Title: High-resolution 3D in situ Spatial Gene Expression Profiling Technology for Human Brain Specimens Description The overall aim of this Phase I project is to apply Expansion Sequencing, a genome-wide in situ transcriptomics profiling technology with unprecedented spatial resolution in 3D, to human brain tissues to empower brain disease research and therapeutic development. Neurodegenerative diseases, such as Alzheimer's disease affects over 11% of the population aged above 65, causing â
of death in seniors, and costs hundreds of billions of dollars a year. Yet, no disease modifying therapeutics have been approved for marketing. The ability to obtain data and validate discoveries directly in human samples is paramount to our ability to characterize and understand brain disorders. Spatially resolved transcriptomics, helps scientists understand how the different cells are organized, using fluorescence microscopy imaging has shown unmatched promise in characterizing different cell types in native tissue, change during development and aging, and how they influence behavior and disease. However, many of existing spatial technologies are limited to thin animal brain sections. They are bound by optical diffraction-limited resolution, restraining the ability to precisely define a large variety of cell types organized in 3D. Tissues from humans and those with neurodegenerative disease have high degree of auto fluorescence caused by protein aggregates (such as Amyloid plaques), lipofuscin granules and dense vessels. Recently published in Science, Expansion Sequencing (ExSeq) is the first in situ genome-wide 3D spatial gene expression profiling technology. It provides unprecedented imaging resolution in 3D using thick mouse brain sections. This allows for clear definition of synapse junctions and mapping genetran scripts with single- and sub-cellular precision, which had not been possible with conventional fluorescence confocal microscopes used by most researchers. In order to make ExSeq suitable for human studies and commercially available, we identified and tested a new set of methods that will allow us to optimise ExSeq for human specimens, and improve sensitivity and specificity. We are building a set of analytical tools to help visualize, debug and improve the robustness of the analytics pipeline. We have also obtained access to a wide variety of precious human brain tissues, to help us test different sample preparation conditions and validate our methods. For this Phase I project, we will develop ExSeq protocol for human brain tissue characterization with a proof-of-concept gene panel, and create a robust image processing and analytical pipeline that can accommodate images generated from different experimental and laboratory settings. Finally, we will process and analyze a set of human normal and Alzheimer's diseased brain tissues, and validate results against published data and prior research. Building upon a strong scientific foundation supported with publications, we are bringing together extensive expertise in protocol optimization and sequencing technology for ExSeq and deep knowledge of Alzheimer's and neurodegenerative disease pathology to make it an impactful tool for both basic science and therapeutic research and development.
Public Health Relevance Statement: Project Narrative Neurodegenerative diseases are an imminent and growing threat to public health globally. Millions of Americans are living with Alzheimer's Disease and other neurodegenerative diseases. It is estimated that by 2050, 1 in 5 of the population above 65 will be affected. Despite the effort into hundreds of investigational drugs over the past 20 years, many that succeed in animal experiments fail in humans, putting the validity of discoveries using animal models into question. Today, most of the advanced tissue profiling technologies are only applicable to animal tissues because human disease tissues have significantly more diverse and profound pathological and heterogeneous conditions than model animals. Hence there is an immediate urgency to have a robust solution for human specimens. The present project will make available a powerful high-resolution spatial profiling technology by which scientists can accurately identify different cell types based on comprehensive gene expression profiles, and determine changes that occur in human brain diseases. The result of this project will comprise both optimized experimental protocols and a robust data pipeline for human tissue analysis, which can be used in a variety of brain research applications. This will catalyze a step change in our ability to interpret, model, diagnose, and eventually treat brain diseases.
Project Terms: Affect, Aging, Alzheimer's Disease, AD dementia, Alzheimer, Alzheimer Type Dementia, Alzheimer disease, Alzheimer sclerosis, Alzheimer syndrome, Alzheimer's, Alzheimer's disease dementia, Alzheimers Dementia, Alzheimers disease, Primary Senile Degenerative Dementia, dementia of the Alzheimer type, primary degenerative dementia, senile dementia of the Alzheimer type, Amyloid, Amyloid Substance, Animals, Astrocytes, Astrocytus, Astroglia, astrocytic glia, Biological Sciences, Biologic Sciences, Bioscience, Life Sciences, Brain, Brain Nervous System, Encephalon, Brain Diseases, Brain Disorders, Encephalon Diseases, Intracranial CNS Disorders, Intracranial Central Nervous System Disorders, Cataloging, Cause of Death, Cells, Cell Body, Chemistry, Chromosome Mapping, Gene Localization, Gene Mapping, Gene Mapping Genetics, Linkage Mapping, Total Human and Non-Human Gene Mapping, genetic mapping, Collagen, Cytoplasmic Granules, granule, Diagnosis, Digestion, Disease, Disorder, Investigational Drugs, Investigational New Drugs, Erythrocytes, Blood erythrocyte, Erythrocytic, Marrow erythrocyte, Red Blood Cells, Red Cell, blood corpuscles, Fluorescence, Formaldehyde, Formic Aldehyde, Methyl Aldehyde, Oxomethane, Foundations, Gene Expression, Genes, Human, Modern Man, Industry, Laboratories, Libraries, Lipofuscin, Marketing, Methods, Microscopy, Fluorescence Microscopy, Fluorescence Light Microscopy, Mission, Mus, Mice, Mice Mammals, Murine, Names, Nerve Cells, Nerve Unit, Neural Cell, Neurocyte, neuronal, Neurons, Noise, optical, Optics, Patents, Legal patent, Pathology, Patients, Antiheparin Factor, Blood Platelet Factor IV, Blood platelet factor 4, Chemokine (C-X-C motif) Ligand 4, Factor 4, Heparin Neutralizing Protein, Platelet Factor 4, Recombinant Platelet Factor 4, SCYB4, Small Inducible Cytokine B4, Small Inducible Cytokine Subfamily B, Member 4, gamma-Thromboglobulin, platelet factor IV, PF4 Gene, Public Health, Scientific Publication, Publications, Publishing, Response RT, Response Time, psychomotor reaction time, Reaction Time, Reagent, Research, Development and Research, R & D, R&D, research and development, Investigators, Researchers, Research Personnel, Non-Polyadenylated RNA, RNA Gene Products, Ribonucleic Acid, RNA, Science, Sensitivity and Specificity, Cell Communication and Signaling, Cell Signaling, Intracellular Communication and Signaling, Signal Transduction Systems, Signaling, biological signal transduction, Signal Transduction, Standardization, Synaptic, synapse, Synapses, Technology, Temperature, Testing, Leanness, Thinness, Tissues, Body Tissues, base, image processing, Microscope, improved, Lateral, Area, Phase, Biological, biologic, Animal Experiments, Microglia, Hortega cell, gitter cell, mesoglia, microglial cell, microgliocyte, perivascular glial cell, Ensure, animal tissue, Individual, Data Bases, data base, Databases, Therapeutic Research, Therapeutic Human Experimentation, Therapeutic, Amyloid Plaques, Neuritic Plaques, amyloid beta plaque, amyloid-b plaque, aβ plaques, cored plaque, diffuse plaque, Senile Plaques, tool, Nature, Research Specimen, Specimen, Knowledge, Scientist, human tissue, Protocol, Protocols documentation, In Situ, cell type, System, 3-D, 3D, three dimensional, 3-Dimensional, brain tissue, Degenerative Neurologic Diseases, Degenerative Neurologic Disorders, Nervous System Degenerative Diseases, Neural Degenerative Diseases, Neural degenerative Disorders, Neurodegenerative Diseases, Neurologic Degenerative Conditions, degenerative diseases of motor and sensory neurons, degenerative neurological diseases, neurodegenerative illness, Neurodegenerative Disorders, American, Animal Models and Related Studies, model of animal, model organism, Animal Model, Speed, Basic Research, Basic Science, validation studies, novel technologies, new technology, Abscission, Extirpation, Removal, Surgical Removal, resection, Excision, Gene Expression Monitoring, Gene Expression Pattern Analysis, Transcript Expression Analyses, Transcript Expression Analysis, gene expression analysis, gene expression assay, transcriptional profiling, Gene Expression Profiling, Modeling, Sampling, behavioral influence, behavior influence, Thickness, Thick, GeneHomolog, Homolog, Homologue, Homologous Gene, global health, Academia, Data, Detection, Reproducibility, Resolution, Transcript, Update, Pathologic, Preparation, Molecular, Process, sample fixation, Fixation, Development, developmental, Image, imaging, cost, image registration, design, designing, protein aggregation, insoluble aggregate, protein aggregate, Visualization software, visualization tool, Population, aged, transcriptomics, analytical tool, human disease, usability, brain research, fluorescence imaging, fluorescent imaging, therapeutic development, therapeutic agent development, genome-wide, genome scale, genomewide, Drug Targeting, gene panel, multigene panel, Metastatic breast cancer, imaging system, invention, Data Analytics, clinical biomarkers, clinically useful biomarkers, biomarker discovery, microscopic imaging, microscope imaging, microscopy imaging, high resolution imaging, data pipeline, data analysis pipeline, data processing pipeline, Alzheimer's disease brain, Alzheimer's brain
