Whole transcriptome spatial profiling for studying CNS disorders
Kit Fuhrman, PhD
Senior Product Manager
Kit Fuhrman has applied his understanding of immunology to solve challenging scientific problems by applying the power of the nCounter and GeoMx platforms. He developed the first 3D Flow protocols to digitally count both RNA and protein in a single tube from sorted populations. He now focuses his time building RNA applications for the GeoMx Digital Spatial Profiling platform for morphology driven gene expression profiling. Kit received his Doctorate from the University of Florida in immunology studying the role of regulatory T cells in type-1 diabetes pathogenesis and his Masters from the University of Central Florida on directed design of HIV entry inhibitors.
Spatial Analysis of Neural Cell Transcript Profiles following Ischemic Stroke in Mice using High-Plex Digital Spatial Profiling
Stroke is ranked as the fifth leading cause of death and the leading cause of adult disability. The progression of neuronal damage after stroke is recognized to be a complex integration of glia, neurons, and the surrounding extracellular matrix, therefore potential treatments must target the detrimental effects created by these interactions. In this study, we examined the spatial cellular and neuroinflammatory mechanisms occurring early after ischemic stroke utilizing Nanostring GeoMx Digital Whole Transcriptome Analysis (WTA) Spatial Profiling (DSP) technology. Male C57bl/6 mice were subjected to photothrombotic middle cerebral artery occlusion (MCAO) and sacrificed at three- and seven-days post-ischemia. Spatial distinction of the ipsilateral hemisphere was studied according to the regions of interest: the ischemic core, peri-infarct, corpus collosum, subcortex, and peri-infarct normal tissue (PiNT) in comparison to the contralateral hemisphere. We demonstrated that early days after ischemia, neuronal cell death and excitotoxicity mechanisms predominate with strong regional distinction centered around core lesion damage. However, approximately a week after ischemia, regions begin to demonstrate less unique distinction with a correlating shift toward repair initiation processes centered around the core border. Overall, our data highlight the importance of identifying ischemic spatial mechanisms to understand the complex, dynamic interactions throughout ischemic progression and repair as well to introduce potential targets for successful ischemic therapeutic interventions.
Jessica Noll received her B.A. degree from Manchester University in Biology-Chemistry and her Biomedical Sciences PhD from the University of California, School of Medicine. She is currently a post-doctoral scholar in her previous advisor, Dr. Byron Ford’s, laboratory who has studied mechanisms of neuroprotection and inflammatory mediators in ischemic stroke for over 20 years. She has three publications, with two in review, and has presented at multiple regional and national conferences on the research topic: “Defining Neuronal Spatiotemporal Profiling in Ischemic Stroke after Neuregulin-1 Treatment”. Additionally, her three-minute presentation, “A Rapid Blood Test for Stroke” won the grand-prize in the 2018 UCR Grad Slam competition. Jessica has also held multiple voluntary leadership roles within her graduate program and graduate division including BMSC Graduate Student Association (GSA) Representative, BMSC Sustainability Officer, and Vice President of Academic Affairs (GSA).
Spatial Transcriptomics of Alzheimer’s Disease Mouse Models with and without Trem2R47H Mutation
In this preliminary experiment, we used spatial transcriptomics to assess the gene expression profiles of microglia or astrocytes in relation to their distance from plaques. We compared 18-month-old APPKI mice (APPNL-F) which carry 2 mutations for familial Alzheimer’s disease to APPNL-F crossed with mice with the Trem2R47H mutation knocked in (APPTREM2KI; n=4 each genotype). In addition, we included Wild Type (WT) and Trem2R47H KI mice (n=2-3). The APPKI mice start to show amyloid plaques at about 9 months of age and by 18 months have a heavy plaque load. To do spatial transcriptomics with the GeoMx® Mouse Whole Transcriptome Atlas, microglia (Iba1 positive cells) areas of interest (AOIs) were divided into 3 groups: those touching plaques; those within an area of heavy plaque load (periplaque) and those far from plaques. Periplaque astrocytes (S100b positive cells) or away from plaque astrocytes were also analyzed.
Frances Edwards, PhD
University College London
Frances Edwards is a CNS synaptic physiologist. After graduating with a BSc Honours and MSc in Behavioural Pharmacology from the University of Sydney in her native Australia, she moved to electrophysiology, gaining her PhD between Australian National University and the Max Planck Institute for Biophysical Chemistry in Goettingen, Germany. In Germany she was involved in developing the application of patch clamp techniques to brain slices working with Bert Sakmann and Arthur Konnerth. This enabled high resolution of synaptic currents between individual neurones in mammalian brain and subsequently led her to a postdoc at UCL and the discovery of the first fast purinergic synapse in the brain. Her ongoing career moved between University College London and University of Sydney until she settled permanently at University College London in the mid-1990s. Over the last decade she has been increasingly involved in Alzheimer’s Research at UCL and is now Professor of Neurodegeneration in the Department of Neuroscience Physiology & Pharmacology. The lab still specialises in electrophysiology but with gene expression, immunohistochemistry and general molecular techniques now equally important. A primary aim is to improve mouse models of Alzheimer’s disease by investigating the role of different Alzheimer’s disease risk factors in knock in mice with Alzheimer’s mutations. Use of technology such as the Nanostring Geomx regional and cell-type enriched gene expression to understand changes in gene expression in these models is a recent exciting addition to these aims.