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Leitner D, Kavanagh T, Kanshin E, Balcomb K, Pires G, Thierry M, Suazo JI, Schneider J, Ueberheide B, Drummond E, Wisniewski T. Differences in the cerebral amyloid angiopathy proteome in Alzheimer's disease and mild cognitive impairment. Acta Neuropathol 2024; 148:9. [PMID: 39039355 PMCID: PMC11263258 DOI: 10.1007/s00401-024-02767-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Cerebral amyloid angiopathy (CAA) is characterized by amyloid beta (Aβ) deposition in cerebrovasculature. It is prevalent with aging and Alzheimer's disease (AD), associated with intracerebral hemorrhage, and contributes to cognitive deficits. To better understand molecular mechanisms, CAA(+) and CAA(-) vessels were microdissected from paraffin-embedded autopsy temporal cortex of age-matched Control (n = 10), mild cognitive impairment (MCI; n = 4), and sporadic AD (n = 6) cases, followed by label-free quantitative mass spectrometry. 257 proteins were differentially abundant in CAA(+) vessels compared to neighboring CAA(-) vessels in MCI, and 289 in AD (p < 0.05, fold-change > 1.5). 84 proteins changed in the same direction in both groups, and many changed in the same direction among proteins significant in at least one group (p < 0.0001, R2 = 0.62). In CAA(+) vessels, proteins significantly increased in both AD and MCI were particularly associated with collagen-containing extracellular matrix, while proteins associated with ribonucleoprotein complex were significantly decreased in both AD and MCI. In neighboring CAA(-) vessels, 61 proteins were differentially abundant in MCI, and 112 in AD when compared to Control cases. Increased proteins in CAA(-) vessels were associated with extracellular matrix, external encapsulating structure, and collagen-containing extracellular matrix in MCI; collagen trimer in AD. Twenty two proteins were increased in CAA(-) vessels of both AD and MCI. Comparison of the CAA proteome with published amyloid-plaque proteomic datasets identified many proteins similarly enriched in CAA and plaques, as well as a protein subset hypothesized as preferentially enriched in CAA when compared to plaques. SEMA3G emerged as a CAA specific marker, validated immunohistochemically and with correlation to pathology levels (p < 0.0001; R2 = 0.90). Overall, the CAA(-) vessel proteomes indicated changes in vessel integrity in AD and MCI in the absence of Aβ, and the CAA(+) vessel proteome was similar in MCI and AD, which was associated with vascular matrix reorganization, protein translation deficits, and blood brain barrier breakdown.
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Affiliation(s)
- Dominique Leitner
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Tomas Kavanagh
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Kaleah Balcomb
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey Pires
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Manon Thierry
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jianina I Suazo
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Julie Schneider
- Department Rush Alzheimer's Disease Center, Rush University Medical Center, 1750 W Harrison Street, Suite 1000, Chicago, IL, 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
- Department of Pathology, Rush University Medical Center, Chicago, IL, USA
| | - Beatrix Ueberheide
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies and Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Eleanor Drummond
- Brain and Mind Centre and School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
| | - Thomas Wisniewski
- Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, 10016, USA.
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2
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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Miranda-Negrón Y, García-Arrarás JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601561. [PMID: 39005414 PMCID: PMC11244903 DOI: 10.1101/2024.07.01.601561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In holothurians, the regenerative process following evisceration involves the development of a "rudiment" or "anlage" at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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Garza R, Atacho DA, Adami A, Gerdes P, Vinod M, Hsieh P, Karlsson O, Horvath V, Johansson PA, Pandiloski N, Matas-Fuentes J, Quaegebeur A, Kouli A, Sharma Y, Jönsson ME, Monni E, Englund E, Eichler EE, Gale Hammell M, Barker RA, Kokaia Z, Douse CH, Jakobsson J. LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. SCIENCE ADVANCES 2023; 9:eadh9543. [PMID: 37910626 PMCID: PMC10619931 DOI: 10.1126/sciadv.adh9543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
The genetic mechanisms underlying the expansion in size and complexity of the human brain remain poorly understood. Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. Using multiomics profiling, we here demonstrate that L1 promoters are dynamically active in the developing and the adult human brain. L1s generate hundreds of developmentally regulated and cell type-specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPR interference silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.
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Affiliation(s)
- Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Diahann A. M. Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Meghna Vinod
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Vivien Horvath
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Pia A. Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Ninoslav Pandiloski
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC B11, Lund University, 221 84 Lund, Sweden
| | - Jon Matas-Fuentes
- Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC B11, Lund University, 221 84 Lund, Sweden
| | - Annelies Quaegebeur
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Clinical Neurosciences, University of Cambridge and Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Antonina Kouli
- Department of Clinical Neuroscience and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge CB2 0PY, UK
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Marie E. Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Emanuela Monni
- Laboratory of Stem Cells and Restorative Neurology, Lund Stem Cell Center, Lund University, SE-22184 Lund, Sweden
| | - Elisabet Englund
- Department of Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Molly Gale Hammell
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Institute for Systems Genetics, Department of Neuroscience and Physiology, NYU Langone Health, New York, NY 10016, USA
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Roger A. Barker
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Clinical Neuroscience and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge CB2 0PY, UK
| | - Zaal Kokaia
- Laboratory of Stem Cells and Restorative Neurology, Lund Stem Cell Center, Lund University, SE-22184 Lund, Sweden
| | - Christopher H. Douse
- Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC B11, Lund University, 221 84 Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
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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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5
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Stetler-Stevenson WG. The Continuing Saga of Tissue Inhibitor of Metalloproteinase 2: Emerging Roles in Tissue Homeostasis and Cancer Progression. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1336-1352. [PMID: 37572947 PMCID: PMC10548276 DOI: 10.1016/j.ajpath.2023.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are a conserved family of proteins that were originally identified as cytokine-like erythroid growth factors. Subsequently, TIMPs were characterized as endogenous inhibitors of matrixin proteinases. These proteinases are the primary mediators of extracellular matrix turnover in pathologic conditions, such as cancer invasion and metastasis. Thus, TIMPs were immediately recognized as important regulators of tissue homeostasis. However, TIMPs also demonstrate unique biological activities that are independent of metalloproteinase regulation. Although often overlooked, these non-protease-mediated TIMP functions demonstrate a variety of direct cellular effects of potential therapeutic value. TIMP2 is the most abundantly expressed TIMP family member, and ongoing studies show that its tumor suppressor activity extends beyond protease inhibition to include direct modulation of tumor, endothelial, and fibroblast cellular responses in the tumor microenvironment. Recent data suggest that TIMP2 can suppress both primary tumor growth and metastatic niche formation. TIMP2 directly interacts with cellular receptors and matrisome elements to modulate cell signaling pathways that result in reduced proliferation and migration of neoplastic, endothelial, and fibroblast cell populations. These effects result in enhanced cell adhesion and focal contact formation while reducing tumor and endothelial proliferation, migration, and epithelial-to-mesenchymal transitions. These findings are consistent with TIMP2 homeostatic functions beyond simple inhibition of metalloprotease activity. This review examines the ongoing evolution of TIMP2 function, future perspectives in TIMP research, and the therapeutic potential of TIMP2.
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Affiliation(s)
- William G Stetler-Stevenson
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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6
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Ferreira AC, Hemmer BM, Philippi SM, Grau-Perales AB, Rosenstadt JL, Liu H, Zhu JD, Kareva T, Ahfeldt T, Varghese M, Hof PR, Castellano JM. Neuronal TIMP2 regulates hippocampus-dependent plasticity and extracellular matrix complexity. Mol Psychiatry 2023; 28:3943-3954. [PMID: 37914840 PMCID: PMC10730400 DOI: 10.1038/s41380-023-02296-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 09/27/2023] [Accepted: 10/06/2023] [Indexed: 11/03/2023]
Abstract
Functional output of the hippocampus, a brain region subserving memory function, depends on highly orchestrated cellular and molecular processes that regulate synaptic plasticity throughout life. The structural requirements of such plasticity and molecular events involved in this regulation are poorly understood. Specific molecules, including tissue inhibitor of metalloproteinases-2 (TIMP2) have been implicated in plasticity processes in the hippocampus, a role that decreases with brain aging as expression is lost. Here, we report that TIMP2 is highly expressed by neurons within the hippocampus and its loss drives changes in cellular programs related to adult neurogenesis and dendritic spine turnover with corresponding impairments in hippocampus-dependent memory. Consistent with the accumulation of extracellular matrix (ECM) in the hippocampus we observe with aging, we find that TIMP2 acts to reduce accumulation of ECM around synapses in the hippocampus. Moreover, its deletion results in hindrance of newborn neuron migration through a denser ECM network. A novel conditional TIMP2 knockout (KO) model reveals that neuronal TIMP2 regulates adult neurogenesis, accumulation of ECM, and ultimately hippocampus-dependent memory. Our results define a mechanism whereby hippocampus-dependent function is regulated by TIMP2 and its interactions with the ECM to regulate diverse processes associated with synaptic plasticity.
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Affiliation(s)
- Ana Catarina Ferreira
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brittany M Hemmer
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah M Philippi
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alejandro B Grau-Perales
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jacob L Rosenstadt
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hanxiao Liu
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey D Zhu
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tatyana Kareva
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Merina Varghese
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph M Castellano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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7
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Jiang Y, Wei D, Xie Y. Functional modular networks identify the pivotal genes associated with morphine addiction and potential drug therapies. BMC Anesthesiol 2023; 23:151. [PMID: 37138216 PMCID: PMC10155436 DOI: 10.1186/s12871-023-02111-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 04/25/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Chronic morphine usage induces lasting molecular and microcellular adaptations in distinct brain areas, resulting in addiction-related behavioural abnormalities, drug-seeking, and relapse. Nonetheless, the mechanisms of action of the genes responsible for morphine addiction have not been exhaustively studied. METHODS We obtained morphine addiction-related datasets from the Gene Expression Omnibus (GEO) database and screened for Differentially Expressed Genes (DEGs). Weighted Gene Co-expression Network Analysis (WGCNA) functional modularity constructs were analyzed for genes associated with clinical traits. Venn diagrams were filtered for intersecting common DEGs (CDEGs). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for functional annotation. Protein-protein interaction network (PPI) and CytoHubba were used to screen for hub genes. Potential treatments for morphine addiction were figured out with the help of an online database. RESULTS Sixty-five common differential genes linked to morphine addiction were identified, and functional enrichment analysis showed that they were primarily involved in ion channel activity, protein transport, the oxytocin signalling pathway, neuroactive ligand-receptor interactions, and other signalling pathways. Based on the PPI network, ten hub genes (CHN2, OLIG2, UGT8A, CACNB2, TIMP3, FKBP5, ZBTB16, TSC22D3, ISL1, and SLC2A1) were checked. In the data set GSE7762, all of the Area Under Curve (AUC) values for the hub gene Receiver Operating Characteristic (ROC) curves were greater than 0.8. We also used the DGIdb database to look for eight small-molecule drugs that might be useful for treating morphine addiction. CONCLUSIONS The hub genes are crucial genes associated with morphine addiction in the mouse striatum. The oxytocin signalling pathway may play a vital role in developing morphine addiction.
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Affiliation(s)
- Yage Jiang
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Donglei Wei
- Department of Traumatology Orthopedic Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
| | - Yubo Xie
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021 China
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8
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Chu-Tan JA, Cioanca AV, Wooff Y, Kirkby M, Ellis M, Gulati P, Karl T, Boatright JH, Bales K, Nickerson J, Natoli R. Voluntary exercise modulates pathways associated with amelioration of retinal degenerative diseases. Front Physiol 2023; 14:1116898. [PMID: 36969592 PMCID: PMC10036398 DOI: 10.3389/fphys.2023.1116898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Background: Exercise has been shown to promote a healthier and longer life and linked to a reduced risk of developing neurodegenerative diseases including retinal degenerations. However, the molecular pathways underpinning exercise-induced cellular protection are not well understood. In this work we aim to profile the molecular changes underlying exercise-induced retinal protection and investigate how exercise-induced inflammatory pathway modulation may slow the progression of retinal degenerations.Methods: Female C57Bl/6J mice at 6 weeks old were given free access to open voluntary running wheels for a period of 28 days and then subjected to 5 days of photo-oxidative damage (PD)-induced retinal degeneration. Following, retinal function (electroretinography; ERG), morphology (optical coherence tomography; OCT) and measures of cell death (TUNEL) and inflammation (IBA1) were analysed and compared to sedentary controls. To decipher global gene expression changes as a result of voluntary exercise, RNA sequencing and pathway and modular gene co-expression analyses were performed on retinal lysates of exercised and sedentary mice that were subjected to PD, as well as healthy dim-reared controls.Results: Following 5 days of PD, exercised mice had significantly preserved retinal function, integrity and reduced levels of retinal cell death and inflammation, compared to sedentary controls. In response to voluntary exercise, inflammatory and extracellular matrix integrity pathways were significantly modulated, with the gene expression profile of exercised mice more closely trending towards that of a healthy dim-reared retina.Conclusion: We suggest that voluntary exercise may mediate retinal protection by influencing key pathways involved in regulating retinal health and shifting the transcriptomic profile to a healthy phenotype.
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Affiliation(s)
- Joshua A. Chu-Tan
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - Adrian V. Cioanca
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - Yvette Wooff
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - Max Kirkby
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - Marissa Ellis
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - Pranay Gulati
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
| | - Tim Karl
- School of Medicine, Western Sydney University, Penrith, NSW, Australia
| | | | - Katie Bales
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - John Nickerson
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Riccardo Natoli
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Acton, ACT, Australia
- *Correspondence: Riccardo Natoli,
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9
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Biasella F, Plössl K, Baird PN, Weber BHF. The extracellular microenvironment in immune dysregulation and inflammation in retinal disorders. Front Immunol 2023; 14:1147037. [PMID: 36936905 PMCID: PMC10014728 DOI: 10.3389/fimmu.2023.1147037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/15/2023] [Indexed: 03/05/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) as well as genetically complex retinal phenotypes represent a heterogenous group of ocular diseases, both on account of their phenotypic and genotypic characteristics. Therefore, overlaps in clinical features often complicate or even impede their correct clinical diagnosis. Deciphering the molecular basis of retinal diseases has not only aided in their disease classification but also helped in our understanding of how different molecular pathologies may share common pathomechanisms. In particular, these relate to dysregulation of two key processes that contribute to cellular integrity, namely extracellular matrix (ECM) homeostasis and inflammation. Pathological changes in the ECM of Bruch's membrane have been described in both monogenic IRDs, such as Sorsby fundus dystrophy (SFD) and Doyne honeycomb retinal dystrophy (DHRD), as well as in the genetically complex age-related macular degeneration (AMD) or diabetic retinopathy (DR). Additionally, complement system dysfunction and distorted immune regulation may also represent a common connection between some IRDs and complex retinal degenerations. Through highlighting such overlaps in molecular pathology, this review aims to illuminate how inflammatory processes and ECM homeostasis are linked in the healthy retina and how their interplay may be disturbed in aging as well as in disease.
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Affiliation(s)
- Fabiola Biasella
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Karolina Plössl
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Paul N. Baird
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Department of Surgery, Ophthalmology, University of Melbourne, Melbourne, VIC, Australia
- *Correspondence: Paul N. Baird, ; Bernhard H. F. Weber,
| | - Bernhard H. F. Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
- *Correspondence: Paul N. Baird, ; Bernhard H. F. Weber,
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10
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Mazzoni M, Todoerti K, Agnelli L, Minna E, Pagliardini S, Di Marco T, Borrello MG, Neri A, Greco A. Transcriptomic landscape of TIMP3 oncosuppressor activity in thyroid carcinoma. Cancer Cell Int 2022; 22:400. [PMID: 36503426 PMCID: PMC9743531 DOI: 10.1186/s12935-022-02811-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most frequent thyroid tumor. The tissue inhibitor of metalloproteinase-3 (TIMP3) gene encodes a matrix metalloproteinases inhibitor that exerts a tumor suppressor role in several tumor types. TIMP3 is frequently downregulated in PTC by promoter methylation. We have previously functionally demonstrated that TIMP3 exerts an oncosuppressor role in PTC: TIMP3 restoration in the PTC-derived NIM1 cell line affects in vitro migration, invasion and adhesive capability, while reduces tumor growth, angiogenesis and macrophage recruitment in vivo. To get a deeper insight on the mediators of TIMP3 oncosuppressor activity in thyroid tumors, here we focused on the TIMP3 related transcriptome. METHODS TCGA database was used for investigating the genes differentially expressed in PTC samples with low and high TIMP3 expression. Genome wide expression analysis of clones NIM1-T23 (expressing a high level of TIMP3 protein) and NIM1-EV (control empty vector) was performed. Gene sets and functional enrichment analysis with clusterProfiler were applied to identify the modulated biological processes and pathways. CIBERSORT was used to evaluate the distribution of different immunological cell types in TCGA-PTC tumor samples with different TIMP3 expression levels. Real time PCR was performed for the validation of selected genes. RESULTS Thyroid tumors with TIMP3-high expression showed a down-modulation of inflammation-related gene sets, along with a reduced protumoral hematopoietic cells fraction; an enrichment of cell adhesion functions was also identified. Similar results were obtained in the TIMP3-overexpessing NIM1 cells in vitro model, where a down-regulation of immune-related function gene sets, some of which also identified in tumor samples, was observed. Interestingly, through enrichment analysis, were also recognized terms related to cell adhesion, extracellular matrix organization, blood vessel maintenance and vascular process functions that have been found modulated in our previous in vitro and in vivo functional studies. CONCLUSIONS Our results highlight the correlation of TIMP3 expression levels with the regulation of inflammatory functions and the immune infiltration composition associated with different PTC prognosis, thus providing a broader view on the oncosuppressor role of TIMP3 in PTC.
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Affiliation(s)
- M. Mazzoni
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - K. Todoerti
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - L. Agnelli
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - E. Minna
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - S. Pagliardini
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - T. Di Marco
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - M. G. Borrello
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - A. Neri
- Scientific Directorate, Azienda USL-IRCCS Reggio Emilia, Reggio Emilia, Italy
| | - A. Greco
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Research Department, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
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11
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Mungale A, McGaughey DM, Zhang C, Yousaf S, Liu J, Brooks BP, Maminishkis A, Fufa TD, Hufnagel RB. Transcriptional mapping of the macaque retina and RPE-choroid reveals conserved inter-tissue transcription drivers and signaling pathways. Front Genet 2022; 13:949449. [PMID: 36506320 PMCID: PMC9732541 DOI: 10.3389/fgene.2022.949449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022] Open
Abstract
The macula and fovea comprise a highly sensitive visual detection tissue that is susceptible to common disease processes like age-related macular degeneration (AMD). Our understanding of the molecular determinants of high acuity vision remains unclear, as few model organisms possess a human-like fovea. We explore transcription factor networks and receptor-ligand interactions to elucidate tissue interactions in the macula and peripheral retina and concomitant changes in the underlying retinal pigment epithelium (RPE)/choroid. Poly-A selected, 100 bp paired-end RNA-sequencing (RNA-seq) was performed across the macular/foveal, perimacular, and temporal peripheral regions of the neural retina and RPE/choroid tissues of four adult Rhesus macaque eyes to characterize region- and tissue-specific gene expression. RNA-seq reads were mapped to both the macaque and human genomes for maximum alignment and analyzed for differential expression and Gene Ontology (GO) enrichment. Comparison of the neural retina and RPE/choroid tissues indicated distinct, contiguously changing gene expression profiles from fovea through perimacula to periphery. Top GO enrichment of differentially expressed genes in the RPE/choroid included cell junction organization and epithelial cell development. Expression of transcriptional regulators and various disease-associated genes show distinct location-specific preference and retina-RPE/choroid tissue-tissue interactions. Regional gene expression changes in the macaque retina and RPE/choroid is greater than that found in previously published transcriptome analysis of the human retina and RPE/choroid. Further, conservation of human macula-specific transcription factor profiles and gene expression in macaque tissues suggest a conservation of programs required for retina and RPE/choroid function and disease susceptibility.
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Affiliation(s)
- Ameera Mungale
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - David M. McGaughey
- Bioinformatics Group, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Congxiao Zhang
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Sairah Yousaf
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - James Liu
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P. Brooks
- Pediatric, Developmental and Genetic Ophthalmology, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Arvydas Maminishkis
- Section on Epithelial and Retinal Physiology and Disease, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Temesgen D. Fufa
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Robert B. Hufnagel
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States,*Correspondence: Robert B. Hufnagel,
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12
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Lynn SA, Soubigou F, Dewing JM, Smith A, Ballingall J, Sass T, Nica I, Watkins C, Gupta B, Almuhtaseb H, Lash SC, Yuen HM, Cree A, Newman TA, Lotery AJ, Ratnayaka JA. An Exploratory Study Provides Insights into MMP9 and Aβ Levels in the Vitreous and Blood across Different Ages and in a Subset of AMD Patients. Int J Mol Sci 2022; 23:ijms232314603. [PMID: 36498929 PMCID: PMC9736887 DOI: 10.3390/ijms232314603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Matrix metalloproteinase-9 (MMP9) and total amyloid-beta (Aβ) are prospective biomarkers of ocular ageing and retinopathy. These were quantified by ELISA in the vitreous and blood from controls (n = 55) and in a subset of age-related macular degeneration (AMD) patients (n = 12) for insights and possible additional links between the ocular and systemic compartments. Vitreous MMP9 levels in control and AMD groups were 932.5 ± 240.9 pg/mL and 813.7 ± 157.6 pg/mL, whilst serum levels were 2228 ± 193 pg/mL and 2386.8 ± 449.4 pg/mL, respectively. Vitreous Aβ in control and AMD groups were 1173.5 ± 117.1 pg/mL and 1275.6 ± 332.9 pg/mL, whilst plasma Aβ were 574.3 ± 104.8 pg/mL and 542.2 ± 139.9 pg/mL, respectively. MMP9 and Aβ showed variable levels across the lifecourse, indicating no correlation to each other or with age nor AMD status, though the smaller AMD cohort was a limiting factor. Aβ and MMP9 levels in the vitreous and blood were unrelated to mean arterial pressure. Smoking, another modifiable risk, showed no association with vitreous Aβ. However, smoking may be linked with vitreous (p = 0.004) and serum (p = 0.005) MMP9 levels in control and AMD groups, though this did not reach our elevated (p = 0.001) significance. A bioinformatics analysis revealed promising MMP9 and APP/Aβ partners for further scrutiny, many of which are already linked with retinopathy.
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Affiliation(s)
- Savannah A. Lynn
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
| | - Flavie Soubigou
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
| | - Jennifer M. Dewing
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
| | - Amanda Smith
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Joanna Ballingall
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Thea Sass
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Isabela Nica
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Catrin Watkins
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Bhaskar Gupta
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Hussein Almuhtaseb
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Stephen C. Lash
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Ho Ming Yuen
- Primary Care, Population Sciences and Medical Education, Faculty of Medicine, University of Southampton, MP 801, Tremona Road, Southampton SO16 6YD, UK
| | - Angela Cree
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
| | - Tracey A. Newman
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
| | - Andrew J. Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
- Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
- Correspondence: (A.J.L.); (J.A.R.)
| | - J. Arjuna Ratnayaka
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK
- Correspondence: (A.J.L.); (J.A.R.)
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13
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Elsayed MEAA, Kaukonen M, Kiraly P, Kapetanovic JC, MacLaren RE. Potential CRISPR Base Editing Therapeutic Options in a Sorsby Fundus Dystrophy Patient. Genes (Basel) 2022; 13:2103. [PMID: 36421778 PMCID: PMC9690532 DOI: 10.3390/genes13112103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 07/30/2023] Open
Abstract
TIMP3 mutations are associated with early-onset macular choroidal neovascularisation for which no treatment currently exists. CRISPR base editing, with its ability to irreversibly correct point mutations by chemical modification of nucleobases at DNA level, may be a therapeutic option. We report a bioinformatic analysis of potential therapeutic options in a patient presenting with Sorsby fundus dystrophy. Genetic testing in a 35-year-old gentleman with bilateral macular choroidal neovascularisation revealed the patient to be heterozygous for a TIMP3 variant c.610A>T, p.(Ser204Cys). Using a glycosylase base editor (GBE), another DNA-edit could be introduced that would revert the variant back to wild-type on amino acid level. Alternatively, the mutated residue could be changed to another amino acid that would be better tolerated, and for that, an available 'NG'-PAM site was found to be available for the SpCas9-based adenine base editor (ABE) that would introduce p.(Ser204Arg). In silico analyses predicted this variant to be non-pathogenic; however, a bystander edit, p.Ile205Thr, would be introduced. This case report highlights the importance of considering genetic testing in young patients with choroidal neovascularisation, particularly within the context of a strong family history of presumed wet age-related macular degeneration, and describes potential therapeutic options.
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Affiliation(s)
| | - Maria Kaukonen
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
| | - Peter Kiraly
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Jasmina Cehajic Kapetanovic
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
| | - Robert E. MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
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14
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Ahmad I. CRISPR/Cas9—A Promising Therapeutic Tool to Cure Blindness: Current Scenario and Future Prospects. Int J Mol Sci 2022; 23:ijms231911482. [PMID: 36232782 PMCID: PMC9569777 DOI: 10.3390/ijms231911482] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR-based targeted genome editing is bringing revolutionary changes in the research arena of biological sciences. CRISPR/Cas9 has been explored as an efficient therapeutic tool for the treatment of genetic diseases. It has been widely used in ophthalmology research by using mouse models to correct pathogenic mutations in the eye stem cells. In recent studies, CRISPR/Cas9 has been used to correct a large number of mutations related to inherited retinal disorders. In vivo therapeutic advantages for retinal diseases have been successfully achieved in some rodents. Current advances in the CRISPR-based gene-editing domain, such as modified Cas variants and delivery approaches have optimized its application to treat blindness. In this review, recent progress and challenges of the CRISPR-Cas system have been discussed to cure blindness and its prospects.
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Affiliation(s)
- Irshad Ahmad
- Department of Bioengineering, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia; ; Tel.: +966-13-8608393
- Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia
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15
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Liu CC, Zhao J, Fu Y, Inoue Y, Ren Y, Chen Y, Doss SV, Shue F, Jeevaratnam S, Bastea L, Wang N, Martens YA, Qiao W, Wang M, Zhao N, Jia L, Yamazaki Y, Yamazaki A, Rosenberg CL, Wang Z, Kong D, Li Z, Kuchenbecker LA, Trottier ZA, Felton L, Rogers J, Quicksall ZS, Linares C, Knight J, Chen Y, Kurti A, Kanekiyo T, Fryer JD, Asmann YW, Storz P, Wang X, Peng J, Zhang B, Kim BYS, Bu G. Peripheral apoE4 enhances Alzheimer's pathology and impairs cognition by compromising cerebrovascular function. Nat Neurosci 2022; 25:1020-1033. [PMID: 35915180 PMCID: PMC10009873 DOI: 10.1038/s41593-022-01127-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 06/22/2022] [Indexed: 12/21/2022]
Abstract
The ε4 allele of the apolipoprotein E (APOE) gene, a genetic risk factor for Alzheimer's disease, is abundantly expressed in both the brain and periphery. Here, we present evidence that peripheral apoE isoforms, separated from those in the brain by the blood-brain barrier, differentially impact Alzheimer's disease pathogenesis and cognition. To evaluate the function of peripheral apoE, we developed conditional mouse models expressing human APOE3 or APOE4 in the liver with no detectable apoE in the brain. Liver-expressed apoE4 compromised synaptic plasticity and cognition by impairing cerebrovascular functions. Plasma proteome profiling revealed apoE isoform-dependent functional pathways highlighting cell adhesion, lipoprotein metabolism and complement activation. ApoE3 plasma from young mice improved cognition and reduced vessel-associated gliosis when transfused into aged mice, whereas apoE4 compromised the beneficial effects of young plasma. A human induced pluripotent stem cell-derived endothelial cell model recapitulated the plasma apoE isoform-specific effect on endothelial integrity, further supporting a vascular-related mechanism. Upon breeding with amyloid model mice, liver-expressed apoE4 exacerbated brain amyloid pathology, whereas apoE3 reduced it. Our findings demonstrate pathogenic effects of peripheral apoE4, providing a strong rationale for targeting peripheral apoE to treat Alzheimer's disease.
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Affiliation(s)
- Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
| | - Jing Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yuan Fu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yasuteru Inoue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yingxue Ren
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Yuanxin Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Sydney V Doss
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Francis Shue
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Ligia Bastea
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Na Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yuka A Martens
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Wenhui Qiao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Minghui Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Na Zhao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Lin Jia
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yu Yamazaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Akari Yamazaki
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dehui Kong
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Zonghua Li
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | | | - Lindsey Felton
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Justin Rogers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Cynthia Linares
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Joshua Knight
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yixing Chen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Aishe Kurti
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Yan W Asmann
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Peter Storz
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, USA
| | - Xusheng Wang
- Department of Biology, University of North Dakota, Grand Forks, ND, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Betty Y S Kim
- Department of Neurosurgery, The Brain Tumor Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
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16
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Keeling E, Lynn SA, Koh YM, Scott JA, Kendall A, Gatherer M, Page A, Cagampang FR, Lotery AJ, Ratnayaka JA. A High Fat "Western-style" Diet Induces AMD-Like Features in Wildtype Mice. Mol Nutr Food Res 2022; 66:e2100823. [PMID: 35306732 PMCID: PMC9287010 DOI: 10.1002/mnfr.202100823] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 03/01/2022] [Indexed: 12/20/2022]
Abstract
Scope The intake of a “Western‐style” diet rich in fats is linked with developing retinopathies including age‐related macular degeneration (AMD). Wildtype mice are given a high fat diet (HFD) to determine how unhealthy foods can bring about retinal degeneration. Methods and results Following weaning, female C57BL/6 mice are maintained on standard chow (7% kcal fat, n = 29) or a HFD (45% kcal fat, n = 27) for 12 months. Animals were sacrificed following electroretinography (ERG) and their eyes analyzed by histology, confocal immunofluorescence, and transmission electron microscopy. HFD mice become obese, but showed normal retinal function compared to chow‐fed controls. However, diminished β3tubulin labeling of retinal cross‐sections indicated fewer/damaged neuronal processes in the inner plexiform layer. AMD‐linked proteins clusterin and TIMP3 accumulated in the retinal pigment epithelium (RPE) and Bruch's membrane (BrM). Neutral lipids also deposited in the outer retinae of HFD mice. Ultrastructural analysis revealed disorganized photoreceptor outer segments, collapsed/misaligned RPE microvilli, vacuoles, convoluted basolateral RPE infolds and BrM changes. Basal laminar‐like deposits were also present alongside abnormal choroidal endothelial cells. Conclusions We show that prolonged exposure to an unhealthy “Western‐style” diet alone can recapitulate early‐intermediate AMD‐like features in wildtype mice, highlighting the importance of diet and nutrition in the etiology of sight‐loss.
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Affiliation(s)
- Eloise Keeling
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
| | - Savannah A Lynn
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
| | - Yen Min Koh
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
| | - Jenny A Scott
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
| | - Aaron Kendall
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
| | - Maureen Gatherer
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
| | - Anton Page
- Biomedical Imaging Unit, University of Southampton, MP12, Tremona Road, Southampton, SO16 6YD, UK
| | - Felino R Cagampang
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew J Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK.,Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, UK
| | - J Arjuna Ratnayaka
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton, SO16 6YD, UK
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17
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Park JH, Cho SJ, Jo C, Park MH, Han C, Kim EJ, Huh GY, Koh YH. Altered TIMP-3 Levels in the Cerebrospinal Fluid and Plasma of Patients with Alzheimer’s Disease. J Pers Med 2022; 12:jpm12050827. [PMID: 35629249 PMCID: PMC9144624 DOI: 10.3390/jpm12050827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/07/2022] [Accepted: 05/14/2022] [Indexed: 02/04/2023] Open
Abstract
Tissue inhibitor of metalloproteinase-3 (TIMP-3) is a component of the extracellular environment and is suggested to play an indirect role in regulating Aβ production and the pathophysiology of Aβ deposition in brains. However, studies on the amount of TIMP-3 in bodily fluids of Alzheimer’s disease (AD) patients have not been conducted. Here, we investigated the relationship between fluid TIMP-3 levels and AD pathology. We first showed that the fluid levels of TIMP-3 were lower in AD dementia patients compared with in non-AD patients. ELISA results revealed that plasma levels of TIMP-3 in 65 patients with AD were significantly lower than those in 115 healthy control subjects and 71 mild cognitive impairment (MCI) subjects. Furthermore, we found that cerebrospinal fluid (CSF) level of TIMP-3 was decreased in AD compared with that in healthy control. These data suggest that fluid TIMP-3 levels negatively correlated with progress of cognitive decline. Collectively, our study suggests that alterations of fluid TIMP-3 levels might be associated with AD pathology.
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Affiliation(s)
- Jung Hyun Park
- Department of Chronic Disease Convergence Research, Division of Brain Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Korea; (J.H.P.); (S.-J.C.); (C.J.)
| | - Sun-Jung Cho
- Department of Chronic Disease Convergence Research, Division of Brain Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Korea; (J.H.P.); (S.-J.C.); (C.J.)
| | - Chulman Jo
- Department of Chronic Disease Convergence Research, Division of Brain Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Korea; (J.H.P.); (S.-J.C.); (C.J.)
| | - Moon Ho Park
- Departments of Neurology, Korea University Medical College, Ansan Hospital, 123 Jeokgeum-ro, Danwon-gu, Ansan-si 15355, Korea;
| | - Changsu Han
- Departments of Psychiatry, Korea University Medical College, Ansan Hospital, 123 Jeokgeum-ro, Danwon-gu, Ansan-si 15355, Korea;
| | - Eun-Joo Kim
- Department of Neurology, Pusan National University Hospital, 179 Gudeok-ro, Seo-gu, Busan 49241, Korea;
| | - Gi Yeong Huh
- Department of Forensic Medicine, Pusan National University School of Medicine, 49 Busandaehak-ro, Mulgeum-eup, Yangsan-si 50612, Korea;
| | - Young Ho Koh
- Department of Chronic Disease Convergence Research, Division of Brain Disease Research, Korea National Institute of Health, 187 Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu, Cheongju-si 28159, Korea; (J.H.P.); (S.-J.C.); (C.J.)
- Correspondence:
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18
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Peeney D, Liu Y, Lazaroff C, Gurung S, Stetler-Stevenson WG. OUP accepted manuscript. Carcinogenesis 2022; 43:405-418. [PMID: 35436325 PMCID: PMC9167030 DOI: 10.1093/carcin/bgac037] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/23/2022] [Accepted: 04/15/2022] [Indexed: 11/12/2022] Open
Abstract
Tissue inhibitors of metalloproteinases (TIMPs) are a conserved family of proteins that were originally identified as endogenous inhibitors of matrixin and adamalysin endopeptidase activity. The matrixins and adamalysins are the major mediators of extracellular matrix (ECM) turnover, thus making TIMPs important regulators of ECM structure and composition. Despite their high sequence identity and relative redundancy in inhibitory profiles, each TIMP possesses unique biological characteristics that are independent of their regulation of metalloproteinase activity. As our understanding of TIMP biology has evolved, distinct roles have been assigned to individual TIMPs in cancer progression. In this respect, data regarding TIMP2's role in cancer have borne conflicting reports of both tumor suppressor and, to a lesser extent, tumor promoter functions. TIMP2 is the most abundant TIMP family member, prevalent in normal and diseased mammalian tissues as a constitutively expressed protein. Despite its apparent stable expression, recent work highlights how TIMP2 is a cell stress-induced gene product and that its biological activity can be dictated by extracellular posttranslational modifications. Hence an understanding of TIMP2 molecular targets, and how its biological functions evolve in the progressing tumor microenvironment may reveal new therapeutic opportunities. In this review, we discuss the continually evolving functions of TIMP proteins, future perspectives in TIMP research, and the therapeutic utility of this family, with a particular focus on TIMP2.
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Affiliation(s)
- David Peeney
- To whom correspondence should be addressed. Tel: 240-858-3233;
| | - Yueqin Liu
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Carolyn Lazaroff
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Sadeechya Gurung
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
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19
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The α-dystrobrevins play a key role in maintaining the structure and function of the extracellular matrix-significance for protein elimination failure arteriopathies. Acta Neuropathol Commun 2021; 9:171. [PMID: 34674769 PMCID: PMC8532274 DOI: 10.1186/s40478-021-01274-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023] Open
Abstract
The extracellular matrix (ECM) of the cerebral vasculature provides a pathway for the flow of interstitial fluid (ISF) and solutes out of the brain by intramural periarterial drainage (IPAD). Failure of IPAD leads to protein elimination failure arteriopathies such as cerebral amyloid angiopathy (CAA). The ECM consists of a complex network of glycoproteins and proteoglycans that form distinct basement membranes (BM) around different vascular cell types. Astrocyte endfeet that are localised against the walls of blood vessels are tethered to these BMs by dystrophin associated protein complex (DPC). Alpha-dystrobrevin (α-DB) is a key dystrophin associated protein within perivascular astrocyte endfeet; its deficiency leads to a reduction in other dystrophin associated proteins, loss of AQP4 and altered ECM. In human dementia cohorts there is a positive correlation between dystrobrevin gene expression and CAA. In the present study, we test the hypotheses that (a) the positive correlation between dystrobrevin gene expression and CAA is associated with elevated expression of α-DB at glial-vascular endfeet and (b) a deficiency in α-DB results in changes to the ECM and failure of IPAD. We used human post-mortem brain tissue with different severities of CAA and transgenic α-DB deficient mice. In human post-mortem tissue we observed a significant increase in vascular α-DB with CAA (CAA vrs. Old p < 0.005, CAA vrs. Young p < 0.005). In the mouse model of α-DB deficiency, there was early modifications to vascular ECM (collagen IV and BM thickening) that translated into reduced IPAD efficiency. Our findings highlight the important role of α-DB in maintaining structure and function of ECM, particularly as a pathway for the flow of ISF and solutes out of the brain by IPAD.
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20
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Kuo S, Chio C, Yeh C, Ma J, Liu W, Lin M, Lin K, Chang C. Mesenchymal stem cell-conditioned medium attenuates the retinal pathology in amyloid-β-induced rat model of Alzheimer's disease: Underlying mechanisms. Aging Cell 2021; 20:e13340. [PMID: 33783931 PMCID: PMC8135003 DOI: 10.1111/acel.13340] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/08/2020] [Accepted: 02/14/2021] [Indexed: 12/11/2022] Open
Abstract
Amyloid‐beta (Aβ) oligomer is known to contribute to the pathophysiology of age‐related macular degeneration. Herein, we aimed to elucidate the in vivo and in vitro effects of Aβ1‐42 application on retinal morphology in rats. Our in vivo studies revealed that intracerebroventricular administration of Aβ1‐42 oligomer caused dysmorphological changes in both retinal ganglion cells and retinal pigment epithelium. In addition, in vitro studies revealed that ARPE‐19 cells following Aβ1‐42 oligomer application had decreased viability along with apoptosis and decreased expression of the tight junction proteins, increased expression of both phosphor‐AKT and phosphor‐GSK3β and decreased expression of both SIRT1 and β‐catenin. Application of conditioned medium (CM) obtained from mesenchymal stem cells (MSC) protected against Aβ1‐42 oligomer‐induced retinal pathology in both rats and ARPE‐19 cells. In order to explore the potential role of peptides secreted from the MSCs, we applied mass spectrometry to compare the peptidomics profiles of the MSC‐CM. Gene ontology enrichment analysis and String analysis were performed to explore the differentially expressed peptides by predicting the functions of their precursor proteins. Bioinformatics analysis showed that 3‐8 out of 155–163 proteins in the MSC‐CM maybe associated with SIRT1/pAKT/pGSK3β/β‐catenin, tight junction proteins, and apoptosis pathway. In particular, the secretomes information on the MSC‐CM may be helpful for the prevention and treatment of retinal pathology in age‐related macular degeneration.
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Affiliation(s)
- Shu‐Chun Kuo
- Department of Ophthalmology Chi Mei Medical Center Tainan Taiwan
- Department of Optometry Chung Hwa University of Medical Technology Tainan Taiwan
| | - Chung‐Ching Chio
- Division of Neurosurgery Department of Surgery Chi Mei Medical Center Tainan Taiwan
| | - Chao‐Hung Yeh
- Department of Optometry Chung Hwa University of Medical Technology Tainan Taiwan
- Division of Neurosurgery Department of Surgery Chi Mei Medical Center Tainan Taiwan
| | - Jui‐Ti Ma
- Department of Medical Research Chi Mei Medical Center Tainan Taiwan
| | - Wen‐Pin Liu
- Department of Medical Research Chi Mei Medical Center Tainan Taiwan
| | - Mao‐Tsun Lin
- Department of Medical Research Chi Mei Medical Center Tainan Taiwan
| | - Kao‐Chang Lin
- Department of Holistic Care Chi Mei Medical Center Tainan Taiwan
- Department of Neurology Chi Mei Medical Center Tainan Taiwan
| | - Ching‐Ping Chang
- Department of Medical Research Chi Mei Medical Center Tainan Taiwan
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21
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He J, Yang J, Shen T, He J. Overexpression of long non-coding RNA XIST promotes IL-1β-induced degeneration of nucleus pulposus cells through targeting miR-499a-5p. Mol Cell Probes 2021; 57:101711. [PMID: 33722663 DOI: 10.1016/j.mcp.2021.101711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/07/2021] [Accepted: 03/08/2021] [Indexed: 01/20/2023]
Abstract
BACKGROUND Long non-coding RNA X-interactive specific transcript (XIST) is implicated in many diseases. However, its role and interaction with microRNA (miR)-499a-5p in intervertebral disc degeneration (IDD) remained unclear. METHODS Nucleus pulposus (NP) tissue samples were collected and nucleus pulposus cells (NPCs) were isolated for Interleukin-1β (IL-1β) treatment and identification. XIST and miR-499a-5p expressions in the tissue were measured with quantitative real-time polymerase chain reaction (qRT-PCR). After IL-1β treatment, NPC apoptosis was detected by flow cytometry. The potential binding sites of XIST and miR-499a-5p were predicted by starBase and confirmed by dual-luciferase reporter assay. Relative expressions of tissue inhibitor of metalloproteinases-3 (TIMP-3), Matrix metalloproteinases-3 (MMP-3), MMP-13, Collagen II, Aggrecan and apoptosis-related proteins (Bcl-2 associated X protein, Bax; B-cell lymphoma 2, Bcl-2; cleaved caspase-3) were measured by qRT-PCR and Western blot as needed. RESULTS XIST expression was upregulated in the NP tissues of patients with IDD, and IL-1β treatment resulted in a degradation of NPCs. Overexpressed XIST promoted the effects of IL-1β on increasing NPC apoptosis and expressions of XIST, MMP-3, MMP-13, Bax and Cleaved caspase-3, but down-regulated TIMP-3, Collagen II, Aggrecan and Bcl-2 expressions. Silencing XIST, however, showed the opposite effects to its overexpression. MiR-499a-5p expression was downregulated in NP tissues of IDD patients and could bind with XIST, while its upregulation reversed the effects of overexpressed XIST in the IL-1β-treated NPCs. CONCLUSION Overexpressed XIST caused NPC degeneration through promoting apoptosis and extracellular matrix degradation of IL-1β-treated NPCs through targeting miR-499a-5p, and therefore can serve as a potential treatment for IDD.
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Affiliation(s)
- Jun He
- Department of Orthopedics, Zhejiang Hospital, Xihu District, Hangzhou City, Zhejiang Province, 310030, China
| | - Jing Yang
- Department of Cardiology, Zhejiang Hospital, Xihu District, Hangzhou, Zhejiang, 310013, China
| | - Tulan Shen
- Outpatient Department, Zhejiang Hospital, Xihu District, Hangzhou City, Zhejiang Province, 310030, China
| | - Jian He
- Department of Orthopedics, Zhejiang Hospital, Xihu District, Hangzhou City, Zhejiang Province, 310030, China.
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22
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García-Onrubia L, Valentín-Bravo FJ, Coco-Martin RM, González-Sarmiento R, Pastor JC, Usategui-Martín R, Pastor-Idoate S. Matrix Metalloproteinases in Age-Related Macular Degeneration (AMD). Int J Mol Sci 2020; 21:ijms21165934. [PMID: 32824762 PMCID: PMC7460693 DOI: 10.3390/ijms21165934] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
Age-related macular degeneration (AMD) is a complex, multifactorial and progressive retinal disease affecting millions of people worldwide. In developed countries, it is the leading cause of vision loss and legal blindness among the elderly. Although the pathogenesis of AMD is still barely understood, recent studies have reported that disorders in the regulation of the extracellular matrix (ECM) play an important role in its etiopathogenesis. The dynamic metabolism of the ECM is closely regulated by matrix metalloproteinases (MMPs) and the tissue inhibitors of metalloproteinases (TIMPs). The present review focuses on the crucial processes that occur at the level of the Bruch’s membrane, with special emphasis on MMPs, TIMPs, and the polymorphisms associated with increased susceptibility to AMD development. A systematic literature search was performed, covering the years 1990–2020, using the following keywords: AMD, extracellular matrix, Bruch’s membrane, MMPs, TIMPs, and MMPs polymorphisms in AMD. In both early and advanced AMD, the pathological dynamic changes of ECM structural components are caused by the dysfunction of specific regulators and by the influence of other regulatory systems connected with both genetic and environmental factors. Better insight into the pathological role of MMP/TIMP complexes may lead to the development of new strategies for AMD treatment and prevention.
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Affiliation(s)
- Luis García-Onrubia
- Clinical University Hospital of Valladolid, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain; (L.G.-O.); (F.J.V.-B.); (J.C.P.)
| | - Fco. Javier Valentín-Bravo
- Clinical University Hospital of Valladolid, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain; (L.G.-O.); (F.J.V.-B.); (J.C.P.)
| | - Rosa M. Coco-Martin
- Institute of Applied Ophthalmobiology (IOBA), University of Valladolid, 47011 Valladolid, Spain;
- Cooperative Health Network for Research in Ophthalmology (Oftared), National Institute of Health Carlos III, ISCIII, 28040 Madrid, Spain
| | - Rogelio González-Sarmiento
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain;
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca—CSIC, 37007 Salamanca, Spain
| | - J. Carlos Pastor
- Clinical University Hospital of Valladolid, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain; (L.G.-O.); (F.J.V.-B.); (J.C.P.)
- Institute of Applied Ophthalmobiology (IOBA), University of Valladolid, 47011 Valladolid, Spain;
- Cooperative Health Network for Research in Ophthalmology (Oftared), National Institute of Health Carlos III, ISCIII, 28040 Madrid, Spain
| | - Ricardo Usategui-Martín
- Institute of Applied Ophthalmobiology (IOBA), University of Valladolid, 47011 Valladolid, Spain;
- Correspondence: (R.U.-M.); (S.P.-I.)
| | - Salvador Pastor-Idoate
- Clinical University Hospital of Valladolid, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain; (L.G.-O.); (F.J.V.-B.); (J.C.P.)
- Institute of Applied Ophthalmobiology (IOBA), University of Valladolid, 47011 Valladolid, Spain;
- Cooperative Health Network for Research in Ophthalmology (Oftared), National Institute of Health Carlos III, ISCIII, 28040 Madrid, Spain
- Correspondence: (R.U.-M.); (S.P.-I.)
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23
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Hongisto H, Dewing JM, Christensen DR, Scott J, Cree AJ, Nättinen J, Määttä J, Jylhä A, Aapola U, Uusitalo H, Kaarniranta K, Ratnayaka JA, Skottman H, Lotery AJ. In vitro stem cell modelling demonstrates a proof-of-concept for excess functional mutant TIMP3 as the cause of Sorsby fundus dystrophy. J Pathol 2020; 252:138-150. [PMID: 32666594 DOI: 10.1002/path.5506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 06/06/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
Sorsby fundus dystrophy (SFD) is a rare autosomal dominant disease of the macula that leads to bilateral loss of central vision and is caused by mutations in the TIMP3 gene. However, the mechanisms by which TIMP3 mutations cause SFD are poorly understood. Here, we generated human induced pluripotent stem cell-derived retinal pigmented epithelial (hiPSC-RPE) cells from three SFD patients carrying TIMP3 p.(Ser204Cys) and three non-affected controls to study disease-related structural and functional differences in the RPE. SFD-hiPSC-RPE exhibited characteristic RPE structure and physiology but showed significantly reduced transepithelial electrical resistance associated with enriched expression of cytoskeletal remodelling proteins. SFD-hiPSC-RPE exhibited basolateral accumulation of TIMP3 monomers, despite no change in TIMP3 gene expression. TIMP3 dimers were observed in both SFD and control hiPSC-RPE, suggesting that mutant TIMP3 dimerisation does not drive SFD pathology. Furthermore, mutant TIMP3 retained matrix metalloproteinase activity. Proteomic profiling showed increased expression of ECM proteins, endothelial cell interactions and angiogenesis-related pathways in SFD-hiPSC-RPE. By contrast, there were no changes in VEGF secretion. However, SFD-hiPSC-RPE secreted higher levels of monocyte chemoattractant protein 1, PDGF and angiogenin. Our findings provide a proof-of-concept that SFD patient-derived hiPSC-RPE mimic mature RPE cells and support the hypothesis that excess accumulation of mutant TIMP3, rather than an absence or deficiency of functional TIMP3, drives ECM and angiogenesis-related changes in SFD. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Heidi Hongisto
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Tampere, Finland
| | - Jennifer M Dewing
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - David Rg Christensen
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jennifer Scott
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Angela J Cree
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Janika Nättinen
- SILK, Department of Ophthalmology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juha Määttä
- SILK, Department of Ophthalmology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Antti Jylhä
- SILK, Department of Ophthalmology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ulla Aapola
- SILK, Department of Ophthalmology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Hannu Uusitalo
- SILK, Department of Ophthalmology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Tays Eye Centre, Tampere University Hospital, Tampere, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland
| | - J Arjuna Ratnayaka
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Heli Skottman
- Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Tampere, Finland
| | - Andrew J Lotery
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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24
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Eyeing the Extracellular Matrix in Vascular Development and Microvascular Diseases and Bridging the Divide between Vascular Mechanics and Function. Int J Mol Sci 2020; 21:ijms21103487. [PMID: 32429045 PMCID: PMC7278940 DOI: 10.3390/ijms21103487] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
The extracellular matrix (ECM) is critical in all aspects of vascular development and health: supporting cell anchorage, providing structure, organization and mechanical stability, and serving as a sink for growth factors and sustained survival signals. Abnormal changes in ECM protein expression, organization, and/or properties, and the ensuing changes in vascular compliance affect vasodilator responses, microvascular pressure transmission, and collateral perfusion. The changes in microvascular compliance are independent factors initiating, driving, and/or exacerbating a plethora of microvascular diseases of the eye including diabetic retinopathy (DR) and vitreoretinopathy, retinopathy of prematurity (ROP), wet age-related macular degeneration (AMD), and neovascular glaucoma. Congruently, one of the major challenges with most vascular regenerative therapies utilizing localized growth factor, endothelial progenitor, or genetically engineered cell delivery, is the regeneration of blood vessels with physiological compliance properties. Interestingly, vascular cells sense physical forces, including the stiffness of their ECM, through mechanosensitive integrins, their associated proteins and the actomyosin cytoskeleton, which generates biochemical signals that culminate in a rapid expression of matricellular proteins such as cellular communication network 1 (CCN1) and CCN2 (aka connective tissue growth factor or CTGF). Loss or gain of function of these proteins alters genetic programs of cell growth, ECM biosynthesis, and intercellular signaling, that culminate in changes in cell behavior, polarization, and barrier function. In particular, the function of the matricellular protein CCN2/CTGF is critical during retinal vessel development and regeneration wherein new blood vessels form and invest a preformed avascular neural retina following putative gradients of matrix stiffness. These observations underscore the need for further in-depth characterization of the ECM-derived cues that dictate structural and functional properties of the microvasculature, along with the development of new therapeutic strategies addressing the ECM-dependent regulation of pathophysiological stiffening of blood vessels in ischemic retinopathies.
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