Grant List
Represents Grant table in the DB
GET /v1/grants?page%5Bnumber%5D=4&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=1405&sort=start_date", "next": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=5&sort=start_date", "prev": "https://cic-apps.datascience.columbia.edu/v1/grants?page%5Bnumber%5D=3&sort=start_date" }, "data": [ { "type": "Grant", "id": "7768", "attributes": { "award_id": "1ZIADK071014-13", "title": "Development of obesity and metabolic clinical research programs", "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": 869835, "principal_investigator": { "id": 23570, "first_name": "Kong", "last_name": "Chen", "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": "In FY20, we made progresses in the following areas. 1. Our ongoing clinical protocol titled Energy expenditure responses to a range of environmental temperatures around the thermal neutral zone (12-DK-0097, NCT01568671) was designed to improve our understanding of dynamic regulation of energy expenditure in response to subtle changes in environmental temperature. In particular, we are interested in studying the capacity of (facultative) cold-induced thermogenesis in humans, defined as an increase in energy expenditure (EE or heat production) to a changed environmental temperature. Combined with the ongoing research on brown adipose tissue (BAT) and its role in cold-induced thermogenesis (CIT) in our and other labs, such clinical research is generating substantial interests in the field of energy metabolism and obesity. We measure resting energy expenditure in a 5-hour period in the room calorimeter with randomized environmental temperature ranging between 16 - 31C (61-88F), in 10-13 consecutive days (a 2-week inpatient protocol). We also carefully measure potential shivering, body movements, and heart rate, skin and core body temperatures, and stress responses by blood and urinary markers, while controlling for physical activity, clothing, and dietary intake. To date, we successfully studied fifteen (15) healthy lean male volunteers as our normative control group, nine (9) healthy obese male volunteers matched for age and race/ethnicity, sixteen (16) lean female volunteers (11 had repeated measurements in follicular and luteal menstrual phases), twelve (13) older lean male volunteers (11 with complete data), and thirteen (13) young lean African-American male (12 with complete data) volunteers. Due to the COVID-19 delays, we aim to recruit and complete the studies in 2-3 more older lean male volunteers this coming year. This data in lean and obese men was published in Journal of Clinical Endocrinology and Metabolism in 2019, the data from other cohorts are currently being analyzed. Since our current protocol only includes one small and homogeneous cohort of female volunteers (young, lean, and Caucasian), we plan to amend the protocol to include equal numbers of female volunteers of different adiposity, age, and race to be compared with the male volunteers studied so far. 2. The interests for brown adipose tissue (BAT) continue to grow. We performed BAT FDG-PET/CT scans for all the study subjects in 12-DK-0097. The publication (PNAS) in 2017 from our group showed that by making improvements to the image analysis methodologies, we could better quantify BAT volume, activity, and distribution in lean and obese subjects. We have trained several research groups to perform the same image analysis using our approaches. We used this rigorous approach in our PET/CT scans in our lean young women cohort and identified the existence of a unique depot of active BAT in women dorsocervical region which is the most superficial depot compare to other six deeper BAT depots that we previous quantified: cervical, supraclavicular, axillary, mediastinal, paraspinal, and abdominal. This paper was published by Obesity in 2020. In addition, we collaborated with our MRI colleagues in developing a novel non-radioactive technique to potentially identify human BAT. We have a paper accepted by Radiology, which we used localized 1H-MRS relaxometry to measure proton densities (T1s and T2s) in cold-activated BAT (confirmed by FDG-PET/CT) in our study subjects and compared to distal subcutaneous white adipose regions. reveals biophysical and biochemical differences between BAT and white fat. Our data suggest that it is feasible to identify BAT by MRS signatures, perhaps even without cold stimulation, which will improve the understanding of BAT in humans. 3. For the protocol 13-DK-0200, NCT01950520, we completed Cohort 1 studies (n=16) of using a pharmacologic approach to regulating sympathetic nervous system (SNS) by different beta-adrenergic receptors varying receptor specificity and agonist/antagonist properties and measure their effects on resting EE in thermoneutral vs. cold-stimulated states. We are currently analyzing the data and preparing manuscripts. We continue to recruit study participants for Cohort 2 (studying the single-dose effects of 4 different FDA approved anti-obesity drugs. Before the COVID-19 pandemic that paused our studies, we accrued 9 study participants so far (8 completed, one study was interrupted). An interim analysis showed that we would reach our primary outcome (5% increase of BMR in one drug) with 16 subjects. In addition, our collaboration with Dr. Aaron Cypess in the Cohort 3 study (n=13) on the dose-response of a 3-adrenergic agonists (mirabegron) to stimulate human BAT and energy expenditure resulted in a publication in Diabetes in FY19, which then emerged into a chronic mirabegron study (4-weeks) in women. This study has also resulted in a publication in the Journal of Clinical Investigation in 2020.", "keywords": [ "Abdomen", "Adipose tissue", "Adrenergic Agonists", "African American", "Age", "Agonist", "Anti-Obesity Agents", "Area", "Axilla", "Basal metabolic rate", "Biochemical", "Biophysics", "Blood", "Body Temperature", "Brown Fat", "COVID-19", "COVID-19 pandemic", "Caucasians", "Cervical", "Chronic", "Clinical", "Clinical Endocrinology", "Clinical Protocols", "Clinical Research", "Clothing", "Collaborations", "Control Groups", "Data", "Data Analyses", "Diabetes Mellitus", "Dietary intake", "Distal", "Dose", "Endocrinology", "Energy Intake", "Energy Metabolism", "Ethnic Origin", "FDA approved", "Fatty acid glycerol esters", "Female", "Food", "Goals", "Heart Rate", "Hour", "Human", "Image Analysis", "Inpatients", "Interruption", "Intervention", "Journals", "Magnetic Resonance Imaging", "Manuscripts", "Measurement", "Measures", "Mediastinal", "Metabolic", "Methodology", "Movement", "Obesity", "PET/CT scan", "Paper", "Participant", "Pharmaceutical Preparations", "Pharmacology", "Phase", "Physical activity", "Property", "Protocols documentation", "Protons", "Publications", "Publishing", "Race", "Radiology Specialty", "Randomized", "Regulation", "Research", "Rest", "Role", "Shivering", "Skin", "Specificity", "Study Subject", "Supraclavicular", "Sympathetic Nervous System", "Techniques", "Temperature", "Thermogenesis", "Thinness", "Training", "Woman", "beta-adrenergic receptor", "biological adaptation to stress", "clinical investigation", "cohort", "density", "design", "environmental change", "fight against", "fluorodeoxyglucose positron emission tomography", "improved", "interest", "male", "men", "novel", "obesity development", "primary outcome", "programs", "receptor", "recruit", "response", "subcutaneous", "total energy expenditure", "urinary", "volunteer", "young woman" ], "approved": true } }, { "type": "Grant", "id": "7691", "attributes": { "award_id": "1ZIADK029046-14", "title": "Methods to accelerate protein structure determination by solution NMR", "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": 995227, "principal_investigator": { "id": 23487, "first_name": "Adriaan", "last_name": "Bax", "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": "For unfolded proteins, the Rh provides a sensitive reporter on the ensemble-averaged conformation and the extent of polypeptide chain expansion as a function of added denaturant. Hydrostatic pressure is a convenient and reversible alternative to chemical denaturants for the study of protein folding, and enables NMR measurements to be performed on a single sample. Pulsed-field gradient NMR spectroscopy is widely used to measure the translational diffusion and hydrodynamic radius (Rh) of biomolecules in solution. However, while the impact of pressure on the viscosity of water is well known, we find that elevated pressures increase the Rh of dioxane, a commonly used reference standard, and other small molecules by amounts that correlate with their hydrophobicity, with parallel increases in rotational friction observed by 13C longitudinal relaxation times. These data point to a tighter coupling with water for hydrophobic surfaces at elevated pressures. Translational diffusion measurements of the unfolded state of a pressure-sensitized ubiquitin mutant (VA2-ubiquitin) as a function of hydrostatic pressure and as a function of urea concentration show that Rh values of both the folded and the unfolded states remain nearly invariant. At ca 23 angstrom, the Rh of the fully pressure-denatured state is essentially indistinguishable from the urea-denatured state, and close to the value expected for an idealized random coil of 76 residues. The intrinsically disordered protein (IDP) alpha-synuclein shows slight compaction at pressures above 2 kbar. Diffusion of both unfolded ubiquitin and alpha-synuclein is significantly impacted by sample concentration, indicating that quantitative measurements need to be carried out under dilute conditions. Small heat-shock proteins (sHSPs) are molecular chaperones that respond to cellular stresses to combat protein aggregation. HSP27 is a critical human sHSP that forms large, dynamic oligomers whose quaternary structures and chaperone activities depend on environmental factors. Upon exposure to cellular stresses, such as heat shock or acidosis, HSP27 oligomers can dissociate into dimers and monomers, which leads to significantly enhanced chaperone activity. The structured core of the protein, the alpha-crystallin domain (ACD), forms dimers and can prevent the aggregation of substrate proteins to a similar degree as does the full-length protein. We have shown that when the ACD dimer dissociates into monomers, it partially unfolds and exhibits enhanced activity. Using solution-state NMR spectroscopy to characterize the structure and dynamics of the HSP27 ACD monomer, we have shown that the monomer is stabilized at low pH and that its backbone chemical shifts, N-15 relaxation rates, and 1H-15N residual dipolar couplings suggest structural changes and rapid motions in the region responsible for dimerization. By analyzing the solvent accessible and buried surface areas of sHSP structures in the context of a database of dimers that are known to dissociate into disordered monomers, we predict that ACD dimers from sHSPs across all kingdoms of life may partially unfold upon dissociation. This resulted in a general model in which conditional disorder-the partial unfolding of ACDs upon monomerization-is a common mechanism for sHSP activity. A series of novel three- and four-dimensional NMR experiments has been developed that provides access to the structure and dynamics of the 608-residue homodimeric Main protease of the SARS-CoV-2 virus. This protein is larger than what is readily accessible to the standard NMR approaches used, but the novel methods combined with 900 MHz high-field measurements provided sufficient data for a detailed structural analysis which reveals subtle but statistically very significant differences relative to all X-ray structures available so far. A characterization of the backbone dynamics shows a strong effect of ligands on the dynamics of the protein backbone in the active site region.", "keywords": [ "2019-nCoV", "3-Dimensional", "Acidosis", "Active Sites", "Algorithms", "Area", "Biological", "Cellular Stress", "Chemicals", "Collection", "Core Protein", "Coupling", "Data", "Data Analyses", "Databases", "Diffusion", "Dimerization", "Dioxanes", "Disease", "Dissociation", "Environmental Risk Factor", "Exhibits", "Exposure to", "Four-dimensional", "Friction", "Goals", "HSPB1 gene", "Heat shock proteins", "Heat-Shock Response", "Human", "Hydrophobic Surfaces", "Hydrophobicity", "Hydrostatic Pressure", "Length", "Life", "Ligands", "Measurement", "Measures", "Methods", "Modeling", "Molecular Chaperones", "Molecular Conformation", "Molecular Structure", "Motion", "NMR Spectroscopy", "Pattern", "Peptide Hydrolases", "Physiologic pulse", "Protein Dynamics", "Proteins", "Radial", "Reference Standards", "Relaxation", "Reporter", "Residual state", "Roentgen Rays", "Rotation", "Sampling", "Series", "Solvents", "Structure", "Surface", "Time", "Ubiquitin", "Urea", "Vertebral column", "Virus", "Viscosity", "Water", "alpha synuclein", "alpha-Crystallins", "combat", "data acquisition", "dimer", "experimental study", "monomer", "mutant", "novel", "polypeptide", "pressure", "prevent", "protein aggregation", "protein folding", "protein structure", "restraint", "small molecule" ], "approved": true } }, { "type": "Grant", "id": "7739", "attributes": { "award_id": "1ZIAAG000581-01", "title": "Molecular Characterization of the SARS-CoV-2 Helicase and High-Throughput Screening to Identify Small Molecule SARS-CoV-2 Helicase Inhibitors as Anti-Viral Medicines", "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": 30287, "principal_investigator": { "id": 23534, "first_name": "Robert", "last_name": "Brosh", "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 COVID-19 Pandemic caused by the novel Severe Acute Respiratory Syndrome (SARS)- Coronavirus (CoV)-2 has necessitated prompt action by biomedical researchers to study key steps in the virus life cycle and identify viral replication targets for molecular interventions leading to therapeutic options. This project focuses on molecular characterization of SARS-CoV-2 (Nsp13) helicase essential for coronavirus replication. Analyses of SARS-CoV-2 helicase will advance our fundamental understanding of its mechanism-of-action and partnership with SARS-CoV-2 Nsp12 RNA-dependent RNA polymerase1. High-throughput screens to identify small molecules that interfere with catalytic functions and interactions of SARS-CoV-2 helicase will provide a strategy for crippling viral replication, a paradigm that builds upon ongoing studies of the Nsp12 polymerase targeting compound Remdesivir2. Discovery of candidate COVID-19 helicase inhibitors may lead to a novel therapeutic anti-viral approach applicable as mono-therapy or combination therapy with anti-viral drugs in use or development. COVID-19 poses a special challenge for the aging population who often have underlying medical conditions3. Age-related comorbid conditions, immuno-senescence, higher risk for infection and sickness in nursing homes, and complications of social distancing for older people likely contribute to elevated risk of mortality for aged individuals. Immune dysfunction and compromised virus (immune) pathogenesis are significant factors influencing the efficacy of future vaccines against COVID-19 for the elderly. Consequently, anti-viral therapies, ultimately combined with immunological strategies, will be advantageous. This COVID-19 research proposal is focused on a key SARS-CoV-2 replication target (helicase) and discovery of small molecule inhibitors as antiviral medicines.", "keywords": [ "2019-nCoV", "Antiviral Agents", "Antiviral Therapy", "Biochemical", "Biological Assay", "COVID-19", "COVID-19 pandemic", "Collection", "Combined Modality Therapy", "Coronavirus", "Crystallization", "Development", "Elderly", "Future", "Goals", "Immune", "Immune System Diseases", "Immunologics", "Individual", "Intervention", "Lead", "Life Cycle Stages", "Medical", "Medicine", "Molecular", "Molecular Bank", "Molecular Target", "Nucleic Acids", "Nucleotides", "Nursing Homes", "Pathogenesis", "Polymerase", "Proteins", "RNA", "RNA Polymerase III", "RNA-Directed RNA Polymerase", "Research Personnel", "Research Proposals", "Resolution", "Social Distance", "Structure", "Structure-Activity Relationship", "Therapeutic", "Vaccines", "Virus", "Virus Replication", "age related", "aged", "aging population", "biophysical properties", "comorbidity", "helicase", "high risk", "high throughput screening", "immunosenescence", "infection risk", "inhibitor/antagonist", "mortality risk", "novel", "novel therapeutics", "repository", "small molecule", "small molecule inhibitor", "small molecule libraries" ], "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": "7731", "attributes": { "award_id": "1ZIABC010671-16", "title": "Genetic Analysis of T-cell Differentiation", "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": 2380130, "principal_investigator": { "id": 23526, "first_name": "remy", "last_name": "bosselut", "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": "We study the transcriptional control of T cell development and function. T cells are essential for immune responses. Most recognize peptide antigens presented by class I (MHC-I) or class II (MHC-II) classical Major Histocompatibility Complex molecules, and express either of two surface glycoproteins that contribute to antigen recognition: CD4, which binds MHC-II, or CD8, which binds MHC-I. Consistent with such binding properties, MHC I-specific T cells generally are CD4-CD8+ (CD8 T cells), whereas MHC II-specific T cells generally are CD4+CD8- (CD4 T cells). CD4 and CD8 T cells differentiate in the thymus from precursors that express both CD4 and CD8 ('double-positive', DP). CD4 T cells are essential for life: CD4 T cell deficiency, whether innate or acquired, leads to recurrent or chronic infections and death. Because of their pivotal role in immune responses, CD4 T cells have remained the main focus of the laboratory research. CD4 T cells responding to infection or immunization (e.g. vaccine) proliferate and, depending on the local inflammatory context, differentiate into effector subtypes endowed with specific functions. Infections by intra-cellular pathogens (e.g. viruses) result in the generation of 'Th1' CD4 T cells producing interferon (IFN)-gamma and of follicular helper CD4 T cells (Tfh), which provide help to B cells for antibody maturation. Such B cell help is a critical function of CD4 T cells, disrupted in various inherited human immunodeficiency syndromes. It is required for durable and protective antibody responses and is considered to be a limiting factor for the generation of broadly neutralizing antibodies against HIV or influenza viruses. Last, long-lived memory CD4 T cells, persisting after pathogen clearance, contribute to durable immunity, together with the B cell response. Efficient differentiation of Tfh and memory CD4 T cells are key objectives of vaccination strategies. Recent work in the laboratory has addressed two aspects of CD4 T cell functions: (i) the mechanisms directing the differentiation of Tfh cells in vivo and (ii) the responses of CD4 T cells to tumor antigens. To address the first question, we primarily studied the CD4 T cell response to a prototypical mouse pathogen, Lymphocytic ChorioMeningitis Virus (LCMV). In a previous report (Ciucci et al., 2019), we characterized the differentiation of LCMV-responsive CD4 T cells by single-cell RNA sequencing (scRNAseq). In these studies, we had observed that the transcription factor Thpok, which promotes the differentiation of CD4 T cells in the thymus, is necessary in post-thymic CD4 T cells for their acquisition of transcriptomic signatures characteristic of Tfh cells. Because both Thpok expression and Tfh differentiation are specific of CD4 T cells, this suggested that Thpok expression could be important for Tfh cell differentiation and proper antibody responses after immunization. Indeed, using genetic strategies to inactivate Thpok in mature CD4 T cells, we verified that Thpok is necessary for the differentiation of Tfh cells, for the formation of germinal centers, the lymphoid organ structure in which B cell-Tfh cell cooperation gives rise to high-affinity antibodies, and for antibody maturation. We further verified that the requirement for Thpok was not unique to virus responses, using immunization with recombinant antigens or parasites. Using RNA sequencing and chromatin immunoprecipitation experiments, we identified potential targets of Thpok, including the surface molecule CD40L, and the transcription factors Bcl6 and Maf. Last, using retroviral transduction experiments, we demonstrated that enforced expression of Bcl6 and Maf into Thpok-deficient CD4 T cells restores at least in part their potential for Tfh differentiation. Altogether, these findings established Thpok as a key controller of Tfh cell differentiation and help to B cells. In addition to their role in fighting infection, CD4 T cells are involved in responses to tumors. Regulatory CD4 T cells often help tumors to escape immune responses, whereas Th1 CD4 T cells contribute to inhibit tumor progression. Clinical and basic studies have emphasized the role of MHC II-presented antigens and of CD4 T cells in tumor control, and established the anti-tumor potential of CD4 T cells. However, CD4 T cell responses to tumors are highly heterogeneous and incompletely understood. Thus, comparing the CD4 T cell responses to intra-cellular pathogens and to tumor antigens is expected to shed light on strategies to exploit CD4 T cells against tumors. We recently leveraged the expertise we acquired in our investigations of LCMV responses to study the response of CD4 T cells to cancer. As a first step, we generated a simple and tractable model of CD4 T cell responses to cancer, by expressing an antigen derived from LCMV in a colon adenocarcinoma cell line; with this approach, analyses of LCMV-antigen responses (in the absence of LCMV infection) serve as surrogate for tumor-specific responses. Combining this approach with high-throughput single-cell RNA sequencing (scRNAseq), we identified unique transcriptomic patterns in tumor-specific CD4 T cells, distinct from those observed in responses to infection. We notably highlighted a transcriptomic signature characteristic of type I IFN signaling, that is also found in human tumors, in which is associates with poor responses to checkpoint therapy. Ongoing research explores the mechanistic basis of CD4 T cell responses to tumors. We are also investigating Ace2 gene responsiveness to improve Covid19 mouse models.", "keywords": [ "Address", "Aging", "Antibodies", "Antibody Affinity", "Antibody Response", "Antigen Targeting", "Antigens", "B-Lymphocytes", "Binding", "Biochemical", "Bone Marrow Transplantation", "CD4 Antigens", "CD4 Positive T Lymphocytes", "CD8-Positive T-Lymphocytes", "CD8B1 gene", "COVID-19", "CRISPR/Cas technology", "Cancer Patient", "Cause of Death", "Cell Differentiation process", "Cell Line", "Cell physiology", "Cells", "Cessation of life", "Characteristics", "Chromatin", "Clinical", "Colon Adenocarcinoma", "DNA-Binding Proteins", "Experimental Neoplasms", "Gene Expression", "Gene Expression Profiling", "Generations", "Genes", "Genetic Transcription", "HIV", "Human", "Immune response", "Immune system", "Immunity", "Immunization", "Immunologic Deficiency Syndromes", "Immunology", "Infection", "Inflammatory", "Inherited", "Interferon Type I", "Interferon Type II", "Investigation", "Laboratories", "Laboratory Research", "Leukocytes", "Life", "Light", "Lymphocytic choriomeningitis virus", "Major Histocompatibility Complex", "Malignant Neoplasms", "Membrane Glycoproteins", "Modeling", "Molecular", "Morbidity - disease rate", "Mus", "Mutant Strains Mice", "Myeloablative Chemotherapy", "Parasites", "Pattern", "Peptides", "Proliferating", "Property", "Protein Analysis", "Puberty", "Recombinants", "Reporting", "Research", "Role", "Shapes", "Signal Transduction", "Structure", "Structure of germinal center of lymph node", "Surface", "T cell differentiation", "T cell response", "T-Cell Depletion", "T-Cell Development", "T-Lymphocyte", "TNFSF5 gene", "Thymus Gland", "Transcriptional Regulation", "Tumor Antigens", "Vaccines", "Viral Antigens", "Virus", "Virus Diseases", "Work", "cell mediated immune response", "checkpoint therapy", "chromatin immunoprecipitation", "chronic infection", "experimental study", "fighting", "genetic analysis", "genetic approach", "genome editing", "high throughput analysis", "improved", "in vivo", "influenzavirus", "lymphoid organ", "memory CD4 T lymphocyte", "mortality", "mouse model", "neutralizing antibody", "novel", "pathogen", "programs", "protein function", "recurrent infection", "response", "retroviral transduction", "single-cell RNA sequencing", "transcription factor", "transcriptome sequencing", "transcriptomics", "tumor", "tumor progression", "vaccination strategy" ], "approved": true } }, { "type": "Grant", "id": "7743", "attributes": { "award_id": "1ZIAAI000938-17", "title": "Paramyxoviruses as Vaccine Vectors Against Highly Pathogenic Viruses", "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": 279642, "principal_investigator": { "id": 23540, "first_name": "Ursula", "last_name": "Buchholz", "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": "We previously constructed a first-generation construct called HPIV3-EbovZ GP, in which the complete genome of the JS strain of HPIV3 was modified by the addition of the EBOV GP gene in the third gene position, between the HPIV3 P and M genes. The JS strain is thought to be an attenuated HPIV3, based on previous clinical studies, although the basis of this attenuation is unknown. EBOV GP is the sole EBOV virion surface protein, the sole EBOV neutralization antigen, and the major protective antigen. The EBOV GP gene was engineered to have the appropriate HPIV3 transcription signals for it to be expressed as a separate mRNA by the HPIV3 polymerase. HPIV3-EbovZ GP was substantially immunogenic and protective when given to non-human primates by combined intranasal (IN) and intratracheal (IT) administration, even in animals previously infected with HPIV3. However, immunogenicity depended on IT delivery of vaccine: IN delivery alone was insufficient. This suggested that vector expression beyond the upper respiratory tract was necessary for immunogenicity. We therefore explored delivery of the HPIV3-EbovZ GP construct by the aerosol route in rhesus macaques. The aerosol route was generally more immunogenic and protective than the combined IN/IT route. This induced generally higher serum and mucosal EBOV-specific IgG, IgA, and neutralizing antibody titers, as well as EBOV-specific cellular responses in the lungs, including polyfunctional CD8+ T cells and CD4+ T helper cells that were predominately Th1. In addition, the HPIV3-EbovZ GP vaccine induced more robust cell-mediated and humoral immune responses than an alphavirus vaccine delivered parenterally in parallel. One aerosol dose of HPIV3-EbovZ GP conferred 100% protection to macaques against EBOV challenge. We developed a second-generation version of this vector, called HPIV3/delHNF/EbovZ-GP, in which the HPIV3 F and HN genes were deleted, leaving EBOV GP as the sole viral surface glycoprotein. A large comparative study in cynomolgus monkeys by our collaborator Alexander Bukreyev at the University of Texas Medical Branch, Galveston, (who made the construct while a Staff Scientist in LID/NIAID) showed that this second-generation version was even more protective than the first-generation even though it was very highly restricted for replication (much more restricted than the first-generation construct). We performed (with clinical collaborators at the Johns Hopkins Bloomberg School of Public Health) an open label phase 1 clinical trial to determine the safety, tolerability, and immunogenicity of HPIV3-EbovZ GP delivered IN in healthy adults in an inpatient setting (NCT025645750), which was intended to be a safety study prior to evaluating aerosol delivery. Ten subjects received two doses (4- to 8-week interval) of 6.0 log10 PFU of vaccine. The first dose was moderately infectious (7/10 subjects shed virus detected by qRT-PCR, mean peak titer 3.8 log10 genomic equivalents/ml, mean duration of shedding 7.9 days). Little shedding was detected after the second dose. A second cohort (n=20) received one of two planned doses of 7.0 log10 PFU of vaccine. Shedding was similar but of shorter duration (mean of 3.7 days). The vaccine was well tolerated, with the exception that asymptomatic ALT elevations were noted in 5 volunteers (3 mild, 2 moderate) in cohort 2 after vaccination and associated with shedding. All resolved by day 28. The study was halted due to these elevations of ALTs, but their significance is unclear. Because of this, this vaccine will not be administered further at this time. Induction of serum antibodies was poor (mucosal antibodies not yet analyzed), but this was expected since, as noted above, we had previously observed that administration by the IN route alone was poorly immunogenic in rhesus monkeys. We have initiated a Phase 1 study to evaluate the safety, infectivity, and immunogenicity of two doses of the HPIV3/HNF/EbovZ GP vaccine candidate when administered intranasally in healthy adults in an inpatient setting (NCT03462004). Participants are being enrolled sequentially in two cohorts. Participants in Cohort 1 have been randomly assigned to receive two doses of either 6.0 log10 PFU/mL of HPIV3/delHNF/EbovZ-GP vaccine or placebo. The first dose was given on Day 0 and the second dose was given 35 days later. Vaccine replication was evaluated by nasal wash and RT-qPCR and infectivity assays, and serum antibody responses will be measured. As expected, at the 6.0 log10 PFU dose, the HPIV3/HNF/EbovZ-GP vaccine was marginally infectious, and adverse events were generally mild to moderate. The study was deemed safe to proceed to the evaluation of the higher 7.0 log10 PFU dose after the closures due to the current SARS-CoV-2 pandemic will be lifted. Participants in Cohort 2 will be randomly assigned to receive two doses of either 7.0 log10PFU/mL of HPIV3/HNF/EbovZ-GP vaccine or placebo on Days 0 and 28.", "keywords": [ "2019-nCoV", "Adult", "Adverse event", "Aerosols", "Alphavirus", "Animals", "Antibodies", "Antibody Response", "Antibody titer measurement", "Antigens", "Attenuated", "Avian Influenza A Virus", "Avulavirus", "Biological Assay", "CD4 Positive T Lymphocytes", "CD8-Positive T-Lymphocytes", "Cattle", "Cavia", "Cell Culture Techniques", "Cells", "Child", "Chimera organism", "Clinical", "Clinical Research", "Comparative Study", "Coronavirus spike protein", "Development", "Dose", "Ebola virus", "Ebola virus envelope glycoprotein", "Effectiveness", "Engineering", "Enrollment", "Evaluation", "Family member", "Gene Order", "Generations", "Genes", "Genetic Transcription", "Genome", "Genomics", "Glycoproteins", "Human", "Immune response", "Immunity", "Immunoglobulin A", "Immunoglobulin G", "Infant", "Infection", "Influenza Hemagglutinin", "Inpatients", "Intranasal Administration", "Lifting", "Lung", "Macaca", "Macaca fascicularis", "Macaca mulatta", "Measures", "Mediating", "Medical", "Membrane Glycoproteins", "Membrane Proteins", "Messenger RNA", "Modification", "Mucosal Immunity", "Mucous Membrane", "National Institute of Allergy and Infectious Disease", "Newcastle disease virus", "Nose", "Para-Influenza Virus Type 1", "Para-Influenza Virus Type 3", "Paramyxovirus", "Participant", "Pathogenicity", "Phase I Clinical Trials", "Placebos", "Polymerase", "Population", "Primates", "Proteins", "Public Health Schools", "Quantitative Reverse Transcriptase PCR", "RNA", "Randomized", "Respiratory System", "Rodent", "Route", "SARS coronavirus", "Safety", "Scientist", "Serotyping", "Serum", "Severe Acute Respiratory Syndrome", "Signal Transduction", "Structure of respiratory epithelium", "Surface Antigens", "System", "TRIP10 gene", "Testing", "Texas", "Time", "United States National Institutes of Health", "Universities", "Upper respiratory tract", "Vaccination", "Vaccines", "Viral", "Viral Vaccines", "Virion", "Virus", "Virus Replication", "Virus Shedding", "Work", "attenuation", "base", "cohort", "conjunctiva", "design", "expression vector", "immunogenic", "immunogenicity", "neutralizing antibody", "nonhuman primate", "open label", "pandemic disease", "parainfluenza virus", "pathogen", "pathogenic virus", "phase 1 study", "respiratory", "response", "reverse genetics", "safety study", "seropositive", "tissue tropism", "vaccine candidate", "vaccine delivery", "vaccine development", "vector", "vecto" ], "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": "7756", "attributes": { "award_id": "1ZICBC011236-12", "title": "CCR-Frederick Flow Cytometry Core", "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": 448770, "principal_investigator": { "id": 23556, "first_name": "Jeffrey", "last_name": "Carrell", "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": "To date in FY2020, the Core has performed 1170 billable services including 163 cell sorts. The Core recorded 62 users from the following programs: Cancer and Developmental Biology Lab, Division of Cancer Treatment and Diagnosis, HIV Dynamics and Replication Laboratory, Animal Sciences Program, Laboratory of Cancer Immunometabolism, Laboratory of Cell and Developmental Signaling, Laboratory of Integrative Cancer Immunology, Laboratory of Molecular Cell Biology, Laboratory of Protein Dynamics and Signaling, Mouse Cancer Genetics Program, and the RNA Biology Lab. SIGNIFICANT ACHIEVEMENTS: -Response to COVID-19: The Core leadership joined with other NCI cytometry cores to draft and publish guidelines for handling human samples within NCI flow cytometry laboratories; guidance was reviewed by laboratory chiefs and distributed to Investigators. Recognizing the need for clear communication to users of the Core describing precautions and evolving guidance, a modified reservation policy was developed and distributed to investigators in a one-sheet visual summary. -Enhancement of Training Program: The Core joined with other NCI cytometry cores to develop and present flow cytometry educational lectures at the NIH Bethesda campus in May and November 2019. We coordinated vendor training days for 2 new cytometers procured and installed in 2019 by Miltenyi Biotec and BDBiosciences. We continue to improve our ad-hoc user trainings with facility-specific software tutorials recently converted to self-paced 'youtube' style video. -Keeping Pace with Evolving Cytometry: As of this writing, the Core is installing two high-dimensional cytometers, each with 5 lasers and capable of measuring more than 30 simultaneous parameters, thus keeping pace with emerging trends in cytometry and proteomics. The Cytek Aurora represents a new class of cytometer that uses the entire spectrum from ultraviolet to infrared to deconvolute fluorescent signals; this added analytical power can derive more usable data from limited samples like tumor infiltrating leukocytes. The BD Biosciences Symphony S6 is capable of high-speed separation of finely defined immune cell subsets into up to six distinct types simultaneously or depositing single defined cells into 96 or 384-well plates for cloning or deep-sequencing. Two instruments manufactured in 2007 and 2009 with pending vendor obsolescence will be retired. -Special Recognition: A member of the Core team earned the Specialist in Cytometry (SCYM) credential by the American Society of Clinical Pathology, indicating \"broad proficiency of technical and operational aspects of cytometry and shared resource (core) labs\".In July 2020, the lab staff was notified of a NCI Director's Award for \"For exceptional initiative and leadership in enhancing flow cytometry support in the NCI through improved facility coordination, training and strategic planning\".", "keywords": [ "Achievement", "American", "Award", "Biological Sciences", "Biology", "CCR", "COVID-19", "Cancer Biology", "Cell Separation", "Cells", "Cellular biology", "Clinical Pathology", "Cloning", "Communication", "Computer software", "Consult", "Cytometry", "Data", "Data Collection", "Deposition", "Development", "Developmental Biology", "Division of Cancer Treatment and Diagnosis", "Evaluation", "Flow Cytometry", "Guidelines", "HIV", "Human", "Immune", "Laboratories", "Laboratory Animal Science", "Lasers", "Leadership", "Leukocytes", "Life Cycle Stages", "Maintenance", "Malignant Neoplasms", "Measures", "Molecular", "Mus", "Optics", "Policies", "Protein Dynamics", "Proteomics", "Publishing", "RNA", "Reagent", "Research Personnel", "Reservations", "Resource Sharing", "Resources", "Sampling", "Schedule", "Services", "Signal Transduction", "Societies", "Sorting - Cell Movement", "Specialist", "Speed", "Strategic Planning", "Technology", "Training", "Training Programs", "United States National Institutes of Health", "Vendor", "Visual", "Writing", "assay development", "cancer genetics", "deep sequencing", "design", "experimental study", "flexibility", "high dimensionality", "improved", "instrument", "investigator training", "lectures", "member", "physical separation", "programs", "quality assurance", "response", "trend", "tumor", "tumor immunology", "ultraviolet" ], "approved": true } }, { "type": "Grant", "id": "7727", "attributes": { "award_id": "1ZICES103326-04", "title": "NIEHS Cryo-EM Core Facility", "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": 2904674, "principal_investigator": { "id": 23521, "first_name": "Mario", "last_name": "Borgnia", "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": "During FY2020, the Cryo-EM Core continued to collaborate with regional researchers through the Molecular Microscopy Consortium. The high productivity of the past year is reflected in the number of publications that resulted from over two dozen collaborations. This year we had our first Regional Symposium in cryo-EM organized by NIEHS, Duke and UNC. The symposium featured over 20 speakers and was attended by over 100 local scientists. Most of the work presented in the symposium was performed in collaboration with Core personnel in the context of the Molecular Microscopy Consortium. At the onset of the COVID-19 pandemic, we had been actively collaborating with Dr. Priyamvada Acharya at the Duke Human Vaccine Institute and with Dr. Eric Freed at NCI-Frederick on various structural questions involving the main viral antigen of HIV, the envelope glycoprotein Env. In response, we rapidly repurposed our structural virology pipelines to study the analogous SARS-CoV-2 S-protein. This prompted additional collaborations in the IRP, most notably an effort to map the binding sites of nanobodies developed by the group of Dr. Matt Hall at NCATS. We are also collaborating with others at NIEHS to solve the structure of a variety of SARS-CoV-2 non-structural proteins. The collaborations of the Cryo-EM Core have also grown in the NIH Intramural Program. In addition to ongoing work with colleagues at NCI, through the first half of FY2020 we have discussed a series of prospective collaborative projects with other ICs. These include both providing access to current technologies in single particle cryo-EM as well as the development of new capabilities in cryo-electron tomography and in situ structure determination. The interactions led to the organization of an intramural consortium between NIEHS, NCATS, NIA, NIBIB and NIDA for the purchase of a state of the art 300 keV TFS Titan Krios cryo-electron microscope which is expected to be operational at NIEHS by the spring of 2021.", "keywords": [ "2019-nCoV", "Binding Sites", "COVID-19 pandemic", "Collaborations", "Complex", "Core Facility", "Cryo-electron tomography", "Cryoelectron Microscopy", "Crystallization", "Development", "Electron Microscope", "Electron Microscopy", "Ensure", "Goals", "HIV Antigens", "Human", "Human Resources", "In Situ", "Institutes", "Intramural Research Program", "Macromolecular Complexes", "Maps", "Membrane Proteins", "Methods", "Microscopy", "Mission", "Molecular", "Molecular Structure", "National Institute of Biomedical Imaging and Bioengineering", "National Institute of Drug Abuse", "National Institute of Environmental Health Sciences", "Nonstructural Protein", "Nuclear Magnetic Resonance", "Preparation", "Process", "Productivity", "Proteins", "Publications", "Research", "Research Personnel", "Resolution", "Scientist", "Series", "Specimen", "Structural Biologist", "Structure", "Techniques", "Technology", "Titan", "Training", "United States National Institutes of Health", "Vaccines", "Viral Antigens", "Work", "X-Ray Crystallography", "collaborative environment", "env Glycoproteins", "image processing", "macromolecule", "nanobodies", "new technology", "novel strategies", "particle", "prospective", "response", "structural biology", "symposium", "tool", "virology" ], "approved": true } }, { "type": "Grant", "id": "7754", "attributes": { "award_id": "1ZICBC010981-13", "title": "Biomarker Investigations for Clinical Trials", "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": 1025905, "principal_investigator": { "id": 23554, "first_name": "Liang", "last_name": "Cao", "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": "Related to the specific goals above, we conducted various studies to support biomarker driven early-stage drug development: 1) Application of new or novel biomarkers in early stage trials of highly unique therapeutic agents. A) We were involved the biomarker studies for the first in phase Ia human study of a dual function immune-targeting agent M7824 by Dr. James Gulley. Our data was the first for the mechanism of action of this agent. Our data also provided the first set of information on the dose-response relationship, which is necessary for drug dose selection (Clin. Cancer Res. 24: 1287-1295, 2018). We continue to support the follow up work. B) We conduct the biomarkers studies in a trial by Dr. Vladimir Valera on an EpCAM antibody, vicinium, in combination with immunotherapy. In the study, we develop both PD and PK assays for the drug, as well as conduct immune cytokine profiling for the trial. Our results provided the first informative PK data on vicinium and the trial is on-going. C) We developed a cell free DNA detection for cervical cancer and use it for treatment monitoring, MRD detection, cancer genotyping for patient selection. Some of the work was published (Clin Cancer Res. 23:6856-6862, 2017). We are currently support about 5 trials by Dr. Christian Henrichs. D) We support marker investigation of Dr. Andrea Apolo by investigating the drugs effects on angiogenesis and inflammation. The work was recently published (Lancet Oncol. doi: 10.1016/S1470-2045(20)30202-3, 2020). 2) Identification of new biomarkers. A) We collaborate with Dr. Brid Ryan in biomarker discovery work, and work results in several publications (Cancer Epidemiol Biomarkers Prev, doi: 10.1158/1055-9965, 2019; J Thorac Oncol. 14:1192-1203, 2019). The tests involved highly plex clinical grade assays with thousands of samples, produced over 100,000 test results. B) We worked with Dr. Ira Pastan and Raffit Hassan to uncover biomarkers for treatment monitoring and response prediction. The early results were published (JCO Precis Oncol. doi: 10.1200/PO.17.00282, 2018), and we continuously support a number of NCI trials by Dr. Hassan and Dr. Alewine on mesothelin-targeted agents. C) In working with Dr. Steven Pavletic, we developed new cytokine tests for the investigation of graft vs host disease (Am J Hematol. doi: 10.1002/ajh.25717, 2020). 3) Assay development and validation. A) We developed a new tumor antigen test and carried extensive analytic and clinical validation, leading to the approval of the test by NCI Biomarker Committee for applications of multiple NCI-sponsored multicenter trials (J Appl Lab Med. 3: 166-177, 2018). We currently three multicenter trials with this test to assess its ability for treatment monitoring and patient selection. B) We developed a cell free DNA for patient selection and treatment monitoring of HPV positive cancer patients on adoptive T cell therapies. We have conducted a joint assay validation with Kite Pharma and have the assay transfer to their operation for treatment monitoring and patient selection. C) In response to COVID-19, we initiated a serology assay development effort. Based on our preliminary data, our assay would likely have the performance comparable to these by Roche and Abbott. However, a potential advantage of our assay over these two is the ability to detect antibodies required for virus neutralization. I believe that this would allow to address future issues such as immunization, immunity, and repeat infections. This work is not included in the time allocation of FY2020. 4) New technology development. A) We focus on the development of a circulating tumor DNA based technology for determining cancer gene mutations associated with treatment responses, and for the identification of mutations associated with resistance. Our current work is on the analysis of HPV positive tumors escaping from adoptive T cell immunotherapies. The work is to support trials by Dr. Christian Hinrichs. B) We work on cell free DNA test to support cancer diagnosis in pregnant women in a trial by Dr. Christina Annunziata.", "keywords": [ "Address", "Antibodies", "Biological Assay", "Biological Markers", "COVID-19", "Cancer Gene Mutation", "Cancer Patient", "Clinical", "Clinical Drug Development", "Clinical Trials", "Data", "Detection", "Development", "Disease", "Dose", "Drug Kinetics", "Evaluation", "Future", "Goals", "HPV analysis", "Human Papillomavirus", "Immune", "Immune response", "Immunity", "Immunization", "Immunotherapy", "Infection", "Inflammation", "Investigation", "Investigational Therapies", "Joints", "Laboratories", "Malignant Neoplasms", "Malignant neoplasm of cervix uteri", "Monitor", "Multicenter Trials", "Mutation", "Patient Monitoring", "Patient Selection", "Patient-Focused Outcomes", "Performance", "Pharmaceutical Preparations", "Pharmacodynamics", "Phase", "Pregnant Women", "Publications", "Publishing", "Resistance", "Sampling", "Selection for Treatments", "Serologic tests", "T cell therapy", "T-Lymphocyte", "TACSTD1 gene", "Technology", "Test Result", "Testing", "Therapeutic", "Therapeutic Agents", "Time", "Tumor Antigens", "Tumor Escape", "Tumor Markers", "Validation", "Virus", "Work", "angiogenesis", "assay development", "base", "biomarker discovery", "biomarker-driven", "cancer diagnosis", "cell free DNA", "clinical development", "clinical investigation", "cytokine", "drug development", "early detection biomarkers", "follow-up", "genotyped patients", "graft vs host disease", "human study", "immune function", "mesothelin", "new technology", "novel", "novel marker", "operation", "patient safety", "predicting response", "response", "targeted agent", "technology development", "treatment response", "tumor DNA" ], "approved": true } } ], "meta": { "pagination": { "page": 4, "pages": 1405, "count": 14046 } } }