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Principal Investigator: Manu Platt
Organization: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
Fiscal Year: 2024
Award: $365,276
Funding agency: National Institute of Biomedical Imaging and Bioengineering
In year two of the MATRICES lab, now that we have been up and running with equipment, focus shifted to hiring and developing our scientific workforce to conduct our studies on sickle cell disease, proteolytic networks and tissue remodeling, and cancer metastasis.
We currently have 3 postbaccalaureate IRTAs in our group: two in their second year, and one OITE-PEP postbac scholar having just started his first year.
This summer we also hosted 3 Biomedical Engineering Summer Internship Program (BESIP) scholars: Jeremy Hannon, Maya Evohr, and Sreenidhi Elayaperumal.
They all presented during NIH Summer Poster Day 2024 and have had their submitted abstracts accepted to the Biomedical Engineering Society Annual Meeting.
Our team also has one staff scientist, a lab manager/animal surgeon, and three postdoctoral fellows.
Project 1: Sickle Cell Disease Mediated Arteriopathy
We study the role of cathepsins in sickle cell disease mediated vasculopathy (elastin breaks and collagen degradation in arteries) causing stroke and bone disease in the mouse models. Single cell RNA seq and spatial RNA seq will help to tease out changes in molecular signatures due to sickle cell disease. We pursue to identify signaling pathways leading to arterial wall thinning and to determine how lack of cathepsin K mitigate it to identify pharmacological targets.
Single cell RNA sequencing of key tissues and arteries to compare wildtype to sickle cell trait and sickle cell disease phenotypes has been completed and data being mined. Elastin stain on carotid arteries from sickle cell disease and cathepsin K knock out/sickle cell disease mouse model (AA, AS, SS, AA/catK KO, AS/catK KO, SS/catK KO) to quantify arterial wall thickness, perimeter, and elastin breaks. Electron Microscopy of elastin imaging from carotid arteries to identify elastin breaks in 3D and with substructural analysis. Diffusion Tensor Imaging with MRI on ex-vivo fixed brain from sickle cell disease to identify microinfarcts in humanized sickle cell mouse model.
Project 2: Computational Fluid Dynamics Reveals Flow Disturbances in Carotid Arteries of Mice with Sickle Cell Disease
To investigate how changes in the geometries of arteries due to sickle cell disease causes regions of disturbed flow, we used magnetic resonance angiography (MRA) to longitudinally image the Townes humanized sickle cell transgenic mouse models of wild-type (AA), sickle-trait (AS), and sickle cell (SS) genotypes as they age. We then used RadiAnt DICOM Viewer, Materialise Mimics, and Materialise 3-Matic to reconstruct the MRA data into 3-dimensional finite element mesh models of the common carotid artery. These models were then simulated with SimVascular using computational fluid dynamics (CFD) under steady-state, no-slip boundary conditions. Using ParaView, blood flow and wall shear stress (WSS) profiles were visualized to show regions of flow recirculation over time. Arterial geometries were analyzed using centerlines to determine how changes in cross-sectional area due to stenoses or curvature affected hemodynamics.
These analyses are soon to include fluid-structure interactions and used to test how elastic recoil affects the spatiotemporal distribution of wall shear stress over the cardiac cycle. Specifically, constitutive models of arterial tissue and reconstructed magnetic resonance images of AA (homozygous wildtype hemoglobin), AS (heterozygous mutation), SS mice, will be used as simulation inputs. By comparing outputs between AA, AS, and SS mice, we can determine regions of interest for tissue remodeling and elastic lamina degradation.
Project 3: Proteolytic networks and SARS-CoV-2 Spike Protein Cleavage
Work is continuing on the role cysteine cathepsins can play in cleavage of SARS-CoV-2 spike protein in either an activating or inactivating cleavage location which can affect viral infectivity of human cells. This is building on previous work from our group that used a bioinformatic approach to identify multiple, putative cathepsin cleavable sites on spike protein that was validated with molecular biology studies. The next steps are to specifically identify the location of these cleavage sites, their accessibility under physiological conditions, and mathematical modeling and determination of the reaction kinetics of multiple cathepsins towards the different spike cleavage sites. Experimentally, this study has included working with the NCI’s Protein Expression Lab, who have generated recombinant cathepsins, spike proteins and their subunits.
Mass spectrometry is also being used to sequence the protein fragments generated by spike protein cleavage in collaboration with the MTIC in NIBIB.
Terms: <2019-nCoV S protein><2019-nCoV spike glycoprotein><2019-nCoV spike protein><3-D><3-Dimensional><3D><AIDS Virus><Acquired Immune Deficiency Syndrome Virus><Acquired Immunodeficiency Syndrome Virus><Affect><Age><Amino Acid Sequence><Animals><Apoplexy><Area><Arterial Disorder><Arteries><Arteriopathy><Atherosclerosis><Atherosclerotic Cardiovascular Disease><Automobile Driving><Bio-Informatics><Bioinformatics><Biomedical Engineering><Blood flow><Body Tissues><Bone Diseases><Brain><Brain Nervous System><Brain Vascular Accident><Breast Cancer><COVID-19 S protein><COVID-19 spike><COVID-19 spike glycoprotein><COVID-19 spike protein><Cardiac><Cardiovascular Diseases><Carotid Arteries><Cathepsins><Cell Body><Cells><Cerebral Stroke><Cerebrovascular Apoplexy><Cerebrovascular Stroke><Cervical Cancer><Cervix Cancer><Circulation><Collaborations><Collagen><Common carotid artery><Computational toolkit><Cysteine><DICOM><DNA Molecular Biology><DWI (diffusion weighted imaging)><DWI-MRI><Data><Diagnostic><Diffusion MRI><Diffusion Magnetic Resonance Imaging><Diffusion Weighted MRI><Diffusion weighted imaging><Diffusion-weighted Magnetic Resonance Imaging><Digital Imaging and Communications in Medicine><Disease><Disease Progression><Disorder><Drug Targeting><Elasticity><Elastin><Electron Microscopy><Elements><Encephalon><Enzyme Gene><Enzymes><Equipment><Family><Genetic Alteration><Genetic Change><Genetic defect><Genotype><Geometry><HIV><Half-Cystine><Hb SS disease><HbAS><HbSS disease><Hemoglobin><Hemoglobin S Disease><Hemoglobin sickle cell disease><Hemoglobin sickle cell disorder><Heterozygote><Human><Human Immunodeficiency Viruses><Image><Infarction><Investigators><Kinetics><Knock-out><Knockout><L-Cysteine><LAV-HTLV-III><Leanness><Liquid substance><Location><Lymphadenopathy-Associated Virus><MR Imaging><MR Tomography><MRI><MRI Angiography><MRIs><Magnetic Resonance Angiography><Magnetic Resonance Imaging><Malignant Breast Neoplasm><Malignant Cervical Neoplasm><Malignant Cervical Tumor><Malignant Neoplasm of the Cervix><Malignant Tumor of the Cervix><Malignant Tumor of the Cervix Uteri><Malignant Tumor of the Lung><Malignant Tumor of the Prostate><Malignant Uterine Cervix Neoplasm><Malignant Uterine Cervix Tumor><Malignant neoplasm of cervix uteri><Malignant neoplasm of lung><Malignant neoplasm of prostate><Malignant prostatic tumor><Mass Photometry/Spectrum Analysis><Mass Spectrometry><Mass Spectroscopy><Mass Spectrum><Mass Spectrum Analyses><Mass Spectrum Analysis><Math Models><Mechanics><Mediating><Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance><Medicine><Metastasis><Metastasize><Metastatic Lesion><Metastatic Mass><Metastatic Neoplasm><Metastatic Tumor><Mice><Mice Mammals><Modeling><Modern Man><Molecular Biology><Molecular Fingerprinting><Molecular Profiling><Murine><Mus><Mutation><NIBIB><NIH><NMR Imaging><NMR Tomography><National Institute of Biomedical Imaging and Bioengineering><National Institutes of Health><Neoplasm Metastasis><Nuclear Magnetic Resonance Imaging><Output><Pathologic Constriction><Pathological Constriction><Physiologic><Physiological><Play><Postbaccalaureate><Postdoc><Postdoctoral Fellow><Primary Protein Structure><Prostate CA><Prostate Cancer><Prostate malignancy><Prostatic Cancer><Protein Cleavage><Protein Fragment><Proteins><Proteolysis><Publishing><Pulmonary Cancer><Pulmonary malignant Neoplasm><RNA Seq><RNA sequencing><RNAseq><Reaction><Recombinants><Research><Research Associate><Research Personnel><Researchers><Role><Running><SARS-CoV-2 S><SARS-CoV-2 S protein><SARS-CoV-2 spike><SARS-CoV-2 spike glycoprotein><SARS-CoV-2 spike protein><Scholars Program><Scientist><Secondary Neoplasm><Secondary Tumor><Severe acute respiratory syndrome coronavirus 2 S protein><Severe acute respiratory syndrome coronavirus 2 spike glycoprotein><Severe acute respiratory syndrome coronavirus 2 spike protein><Sickle Cell><Sickle Cell Anemia><Sickle Cell Trait><Signal Pathway><Site><Societies><Staining method><Stains><Stenosis><Stroke><Structure><Surgeon><System><Tendinitis><Tendinopathy><Tendonitis><Testing><Thick><Thickness><Thinness><Time><Tissues><Transgenic Mice><United States National Institutes of Health><Up-Regulation><Upregulation><Uterine Cervix Cancer><Vascular Diseases><Vascular Disorder><Viral><Virus-HIV><Visualization><Work><Zeugmatography><ages><atheromatosis><atherosclerotic disease><atherosclerotic vascular disease><bio-engineered><bio-engineers><bioengineering><biological engineering><blood vessel disorder><bone disorder><brain attack><cancer metastasis><cardiovascular disorder><cathepsin K><cathepsin O><cathepsin O2><cerebral vascular accident><cerebrovascular accident><computational toolbox><computational tools><computational toolset><computerized tools><coronavirus disease 2019 S protein><coronavirus disease 2019 spike glycoprotein><coronavirus disease 2019 spike protein><dMRI><diffusion tensor imaging><disease phenotype><driving><endometriosis><fluid><genome mutation><hemodynamics><heterozygosity><imaging><infarct><interest><liquid><longitudinal imaging><lung cancer><malignant breast tumor><mathematic model><mathematical model><mathematical modeling><mechanic><mechanical><meeting><meetings><molecular profile><molecular signature><mouse model><murine model><novel><pharmacologic><post-doc><post-doctoral><post-doctoral trainee><postbac><postbacc><posters><protein expression><protein sequence><research associates><scRNA-seq><serial imaging><shear stress><sickle RBC><sickle cell disease><sickle cell disorder><sickle disease><sickle erythrocyte><sickle red blood cell><sicklemia><sickling><simulation><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell transcriptomic profiling><single-cell RNA sequencing><social role><spatiotemporal><spike proteins on SARS-CoV-2><stroked><strokes><summer intern><summer internship><three dimensional><trait><transcriptome 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