Grant List
Represents Grant table in the DB
GET /v1/grants?page%5Bnumber%5D=1419&sort=-start_date
{ "links": { "first": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1&sort=-start_date", "last": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1424&sort=-start_date", "next": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1420&sort=-start_date", "prev": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=1418&sort=-start_date" }, "data": [ { "type": "Grant", "id": "7699", "attributes": { "award_id": "1ZIAES103345-01", "title": "SARS-CoV-2 Studies", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Environmental Health Sciences (NIEHS)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 438205, "principal_investigator": { "id": 23493, "first_name": "DOUGLAS", "last_name": "BELL", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1605, "ror": "https://ror.org/00j4k1h63", "name": "National Institute of Environmental Health Sciences", "address": "", "city": "", "state": "NC", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1605, "ror": "https://ror.org/00j4k1h63", "name": "National Institute of Environmental Health Sciences", "address": "", "city": "", "state": "NC", "zip": "", "country": "United States", "approved": true }, "abstract": "Smoking, Immune Senescence and COVID-19 morbidity. The general approach is to prospectively establish a bank of cryopreserved PBMCs from smokers and nonsmokers before any COVID-19 exposure and use CyTOF to analyze detailed immune profiles. Subjects will return for second post-COVID-19 pandemic visit to provide a second blood sample for analysis. The focus is primarily on immune profiles compared with COVID-19 incidence (or levels of morbidity) in smokers. As seen in Figure 2, there is a large variance in CD16+CD8+ T cell frequency among smokers. We hypothesize that senescent CD16+CD8+ T cells will be higher in smokers who develop COVID-19 or who have more severe morbidity. Specific Aims and Experimental Plans Specific Aim 1. Establish CyTOF immune profiles in 60 smokers and 60 matched nonsmokers who are COVID-19 negative and will be followed up on and recalled after the COVID-19 pandemic has subsided. Specific Aim 2. Compare immune profiles determined from a post-COVID-19 visit to the pre-COVID-19 negative sample. COVID-19 Diagnostics. Aim 1. Develop cDNA library methods for SARS-CoV-2 and host cells suitable for Next Generation sequencing.", "keywords": [ "2019-nCoV", "Bar Codes", "Blood specimen", "CD8-Positive T-Lymphocytes", "COVID-19", "COVID-19 pandemic", "Cells", "Communicable Diseases", "Cryopreservation", "Diagnostic", "Disease Outbreaks", "FCGR3B gene", "Frequencies", "Genetic Transcription", "Goals", "Guide RNA", "Healthcare Systems", "Immune", "Immune System Diseases", "Incidence", "Infection", "Methods", "Morbidity - disease rate", "Peripheral Blood Mononuclear Cell", "Predisposition", "Premature aging syndrome", "Regulatory T-Lymphocyte", "Sampling", "Screening procedure", "Severe Acute Respiratory Syndrome", "Smoker", "Smoking", "T-Lymphocyte Subsets", "Viral", "Visit", "cDNA Library", "follow-up", "high risk", "indexing", "mortality", "next generation sequencing", "non-smoker", "prospective", "response", "screening", "senescence" ], "approved": true } }, { "type": "Grant", "id": "7706", "attributes": { "award_id": "1ZIABC011941-01", "title": "Studies of the SARS-CoV-2 Spike Protein", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Cancer Institute (NCI)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 512699, "principal_investigator": { "id": 23500, "first_name": "JAY A", "last_name": "BERZOFSKY", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1601, "ror": "", "name": "DIVISION OF BASIC SCIENCES - NCI", "address": "", "city": "", "state": "", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1601, "ror": "", "name": "DIVISION OF BASIC SCIENCES - NCI", "address": "", "city": "", "state": "", "zip": "", "country": "United States", "approved": true }, "abstract": "This project just began in April, 2020, during the COVID-19-induced closure of NIH labs, with very few people allowed to work, so it is very early ( 3 months) and progress is limited on each of the above sub-studies. In vitro studies in macaque bronchioalveolar lavage cells: So far, we have seen some effects in vitro on these cells of stimulating them with recombinant spike protein to affect expression of ACE2 and of interferons, that may play a role in infection. Little effect was seen on other cytokine or chemokine production. This work is in progress. In vivo vaccine studies in macaques: the animals have been primed IM with spike in different adjuvants and boosted systemically with spike in nanoparticles. Some T cell responses have been induced by the different regimens, and serum and BAL fluid for antibody responses have been collected and are being assayed. It is too soon to determine which regimen is more immunogenic. If we can arrange a challenge at a BSL3 facility that can handle the virus (being negotiated), we hope to challenge the animals with SARS-CoV-2 to measure vaccine efficacy and correlate that with different immune responses. In vivo studies in mice: ACE2-transgenic mice have been ordered but their shipment was delayed until the end of July. In wild type B6 mice, we have immunized with recombinant spike protein in several different adjuvants to determine the best formulation. That work is in progress. The DNA vaccine with spike protein coupled to a chemokine is being constructed and that work is in progress. Human cell lines: We have received the immortalized human lung epithelial cell lines, that express ACE2, from John Minna at UTSW, as well as some of his non-small-cell lung cancer cell lines that also express ACE2. We have just obtained (mid-July) an antibody to ACE2 that we will use to verify expression. These lines have now been thawed and are being grown up, but no results of planned studies to stimulate with spike protein have been obtained yet. We intend to measure production of chemokines, cytokines, and other factors that may affect the COVID-19 disease course, as noted above.", "keywords": [ "2019-nCoV", "Adjuvant", "Affect", "Animal Model", "Animals", "Antibodies", "Antibody Response", "Binding", "Bioinformatics", "Biological Assay", "Bronchoalveolar Lavage", "COVID-19", "Cancer cell line", "Cell Line", "Cells", "Clinical Trials", "Coupled", "DNA Vaccines", "Dendritic Cells", "Disease", "Electroporation", "Engineering", "Epithelial Cells", "Epitopes", "Formulation", "Human", "Human Cell Line", "Immune", "Immune response", "Immunize", "In Vitro", "Industrialization", "Infection", "Interferons", "Liquid substance", "Lung", "Macaca", "Malignant neoplasm of lung", "Measures", "Mediation", "Medical center", "Methods", "Modeling", "Morbidity - disease rate", "Mucosal Immunity", "Mucous Membrane", "Mus", "Natural Immunity", "Non-Small-Cell Lung Carcinoma", "Phase", "Play", "Production", "Proteins", "Recombinants", "Regimen", "Respiratory Mucosa", "Role", "Route", "SIV Vaccines", "Serum", "Ships", "Site", "Structure of respiratory epithelium", "T cell response", "Texas", "Transgenic Mice", "United States National Institutes of Health", "Universities", "Vaccines", "Vascular Endothelial Cell", "Viral", "Viral Vaccines", "Virus", "Work", "biosafety level 3 facility", "chemokine", "cytokine", "immunogenic", "immunogenicity", "immunopathology", "in vivo", "mucosal vaccine", "nanoparticle", "neutralizing antibody", "nonhuman primate", "preclinical study", "receptor", "receptor binding", "response", "vaccine candidate", "vaccine efficacy", "vaccine trial", "viral transmission" ], "approved": true } }, { "type": "Grant", "id": "7707", "attributes": { "award_id": "1ZIADK075104-08", "title": "Understanding protein folding, evolution and function via molecular simulation", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 866673, "principal_investigator": { "id": 23501, "first_name": "Robert", "last_name": "Best", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1600, "ror": "https://ror.org/00adh9b73", "name": "National Institute of Diabetes and Digestive and Kidney Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1600, "ror": "https://ror.org/00adh9b73", "name": "National Institute of Diabetes and Digestive and Kidney Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "The project has addressed the following areas in the past year: 1. Studies of SARS-Cov2 Main Protease. In collaboration with John Louis (NIDDK), we have investigated the autoprocessing mechanism of the SARS-Cov2 Main Protease. A reaction coordinate was developed that can describe the conformational change between the native protease structure and a putative transient state required for protease autoprocessing, a key step for viral replication. Simulations show that this state is only slightly higher in free energy than the native state and should be populated on a microsecond to millisecond time scale, making the proposed autoprocessing mechanism extremely plausible. Future work will investigate this mechanism further and whether it can be exploited to design novel inhibitors for SARS proteases (R. Best). 2. Association of highly charged intrinsically disordered proteins. Recent work in collaboration with Ben Schuler's single molecule FRET group in Zurich has shown that high affinity disordered complexes of proteins or proteins and nucleic acids may be ubiquitous in cell nuclei. We are seeking to develop a predictive model for the affinity and structure of these complexes, initially via molecular simulation, but then via a semi-empirical theory fitted to experimental data collected in the Schuler lab (M. Ivanovic). 3. Development of coarse-grained models for complex coacervation of intrinsically disordered proteins with single- and double-stranded nucleic acids. Going beyond the 1:1 complexes studied in project 1, it is also possible for oppositely charged macromolecules such as proteins and DNA or RNA to undergo complex coacervation, forming a separate phase with high macromolecular density, under the correct conditions. Such a phenomenon may provide a physical basis for the formation of some of the membraneless organelles observed in the cell nucleus. We have developed a coarse-grained simulation model of protein-nucleic acid interactions, and used it to study the ordering induced on formation of the condensed phase. Future work will include improving the transferability of the model to different sequences and making it more sensitive to sequence-specific effects (K. Lebold). 4. Development of transferable sequence-specific models for liquid-liquid phase separation (LLPS) of intrinsically disordered proteins. We had previously shown that a simple coarse-grained model could be useful for modelling qualitative effects on protein liquid-liquid phase separation, the basis for formation of many membraneless organelles within cells. However, this model was not very predictive of which proteins would undergo phase separation. We have therefore undertaken a comprehensive refitting of the energy function in order to describe both the properties of isolated disordered chains and also those of proteins which are known to phase separate. The inclusion of the latter data set results in a great improvement of the overall accuracy of the model, owing to some of the effects which are important for driving LLPS not being well represented in the database of isolated (non phase-separating) proteins. This work is currently in preparation for publication (T. Dannenhoffer-Lafage). 5. All-atom simulations of protein phase separation and complex coacervation. Using time obtained on the Anton supercomputer, together with novel multiscale simulation methodology, we have performed the first all-atom simulations of a protein-rich phase representative of those obtained in protein LLPS. We have characterized the interactions driving formation of this phase, the partitioning of ions into the dense phase, and the dynamics of proteins within the phase - paper currently under review. We now intend to apply similar methodology to the more challenging problem of coacervation of oppositely charged proteins, in order to elucidate the interactions responsible for stabilizing these phases (M. Ivanovic). 6. Co-translational protein folding. In collaboration with Gunnar von Heijne, we have used our previously developed model for co-translational folding on the ribosome to investigate more directly the relationship between the forces arising from the folding nascent chain and the yield of full length protein obtained in arrest peptide experiments. We also devised a method for obtaining these forces directly from experiment by using a series of different arrest peptides with the same protein constructs (5). In a second collaboration with the group of Sander Tans, we are using our coarse-grained co-translational folding model to understand the effects of the ribosome on the folding and unfolding rates of ADR1a in the ribosome exit tunnel, as probed by single molecule force and fluorescence spectroscopy. We have recently started a new collaboration with Alexey Amunts in Stockholm to interpret their cryo-EM results on mitochondrial ribosomes (R. Best, P. Tian). 7. Using sequence-based energy functions to describe protein fitness landscapes and for protein design. Building on our success in describing the fitness landscape of a single fold using coevolutionary models, we are seeking to design sequences which can fold into two different structures as envisaged in our recent theoretical work (7). We are collaborating with Susan Marqusee's group to test some of these ideas (P. Tian). We are also looking to develop similar ideas to identify proteins which naturally switch folds (such as RfaH), using sequence information (L. Frechette). 8. Modelling sensitivity of single molecule experiments to protein folding transition paths using molecular simulations. Recent single molecule fluorescence experiments have been able to detect transition paths between folded and unfolded states of proteins by combining photon by photon detection with sophisticated maximum likelihood analysis algorithms. However, it is not clear how the inferred transition path durations relate to the actual folding transition path lengths, since they cannot be independently measured. We have used simulations as a model to generate coarse-grained folding trajectories for two proteins (alpha3D, protein G), in which we can unambiguously assign transition paths. We then generated synthetic photon trajectories from these simulations and analyzed them in the same way as the experimental data. We found that the experimentally inferred transition path durations are of the right magnitude, but systematically shorter than the true durations. Beyond current analysis methods, we are also testing the feasibility of obtaining information besides just the length of the transition path, i.e. transition path \"shape\", from this type of experiment, using synthetic data generated from our simulations (G. Taumoefolau). 9. Using transition-path sampling to study the mechanism and rate of assembly of transmembrane protein dimers, as represented by Glycophorin A. We have used our force field developed to best reproduce the stability of Glycophorin A in POPC membranes to study the dynamics of protein association using enhanced sampling methods (transition-path sampling) (4). We find that association occurs via an intermediate in which non-native interactions are initially formed between the helices, followed by a second step driven by native interactions. The same approach should be applicable to study oligomerization of other transmembrane domains. (J. Domanski). Group members or jointly supervised external collaborators involved in each project are listed at the end of each section.", "keywords": [ "2019-nCoV", "Address", "Affinity", "Algorithmic Analysis", "Area", "Automobile Driving", "Base Sequence", "Cell Nucleus", "Cells", "Charge", "Collaborations", "Complex", "Cryoelectron Microscopy", "Cytoplasmic Granules", "DNA", "Data", "Data Set", "Databases", "Development", "Disease", "Evolution", "Fluorescence", "Fluorescence Spectroscopy", "Free Energy", "Future", "G-substrate", "GYPA gene", "Goals", "Grain", "Integral Membrane Protein", "Ions", "Length", "Liquid substance", "Measures", "Membrane", "Membrane Proteins", "Methodology", "Methods", "Mitochondria", "Modeling", "Molecular", "Molecular Conformation", "National Institute of Diabetes and Digestive and Kidney Diseases", "Nucleic Acids", "Organelles", "Paper", "Peptide Hydrolases", "Peptides", "Phase", "Photons", "Preparation", "Property", "Protein Dynamics", "Protein Engineering", "Proteins", "Publications", "RNA", "Reaction", "Refit", "Resolution", "Ribosomes", "Sampling", "Series", "Severe Acute Respiratory Syndrome", "Shapes", "Structure", "Supervision", "Testing", "Time", "Transmembrane Domain", "Virus Replication", "Work", "amyloid fibril formation", "density", "design", "dimer", "experimental study", "fitness", "improved", "inhibitor/antagonist", "interest", "macromolecule", "member", "millisecond", "models and simulation", "non-Native", "novel", "photon-counting detector", "predictive modeling", "protein aggregation", "protein complex", "protein folding", "protein function", "protein misfolding", "simulation", "single molecule", "single-molecule FRET", "success", "supercomputer", "theories", "time use" ], "approved": true } }, { "type": "Grant", "id": "7708", "attributes": { "award_id": "1ZIAAI001292-01", "title": "Mechanisms of immunopathology of COVID-19/ARDS, and strategies to mitigate detrimental inflammatory responses", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Allergy and Infectious Diseases (NIAID)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 243355, "principal_investigator": { "id": 23502, "first_name": "Sonja", "last_name": "Best", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "The emergence of SARS-CoV-2 rapidly became a global pandemic necessitating the need to understand the mechanisms of disease, and develop vaccines and therapeutics. These efforts are hampered by the fact that the most useful experimental model in these efforts, the mouse, is not susceptible to infection due to an incompatible sequence of the cellular receptor for virus entry, ACE2. Therefore we have initiated two major efforts to develop mouse models that can be utilized in the efforts to understand dysregulation of innate and adaptive immunity associated with severe viral pneumonia. The ultimate goal is to define these processes as they relate to SARS-CoV-2 to identify points of intervention of inflammatory responses that can be targeted therapeutically. The first major initiative is to develop mouse models of severe SARS-CoV-2 infection. To achieve this, we have partnered with Jackson Laboratories to genetically engineer mice that express a humanized ACE2 gene to enable virus replication in tissues. We are currently testing 4 novel mouse models that reflect different strategies to humanize ACE2 at the endogenous locus, or as a transgene. We are also testing mouse backgrounds for susceptibility, including the 8 founder mice of the Collaborative Cross, and our preliminary data suggests that different mouse strains can reflect some aspects of human disease, including a male bias and complications from thrombosis. The ulimate goal will be to fully characterize the host responses as they relate to pathology in these models, and then utilize the models for testing biologics that block various events in inflammatory cascades. The second major initiative is the employment of a lethal influenza infection as a model for severe viral pneumonia that can be used as a test bed for better understanding other viral pulmonary infections such COVID-19 caused by SARS-Cov2. Ongoing studies involve (i) tests of interventions in the lethal influenza model that might have clinical utility and (ii) cell and molecular studies aimed at better understanding the underlying mechanism(s) of tissue damage and why interventions that constrain viral replication or innate immunity often fail after an early point in infection but well before death of the host. Using a severe influenza infection model that bypasses early nasopharyngeal replication and leads to rapid deep lung infection, we found that only very early treatment with the anti-viral (oseltamivir phosphate - Tamiflu) could prevent death of the infected animals. No other drug or anti-inflammatory treatments tested altered the course of disease appreciably, arguing that either multiple damaging activities are involved and blunting only one is insufficient for a clinical effect, or that irreversible tissue damage occurs early and once this occurs, interfering with viral replication or host immunity does not play a major role in loss of pulmonary function. Current work utilizes the highly multiplex imaging methods developed in the Lymphocyte Biology Section, LISB, NIAID, NIH to quantitatively probe the state of key cells and structures in the lung during the critical window in which intervention affects death rates to identify possible sites of damage, while treatment strategies involving pairing of anti-virial and anti-immune drugs are being tested for synergy.", "keywords": [ "2019-nCoV", "Acute", "Adult Respiratory Distress Syndrome", "Affect", "Animals", "Anti-Inflammatory Agents", "Antiviral Agents", "Attention", "Beds", "Biological Testing", "Bypass", "COVID-19", "Cells", "Cellular Structures", "Cessation of life", "Clinical", "Data", "Death Rate", "Disease", "Early treatment", "Employment", "Event", "Experimental Models", "Genes", "Genetically Engineered Mouse", "Goals", "Host Defense Mechanism", "Human", "Immune response", "Immunity", "Immunotherapeutic agent", "Infection", "Inflammatory", "Inflammatory Response", "Influenza", "Intervention", "Laboratories", "Lung", "Lung infections", "Lymphocyte Biology", "Modeling", "Molecular", "Morbidity - disease rate", "Mouse Strains", "Mus", "National Institute of Allergy and Infectious Disease", "Natural Immunity", "Oseltamivir", "Pathologic", "Pathology", "Pharmaceutical Preparations", "Predisposition", "Process", "Role", "Site", "Testing", "Therapeutic", "Thrombosis", "Thrombus", "Tissues", "Transgenes", "United States National Institutes of Health", "Vaccination", "Vaccines", "Viral", "Viral Pneumonia", "Virus Receptors", "Virus Replication", "Work", "adaptive immune response", "adaptive immunity", "clinical effect", "human disease", "imaging modality", "immunopathology", "inflammatory marker", "inorganic phosphate", "male", "mortality", "mouse model", "multiplexed imaging", "novel", "pandemic disease", "preservation", "prevent", "pulmonary function", "response", "synergism", "targeted treatment", "treatment strategy" ], "approved": true } }, { "type": "Grant", "id": "7713", "attributes": { "award_id": "1ZIAEY000559-04", "title": "Developing 3D patient-specific iPS cell derived RPE/choroid models", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Eye Institute (NEI)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 1564812, "principal_investigator": { "id": 23508, "first_name": "Kapil", "last_name": "Bharti", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1611, "ror": "https://ror.org/03wkg3b53", "name": "National Eye Institute", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1611, "ror": "https://ror.org/03wkg3b53", "name": "National Eye Institute", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "Age-related macular degeneration (AMD) is one of the leading causes of blindness among elderly. The disease has two advanced stages, the dry and the wet stage. The dry stage is trigged by the death of retinal pigment epithelium (RPE) cells followed by photoreceptor (PR) cell death and choroidal thinning. In contrast the wet-stage is characterized by overt proliferation of choroidal capillaries. It is thought that disease processes for both these advanced stages initiate in the back of the eye around the PR/RPE/choroid complex. However, due to lacking human models, the disease initiating events that lead to functional and anatomical changes in the PR/RPE/choroid complex are not well understood. We have combined bioprinting, tissue engineering, and induced pluripotent stem (iPS) cell technology to develop a 3D in vitro model of RPE/choroid. Using a collagen-based gel for encapsulation of patient-specific iPS cell-derived endothelial cells, choroidal fibroblasts, and pericytes, we successfully bioprinted a microvascular network on one side of a biodegradable scaffold. On the other side of the scaffold, we grow a RPE monolayer differentiated from the same patients iPS cells. This 3D tissue mimics the anatomy and functional properties of native RPE/choroid unit. Similar to wet-AMD, the in vitro microvascular network also proliferates in response to VEGF. This work provides a platform to discover disease initiating pathways and the possibility of identifying potential therapeutic drugs for wet-AMD. In a parallel approach, we are developing a controlled biomimetic microenvironment based microfluidic culture platform to recapitulated the human outer blood retina barrier using iPSC-derived RPE and endothelial cells. The purpose of this investigation is to serve as a groundwork for developing functional retina degenerative disease models on the microchips and improving upon the existing preclinical drug development process. We successfully designed and developed a microfluidic chip platform that facilitates seamless image acquisition, fluidic connection and disconnection, and in situ assays. Furthermore, we showed that the chip system is capable of co-culturing RPE and endothelial cells in a dual-channel microfluidic chip. This microfluidic chip platform is currently being use to test toxicity of hydroxychloroquine (HCQ), a drug that has been in wide clinical use for COVID-19. HCQ as a side-effect causes retinal toxicity and vision loss via damage to the RPE. We are using our microfluidic platform to determine HCQ toxicity in the RPE. HCQ is pumped in the endothelial channel similar and from there is diffuses to the RPE - similar to what happens in patients eyes. This platform will help discover pathways that are affected by HCQ in RPE cells and lead to RPE degeneration, and help alleviate HCQ toxicity", "keywords": [ "3-Dimensional", "Affect", "Age related macular degeneration", "Anatomy", "Back", "Biological Assay", "Biomimetics", "Blindness", "Blood capillaries", "Blood-Retinal Barrier", "COVID-19", "Cell Death", "Cessation of life", "Choroid", "Clinical", "Coculture Techniques", "Collagen", "Complex", "Development", "Diffuse", "Disease", "Disease model", "Elderly", "Endothelial Cells", "Endothelium", "Event", "Eye", "Fibroblasts", "Gel", "Goals", "Human", "Hydroxychloroquine", "Image", "In Situ", "In Vitro", "Investigation", "Lead", "Liquid substance", "Microfluidic Microchips", "Microfluidics", "Modeling", "Pathway interactions", "Patients", "Pericytes", "Pharmaceutical Preparations", "Photoreceptors", "Preclinical Drug Development", "Process", "Proliferating", "Property", "Pump", "Retina", "Retinal Degeneration", "Retinal Photoreceptors", "Side", "Structure of retinal pigment epithelium", "System", "Testing", "Therapeutic", "Thinness", "Tissue Engineering", "Tissues", "Toxic effect", "Toxicity Tests", "Vascular Endothelial Growth Factors", "Work", "base", "bioprinting", "design", "human model", "improved", "in vitro Model", "induced pluripotent stem cell", "microchip", "monolayer", "response", "retinal damage", "scaffold", "side effect", "stem cell technology" ], "approved": true } }, { "type": "Grant", "id": "7716", "attributes": { "award_id": "1ZIAAG000443-13", "title": "The origin of tBregs and their trans-differentiation in cancer", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute on Aging (NIA)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 1596810, "principal_investigator": { "id": 23510, "first_name": "Arya", "last_name": "Biragyn", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1613, "ror": "https://ror.org/049v75w11", "name": "National Institute on Aging", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1613, "ror": "https://ror.org/049v75w11", "name": "National Institute on Aging", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "We continue our study of regulatory B cells, which we discovered in some mice and humans with cancer (Olkhanud et al, Cancer Research, 2011; Bodogai et al. Cancer Research, 2013). These cells (termed tBregs) are directly induced by cancer cells producing metabolites of 5-lipoxygenase pathway (5-LOX) via activating the proliferator-activated receptor alpha (PPARa) signaling in B cells (Wejksza et al., J. Immunology, 2013). tBregs express high levels of TGFb and support cancer metastasis utilizing several mechanisms, such as by suppressing activity of effector T cells, inducing the generation of FoxP3+ Tregs, and educating the regulatory function of both the monocyte and granulocyte subpopulations of MDSCs via triggering TgfbR1/TgfbR2 signaling. Although Tregs and MDSCs are the key metastasis-supporting cells, our data place tBregs upstream of these two cells, explain why the loss of tBregs alone almost completely abrogates metastasis (Bodogai et al., Cancer Research, 2015; Olkhanud et al, Cancer Research, 2011). Overall, our data indicate that cancer-induced B cells/B regulatory cells play important roles in metastasis (Bodogai et al., Cancer Research, 2015), suggesting that strategies that inactivate tBregs can improve antitumor immune responses (Lee-Chang et al., J. Immunol., 2013; Bodogai et al., Cancer Research, 2013). However, we also demonstrated that some B cell-targeting strategies can instead be harmful. For example, because tBregs express low levels of surface CD20, current FDA-approved antibody that depletes B cells by targeting CD20 (Rituximab/Rituxan) eliminates beneficial B cells but enriches for tBregs and thereby exacerbates metastasis in mice (Bodogai et al., Cancer Research, 2013), explaining a recent failure of this strategy in humans with solid tumors. The source of B cells that become tBregs remained unknown. Here, we report completion of 4-year-long study that revealed that tBregs are derived from the bone marrow (BM) pre-B cells. Mechanistically, cancer promotes premature emigration of pre-B cells from BM and expansion in the circulation by producing thymic stromal lymphopoietin (TSLP). TSLP downregulates CXCR4 and VLA4 expression on pre-B cells and dislodges them from BM. In addition, TSLP also supports survival of pre-B cells in the circulation. Overall, our study revealed previously unknown pathway that cancer utilizes to generate metastasis-promoting regulatory B cells. Moreover, it also suggested that the TSLP/TSLPR axis can be a therapeutic target to control cancer metastasis, because the loss of TSLP expression in cancer cells or TSLPR deficiency in B cells impairs lung metastasis of 4T1 cancer cells. This finding is recently published in Cancer Research (Ragganoud et al, 2019). \tThe second part of this study is to understand the differentiation of pre-B cells in the circulation. We found that these cells can surprisingly trans-differentiate into macrophage-like cells. At present, we are elucidating the mechanism of this unique process and its relevance to cancer escape. Unfortunately, the COVID-19 quarantine temporarily hampered the progress of this exciting study. Several essential strains of mice we were breeding for this study were lost due to the COVI-19 rules of our animal facility. We therefore expect to complete this study and submit paper for publication sometime late 2021.", "keywords": [ "4T1", "Antibodies", "Arachidonate 5-Lipoxygenase", "B-Lymphocytes", "Blood Circulation", "Bone Marrow", "Breeding", "COVID-19", "CXCR4 gene", "Cancer Control", "Cells", "Data", "Emigrations", "FDA approved", "FOXP3 gene", "Failure", "Generations", "Goals", "Human", "Immunology", "Impairment", "LOX gene", "Lung", "MS4A1 gene", "Malignant Neoplasms", "Metastatic Neoplasm to the Lung", "Mouse Strains", "Mus", "Neoplasm Metastasis", "Paper", "Pathway interactions", "Phenotype", "Play", "Process", "Publications", "Publishing", "Quarantine", "Regulatory T-Lymphocyte", "Reporting", "Role", "Signal Transduction", "Solid Neoplasm", "Source", "Supporting Cell", "Surface", "TSLP gene", "Testing", "animal facility", "anti-tumor immune response", "anticancer research", "cancer cell", "effector T cell", "granulocyte", "improved", "macrophage", "malignant breast neoplasm", "monocyte", "premature", "receptor", "rituximab", "therapeutic target", "transdifferentiation" ], "approved": true } }, { "type": "Grant", "id": "7717", "attributes": { "award_id": "1ZIAAG000778-04", "title": "The role of immune cells in Alzheimer's disease", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute on Aging (NIA)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 528921, "principal_investigator": { "id": 23510, "first_name": "Arya", "last_name": "Biragyn", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1613, "ror": "https://ror.org/049v75w11", "name": "National Institute on Aging", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1613, "ror": "https://ror.org/049v75w11", "name": "National Institute on Aging", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "The role of B cells in Alzheimer's disease (AD) remains poorly understood even though we and others showed their benefit as producers of antibody that help to eliminate neurotoxic beta-amyloid depositions (Ab plaques) (Olkhanud et al, Vaccine, 2011). About 6 years ago, we have hypothesized that B cells could also be promoting AD because they upregulate expression of inflammatory factors together with the onset of AD in 3xTgAD mice. We tested this possibility in 3 different mouse models of AD, such as 3xTgAD, APP/PS1 and 5xFAD mice, utilizing complementing experimental strategies. First, we generated B-cell deficient (BKO) mice that develop AD in young and old age, 2xTgAD and 3xTgAD mice by crossing BKO mice with 2xTgAD and 3xTgAD mice, respectively. The loss of B cells in these mice almost completely reversed the AD symptoms despite expression of AD-promoting transgenes. Compared to age/sex-matched B-cell sufficient littermates, 2xTgAD/BKO and 3xTgAD/BKO mice exhibited reduced anxiety and improved memory deficits. Both 2xTgAD/BKO and 3xTgAD/BKO mice contained significantly fewer Ab-plaques in the brain subiculum than their age- and sex-matched littermates. The over activated microglia, another hallmark of AD pathology, in both mice without B cells was also markedly reduced. To confirm this finding, we also transiently depleted B cells from the circulation of mice with AD, such as 3xTgAD, APP/PS1 and 5xFAD mice, by injecting CD20-targeting antibody. The B-cell depletion indeed significantly delayed AD symptoms in all three types of mice. Overall, for the first time we demonstrate that B cells play pathogenic role in AD and, importantly, their transient depletion from the circulation can delay AD onset. The paper, which we recently submitted for publication, came back for revision. Due to the COVID-19 quarantine, we had to terminate experiments and cull essential AD mice, precluding a proper addressing the editor and reviewers comments. We therefore expect to finalize this paper by middle of 2021. Despite this, we have played the key roles in successful completion of 2 papers from our collaborators on Ad and AD-like symptoms in Down syndrome.", "keywords": [ "APP-PS1", "Address", "Age", "Aging", "Alzheimer&apos", "s Disease", "Alzheimer&apos", "s disease model", "Alzheimer&apos", "s disease pathology", "Antibodies", "Anxiety", "B-Lymphocytes", "Back", "Blood Circulation", "Brain", "COVID-19", "Cells", "Complement", "Disease", "Down Syndrome", "Exhibits", "Goals", "Immune", "Inflammatory", "MS4A1 gene", "Memory impairment", "Microglia", "Mus", "Onset of illness", "Paper", "Pathogenicity", "Play", "Publications", "Published Comment", "Quarantine", "Role", "Symptoms", "Testing", "Therapeutic", "Time", "Transgenes", "Vaccines", "abeta deposition", "experimental study", "improved", "mouse model", "neurotoxic", "sex" ], "approved": true } }, { "type": "Grant", "id": "7718", "attributes": { "award_id": "1ZIAAG000444-09", "title": "Development of simple formulations for vaccine use", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute on Aging (NIA)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 1577096, "principal_investigator": { "id": 23510, "first_name": "Arya", "last_name": "Biragyn", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1613, "ror": "https://ror.org/049v75w11", "name": "National Institute on Aging", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1613, "ror": "https://ror.org/049v75w11", "name": "National Institute on Aging", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "This study consists of two sub-projects, 1, To develop COVID-19 vaccine formulation based on our previously devised technology; and 2, to develop CD8+ T cell-targeting technology via their cell surface-expressed receptors. 1, We previously demonstrated that the exposure of B-cell epitopes on the surface of empty viral particles, such as HBsAg-based 22 nm particles, can render them highly immunogenic. For example, Amyloid (A-) beta peptide exposed on the surface of HBsAg particles elicited high levels of A-beta antibody capable of ameliorating and delaying onset of Alzheimers disease in mice. Therefore, here we generated a vaccine construct that expresses receptor-binding fragment of S antigen of SARS-CoV2 virus, a cause of current COVID-19 pandemic. The vaccine is now being tested in mice for induction of SARS-CoV2 neutralizing antibody. 2, To develop CD8+ T cell-targeting strategy , we adapt our in house-developed and patented chemoarp technology that can deliver immune regulatory siRNA/miRNA into T cells (Biragyn et al., J. Immunotherapy, 2013). For example, chemoarp can inactivate expression of IL10 and FoxP3 in CCR4+ Tregs in mice and thereby to block lung metastasis (Biragyn et al., J. Immunotherapy, 2013). We also used chemoarp to deliver immunostimulatory CpG-ODN and activate antitumor responses of B cells in mice with breast cancer (Bodogai et al., 2013). Our chemokine-based technologies have been also used by others to create a number of papers in collaboration with our laboratory, such as Dr. Rivas-Santiago (Mexican Institute of Social Security, Mexico) tested for prevention tuberculosis in mice (Cervantes-Villagrana et al., 2013); professors Nishioka and Sone (University of Tokushima, Japan) to alleviate asthma (Honjo et al., Respir. Investig., 2013); professors Markham from JHU to generate malaria vaccine (Luo et al., PlosOne, 2014; Geoghegan et al., Antimicrob. Agents, 2015); and Dr.Okuma in therapy of ATLL (Hiyoshi et al, Retrovirology, 2015). However, despite importance of CD8+T cells in immunotherapy of cancer or induction of autoimmunity, there are no strategies designed to manipulating these cells due to lack of useful cell surface receptors. For last 6 years, we searched for protein ligands specific to CD8+ T cells and only recently found a hypothetical sperm-expressed protein, which has a high affinity to CD8 T cells. Although its receptor is unknown, we created a recombinant protein containing this unknown protein and showed that it can indeed be used for targeted modulation of function of CD8+ T cells. Overall, both these studies are progressing well, and we expect to complete them in one year.", "keywords": [ "2019-nCoV", "Adult T-Cell Leukemia/Lymphoma", "Affinity", "Alzheimer&apos", "s Disease", "Amyloid", "Amyloid beta-Protein", "Antibodies", "Antitumor Response", "Asthma", "Autoimmunity", "B-Lymphocyte Epitopes", "B-Lymphocytes", "CD8-Positive T-Lymphocytes", "COVID-19 pandemic", "COVID-19 vaccine", "Cell Surface Receptors", "Cell surface", "Cells", "Collaborations", "Development", "FOXP3 gene", "Fab Immunoglobulins", "Formulation", "Goals", "Hepatitis B Surface Antigens", "Immune", "Immunotherapy", "Institutes", "Interleukin-10", "Japan", "Laboratories", "Legal patent", "Ligands", "Malaria Vaccines", "Metastatic Neoplasm to the Lung", "Mexican", "Mexico", "MicroRNAs", "Mus", "Paper", "Prevention", "Proteins", "Recombinant Proteins", "Regulatory T-Lymphocyte", "Retrovirology", "Small Interfering RNA", "Social Security", "Surface", "T-Lymphocyte", "Technology", "Testing", "Therapeutic", "Tuberculosis", "Universities", "Vaccines", "Viral", "Virus", "base", "cancer immunotherapy", "chemokine", "design", "high risk", "immunogenic", "innovation", "malignant breast neoplasm", "neutralizing antibody", "particle", "professor", "receptor", "receptor binding", "sperm cell", "vaccine development" ], "approved": true } }, { "type": "Grant", "id": "7721", "attributes": { "award_id": "1ZIAAI000940-17", "title": "Pathogenesis of Tick-Borne Flavivirus Infections", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Allergy and Infectious Diseases (NIAID)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 1270472, "principal_investigator": { "id": 23513, "first_name": "Marshall", "last_name": "Bloom", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "While the COVID-19 pandemic, caused the novel -coronavirus SARS-CoV-2, ravages the world and has disrupted much biomedical research, infections with vector- borne flaviviruses continue their inexorable march as important emerging and re-emerging viral pathogens. The tick borne flaviviruses (TBFV) include tick borne encephalitis virus (TBEV), Omsk hemorrhagic fever virus, Kyasanur forest disease virus, Alkhurma hemorrhagic fever virus, Powassan/deer tick virus (POWV/DTV) and Langat virus (LGTV). TBFV are generally transmitted to humans by ixodid ticks, and cause a spectrum of disease ranging from mild febrile illness to encephalitis, meningitis or hemorrhagic fevers. In the US, the cases of all tick-borne infections are increasing dramatically. POWV/DTV are the only autochthonous TBFV and case reports of serious illness and death are also on the increase. Importantly, POWV/DTV is transmitted by Ixodes scapularis ticks, the same vector that transmits the agent of Lyme disease, Borrelia burgdorferi, as well as several other emerging agents. Thus, a comprehensive evaluation of various tick-borne infections is needed to fully unravel the biology of the TBFV. These pathogens will continue to pose public health problems even in the face of the coronavirus pandemic. The mosquito borne flaviviruses include West Nile virus (WNV), Japanese encephalitis virus (JEV), dengue virus (DEN) and yellow fever virus (YFV). The dramatic and ongoing pandemic attributed to the MBFV Zika virus is important because of its capacity to cause a severe congenital Zika disease as well an ever increasing spectrum of neurological syndromes in adults. Our current investigations are focused on the TBFV, but studying the biology of TBFV will illuminate the biology of other vector borne viruses. The research in our laboratory employs virology, immunology, entomology, advanced imaging techniques, genomics, cell biology, molecular biology, and vector biology. We study LGTV, a naturally attenuated member of the TBFV that can be safely studied at Biosafety Level-2 (BSL-2) as well as the virulent autochthonous BSL-3 POWV/DTV. These viruses are not Select Agents which greatly facilitates research studies. In addition, we have also continued to study the BSL2 MBFV, Zika virus. With the persistent emergence of Zika in the western hemisphere, similar avenues of inquiry are being explored for that vexatious pathogen. TBFV biology in ex vivo cultures of I. scapularis organs. Infection in ticks is patently a critical feature of TBFV biology, but it is woefully understudied. Transmission of TBFV from the bite an Ixodes scapularis tick can occur in less than 15 minutes; thus virus biology in salivary glands (SG) is of considerable interest. In the past year, we extended our studies of ex vivo SG cultures to include male ticks. The feeding behavior of male ticks differs from that of females and their possible role in pathogen transmission unclear. We demonstrated that TBFV initiate a productive infection in male tick SG cultures, inferring that male ticks may also play a role in virus transmission. Confocal microscopy of SG cultures infected with a GFP-expressing TBFV revealed that not all granular acini support infection. This finding suggested that virus may target specific types of acini and specific cell types in SG. Thus, SG cultures likely provide a convenient and controlled system in which to look for genes associated with POWV replication and to assay antiviral countermeasures. Another aspect of this project involves identifying transcripts in SG cultures of female ixodid ticks that promote infection or are proviral. Since SG are the final barrier to transmission from the tick, identification of such genes would be of considerable interest, because proviral transcripts might serve as potential targets for countermeasure development. To date, four proviral transcripts have been identified via RNA interference assays in flavivirus-infected salivary gland cultures. Current ongoing research will finalize these RNA interference assays using salivary gland cultures from female ixodid ticks. Extending this work to confirm a proviral function of these transcripts in infected whole ticks would be logical. Finally, pathogen-tick interaction studies need to be confirmed in intact ticks, and furthermore emerging evidence from other groups indicates that the physiology of replete and partially fed ticks differs from unfed ticks. For example, TBFV grows to higher levels in fed ticks versus unfed ticks. Thus, it will be key to elucidate TBFV infection in ticks during various stages of blood feeding. We are approaching this issue by studying tick attachment, TBFV uptake and reproduction during blood feeding by means of small capsules with silicone-based membrane submerged in blood.. We have optimized female tick attachment using this setup and have confirmed partial feeding within these ticks. Ongoing work is confirming virus uptake using this method and characterizing virus replication as the ticks feed. This strategy will be very useful for various applications dealing with pathogen-tick studies during feeding. Since it does not involve live mammals as a target, the method will also be convenient for studying high consequence pathogens. This work was done by post-doctoral fellow Dr. Jeffrey Grabowski and post-baccalaureate trainee Luke Kendall. Microbial interactions within the microbiome of the tick Ixodes scapularis Studies indicate that B. burgdorferi can infect over 70% of I. scapularis ticks in some regions of the U.S., while POWV/DTV infects less than 5%. Similarly, the bacterial endosymbiont Rickettsia buchneri can achieve infection rates of 100% of the I. scapularis populations in some U.S. regions. Although there may be multiple reasons to explain this range of infection rates, one intriguing possibility is that ticks infected with one microbe may be less susceptible to infection by a second agent. Dr. Phillip Stewart joined BVBVS last year, bringing a wealth of experience in B. burgdorferi and other tick bacteria. Thus, we were able to establish a new project to probe for interactions (beneficial or antagonistic) between microbial species inhabiting I. scapularis. As this tick species is the leading vector of disease in the U.S., identifying such interactions may highlight methods to disrupt the infectious cycle of pathogens. Progress in this project was also halted by COVID-19, and results are minimal so far. However, the specific aims of this project are: 1.) Establish new techniques to study potential interactions between the microbial symbionts of the tick I. scapularis. We have adapted existing in vitro cell culture systems and in vivo animal models to sequentially introduce specific microbial species and directly assess their impact on the ability of a second agent to infect and persist. For the predominant symbiont R. buchneri, we are establishing methods to eliminate this endosymbiont from I. scapularis individuals, which will allow us to compare infection rates of both B. burgdorferi and POWV in these dysbiosed ticks. 2.) Identify the mechanisms of interactions between these microbes. Molecular pathogenesis of TBFV infections. In the past year Dr. Dylan Flather continued to employ genome wide loss of function studies to identify cellular genes that modulate TBFV infections, notably the autochthonous BSL3 TBFV POWV/DTV. Haploid mutagenized or Genome-Scale CRISPR Knock-Out (GecKO) lentiviral transduced cell pools, which contain individual knockouts of nearly all non-essential human genes, were infected with POWV. Deep sequencing of surviving cell populations allowed for the identification of deleted genes that are putative pro-viral host factors, as cells lacking these genes persist in cell culture following infection. Genes identified in this manner fell into", "keywords": [ "2019-nCoV", "Acinus organ component", "Adult", "Alkhurma Virus", "Animal Model", "Antiviral Agents", "Arthropods", "Attenuated", "Bacteria", "Basic Science", "Biological Assay", "Biology", "Biomedical Research", "Bite", "Black-legged Tick", "Blood", "Borrelia burgdorferi", "COVID-19", "COVID-19 pandemic", "Case Study", "Cell Culture System", "Cell Culture Techniques", "Cells", "Cellular biology", "Cessation of life", "Clustered Regularly Interspaced Short Palindromic Repeats", "Confocal Microscopy", "Coronavirus", "Deer Tick", "Dengue Virus", "Development", "Disease", "Disease Vectors", "Encephalitis", "Entomology", "Evaluation", "Experimental Models", "FDA approved", "Feeding behaviors", "Female", "Fever", "Flavivirus", "Flavivirus Infections", "Genes", "Genomics", "Haploidy", "Human", "Image", "Imaging Techniques", "Immunology", "In Vitro", "Individual", "Infection", "Integration Host Factors", "Investigation", "Ixodes", "Japanese encephalitis virus", "Knock-out", "Kyasanur Forest disease virus", "Laboratories", "Langat virus", "Legal patent", "Lyme Disease", "Mammals", "Membrane", "Meningitis", "Methods", "Microbe", "Molecular", "Molecular Biology", "Neurologic", "Omsk hemorrhagic fever virus", "Organ", "Pathogenesis", "Pharmaceutical Preparations", "Physiology", "Play", "Population", "Postdoctoral Fellow", "Powassan virus", "Public Health", "RNA Interference", "Reporting", "Reproduction", "Research", "Resources", "Rickettsia", "Role", "Salivary Glands", "Silicones", "Syndrome", "System", "Techniques", "Tick-Borne Encephalitis Virus", "Tick-Borne Infections", "Ticks", "Transcript", "Viral", "Viral Hemorrhagic Fevers", "Virulent", "Virus", "Virus Replication", "West Nile virus", "Work", "Yellow fever virus", "ZIKA", "ZIKV disease", "Zika Virus", "base", "capsule", "cell type", "cellular transduction", "deep sequencing", "endosymbiont", "experience", "feeding", "genome-wide", "hemorrhagic fever virus", "in vivo", "infection rate", "interest", "lentivirally transduced", "loss of function", "male", "member", "microbial", "microbiome", "microorganism interaction", "mosquito-borne", "novel", "novel coronavirus", "pandemic disease", "pathogen", "pathogenic virus", "research study", "symbiont", "tick feeding", "tick-borne", "transmission process", "uptake", "vector", "vector-borne", "viral transmission", "virology" ], "approved": true } }, { "type": "Grant", "id": "7722", "attributes": { "award_id": "1ZIAAI001297-01", "title": "Molecular pathogenesis of human coronaviruses", "funder": { "id": 4, "ror": "https://ror.org/01cwqze88", "name": "National Institutes of Health", "approved": true }, "funder_divisions": [ "National Institute of Allergy and Infectious Diseases (NIAID)" ], "program_reference_codes": [], "program_officials": [], "start_date": null, "end_date": null, "award_amount": 9073, "principal_investigator": { "id": 23513, "first_name": "Marshall", "last_name": "Bloom", "orcid": null, "emails": "", "private_emails": "", "keywords": null, "approved": true, "websites": null, "desired_collaboration": null, "comments": null, "affiliations": [ { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true } ] }, "other_investigators": [], "awardee_organization": { "id": 1540, "ror": "https://ror.org/043z4tv69", "name": "National Institute of Allergy and Infectious Diseases", "address": "", "city": "", "state": "MD", "zip": "", "country": "United States", "approved": true }, "abstract": "Since early 2020, the COVID-19 pandemic, caused the novel -coronavirus SARS-CoV-2, has ravaged the world and has disrupted much biomedical research. Consequently, we decided to focus a portion of our efforts on human coronaviruses, like SARS-CoV-2 and the Middle East Respiratory Syndrome coronavirus or MERS-CoV. Both MERS-CoV and SARS-CoV-2 are high consequence viral pathogens with the capacity to cause severe human disease, and SARS-CoV-2 has established a raging pandemic. This very new project will apply pre-existing expertise against this new pathogen. Suppression of SARS-CoV-2 and MERS-CoV replication by FDA-approved drugs The recent emergence of SARS-CoV-2 in 2019 and the emergence of MERS-CoV and SARS-CoV-1 in the past 20 years highlight the necessity of broad-spectrum antivirals that suppress coronaviruses and can be deployed against currently circulating coronaviruses and coronaviruses that emerge in the future. Dr. Stacey Scroggs arrived in BVBVS 4 months before the COVID-19 shutdown truncated research. Briefly, based on her thesis work, we selected several fluoroquinolone antibiotics and evaluated their ability to suppress several SARS-CoV-2 and MERS-CoV. We evaluated the potency of enoxacin, ciprofloxacin, levofloxacin, and moxifloxacin to suppress SARS-CoV-2 and MERS-CoV replication based Dr. Scroggss work cited in the previous section as well as the work of other suggesting anti-SARS activity of these compounds We demonstrated that at micromolar concentrations over 150 all four drugs suppress SARS-CoV-2 replication in Vero cells. The effective concentration 50 values (EC50) of these drugs against SARS-CoV-2 were between153.2M and 531.0M indicating that these 4 fluoroquinolones have low potency against SARS-CoV-2 and are unlikely to elicit a clinical benefit alone. The results for MERS-CoV were similar. Antiviral potency at these concentrations is not due to cellular toxicity as the Cytotoxic Concentration50 for all 4 drugs in both cell types are over 600M. Thus, it appears that the fluoroquinolones tested will not be useful therapeutics for these 2 high consequence coronaviruses. Although this is negative data, we feel it is noteworthy and it is being prepared for publication. Cellular mechanisms modulating replication of high consequence human coronaviruses. As noted in my other annual report, in the past year Dr. Dylan Flather continued to employ genome wide loss of function studies to identify cellular genes that modulate flavivirus infections. He will use his expertise in that area to examine 2 high consequence human coronaviruses, SARS-CoV-2 and MERS-CoV, as well as the common cold coronavirus HCoV-229e. Briefly, haploid mutagenized or Genome-Scale CRISPR Knock-Out (GecKO) lentiviral transduced cell pools, are being infected with MERS and our colleagues at CZ Biohub are doing the same with SARS-CoV-2 and HCoV-229E. Deep sequencing of surviving cell populations should allow for the identification of deleted genes that are putative pro-viral host factors, as cells lacking these genes persist in cell culture following infection. Genes identified in this manner will be grouped into functional groups. We have just initiated the MERS genome-wide screen and validation of protein hits will ensue. The pronounced ability of MERS-CoV to induce syncytia formation is a complicating factor that is being address by manipulating viral MOI and plating density of the cell libraries. SARS-CoV-2 and Animal Cell Lines. Building off of previous work with vector borne flaviviruses, we tested various animal cell lines for permissiveness to SARS-CoV-2 infection. The lines tested were mink lung, ferret brain, raccoon uterine, fox lung, opossum kidney, white tail deer brain, canine kidney, and woodchuck hepatocytes. While infectious virus was seen at 24 hours post infection (hpi), titers dropped throughout the remainder of the timepoints tested. Due to the lack of increasing replication throughout the growth curve, we cannot rule out residual inoculum accounting for the virus seen at 24hpi. We have decided not to further pursue this project. Anti-CD47 and anti-IL6 as SARS-CoV-2 Therapeutics. In collaboration with Dr. Kim Hasenkrugs group, we will be examining the use of anti-CD47 and anti-IL6 antibodies during SARS-CoV-2 infection. We hope to be able to use these antibodies as therapeutics to stop or, potentially, reverse the lung damage caused by SARS-CoV-2 infection. 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