Bruker Brain Day 2025:

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Join us for a celebration of science that brings together fit for purpose neuroscience solutions from Bruker Spatial Biology platforms.

Webinar 1: Retinal changes associated with cerebral small vessel disease

Speakers

Dr. Joseph Beechem

Chief Science Officer, NanoString, a Bruker Company

Dr. Ranga Parthasarathy

SVP of Product Management and Marketing, NanoString, a Bruker Company

Dr. Ram DasGupta

Senior Group Leader, Genome Institute of Singapore

Dr. Arutha Kulasinghe

Senior Research Fellow, University of Queensland

NOW ON DEMAND

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Retinal changes associated with cerebral small vessel disease

With the rapidly expanding aging population, and the incidence of dementia expected to grow with this population, developing sensitive and accessible biomarkers that reveal the pathophysiology occurring in the brain is imperative. Currently, the two leading causes of dementia, Alzheimer’s disease (AD) and vascular contributions to cognitive impairment and dementia (VCID), are best diagnosed clinically with either costly PET or MRI scans and relatively nonspecific neuropsychological evaluations. Since some of these methods lack sensitivity and specificity, there is a clear need to develop novel biomarkers and understand how said biomarkers reflect underlying disease mechanisms. While rapidly emerging plasma biomarkers are gaining traction and specificity for AD, there is a lack of markers for VCID, in particular cerebral small vessel disease (cSVD), the most common VCID pathology.The retina has become a promising biomarker for AD and VCID, but the specific mechanisms underlying retinal changes that reflect brain disease are unclear. Using our model of hyperhomocysteinemia (HHcy)-induced cSVD, we aimed to identify the effects of cSVD on visual sensitivity and cognition, retinal glial and vascular cells, and neuroinflammatory and cardiovascular gene expression changes. Ultimately, HHcy led to visual deficits that specifically affected the reaction to blue and white light, decreased vascular volume and decreased interaction of microglia with the vasculature, as well as the downregulation of inflammatory and vascular genes. These changes provide novel insights and reproduce some prior observations. These studies highlight retinal changes in association with cSVD and serve as a precaution when interpreting vision-dependent cognitive testing of cSVD models.

Erica Weekman, PhD
Assistant Research Professor of Neurology

Stark Neurosciences Research Institute
Indiana University School of Medicine

Connecting form and function: Mapping microglial spatial biology in a mouse model of acute and chronic ischemic stroke

Microglia, the brain’s primary immune cells, are highly responsive to changes in their environment, adapting their behavior through intricate molecular signaling. These functional shifts, from surveillance to injury response, are associated with morphological changes, which can serve as markers of their functional state. Our study uniquely combines cutting edge, high-plex spatial proteomics and traditional immunohistochemistry (IHC) to quantify and correlate microglial morphology with functional changes after ischemic stroke at different timepoints.

Adult male mice were subjected to transient middle cerebral artery occlusion and reperfusion using the filament method. Following this procedure, stroke severity was confirmed using a Bruker Biospec 70/20 7.0T MRI scanner. Brains were extracted at 24 hours, 2 weeks, or 4 weeks post-stroke (3 animals/timepoint), fixed, and sectioned at 10μm (spatial proteomics) or 50μm (IHC). We stained microglia with an IBA1 antibody or, utilizing the high plex Mouse CosMx^® Neuroscience Protein Panel and the CosMx Spatial Molecular Imager (SMI), we detected 68 proteins with single cell resolution, focusing on regions proximal and distal to the infarct.

Leveraging the many microglial and immune markers in the Mouse CosMx Neuroscience Protein Panel, we captured precise cell morphology and quantified it by skeleton analysis focused on microglial process length and endpoints. Our results showed strong correlation between CosMx SMI and IHC morphometric data over time and distance from stroke injury, supporting CosMx SMI as a viable alternative to traditional IHC. Additionally, principal component analysis of select proteins in the CosMx SMI data revealed correlations between microglial form and function across various brain regions. Utilizing the InSituCor analysis toolkit, we further identified a module of spatially correlated proteins in the infarct region two weeks post-stroke, including Cathepsin B—a promising therapeutic target—and phagocytic markers CD11b, CD11c, and DAP12, with their colocalization shifting gradually with distance from the infarct core. By pairing spatial proteomic data with microglial morphology analysis, we gained deeper insights into the complex interactions between microglia and the recovering brain following ischemic stroke, highlighting how these interactions evolve over time and with proximity to the infarct core.

Kimberly Young

Bruker Spatial Biology

Multi-omic profiling of healthy and diseased brains with high-plex single-cell spatial molecular imaging

Single-cell transcriptomics and proteomics can provide complementary information about the form and function of neurons and glia throughout the brain. However, most high-plex spatial analyses to date have primarily utilized one of these two modalities to interrogate cell activity and cell-to-cell communication. Here, we simultaneously leveraged the detection of 68 proteins and over 6,000 RNA targets on the same formalin-fixed paraffin-embedded (FFPE) human brain sections to perform extended segmentation of neural processes and integrated analyses of protein and RNA expression.

Using a mult-iomic approach with the CosMxTM Spatial Molecular Imager (SMI), first high-plex protein panel targets were imaged via cyclic in situ hybridization chemistry. Next RNA targets on the same tissue section were exposed then hybridized, and finally RNAs were imaged using the same chemistry. The human neuro protein panel targets are particularly well-suited for dissecting neurodegenerative disease pathology, including various phospho-tau species and amyloid beta variants. Moreover, the protein panel includes markers for diverse neural cell types and enables robust cell typing, especially alongside the over 4,900 neuroscience-related genes covered by the Human 6K Discovery Panel. RNA targets focus on over 80 pathways, cell typing, and key ligand-receptor interactions. To demonstrate the capability of the single-cell high-plex multi-omic technique, we collected data from sections of FFPE male human brains, with samples derived from frontal, parietal, and occipital lobes, as well as the precentral/ postcentral gyri and cerebellum, of healthy individuals and Alzheimer’s Disease patients.

Drawing on both the protein and RNA data, we achieved unparalleled segmentation of neurons and glia and increased transcript counts per cell. We also annotated cells with neuronal, glial, and vascular subtypes. By comparing RNA and protein expression, we identified genes and proteins with correlated and divergent patterns across our tissue space, highlighting the advantage of including the functional readout, protein, in understanding cell activity. Using open-source tools, we assigned cells into niches based on protein patterns and then applied differential expression models to identify genes and gene sets which varied based on niche for individual cell types. Overall, by applying the SMI multi-omic platform to human brain samples, we were able to simultaneously probe cell shapes, cell types, cell neighborhoods, and cell activity in one experiment on a single slide.

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Join us in a celebration of science that brings together fit for purpose neuroscience solutions from Bruker Spatial Biology platforms.

Discovering Novel Biomarkers: Learn about new biomarkers for cerebral small vessel disease (cSVD) and their role in diagnosing dementia with the nCounter^® Analysis Platform.
Exploring Microglial Function: Hear about the mapping of microglial morphology and function in ischemic stroke recovery with the CosMx^® Neuroscience Protein Panel.
Integrating Multiomic Data: Gain insights into high-plex single-cell spatial molecular imaging with CosMx SMI for comprehensive neural analysis.

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BONUS EVENT: Retinal changes associated with cerebral small vessel disease

Thursday, March 13th | 10AM GMT / 11AM CET

Using our model of hyperhomocysteinemia (HHcy)-induced cSVD, we aimed to identify the effects of cSVD on visual sensitivity and cognition, retinal glial and vascular cells, and neuroinflammatory and cardiovascular gene expression changes. Ultimately, HHcy led to visual deficits that specifically affected the reaction to blue and white light, decreased vascular volume and decreased interaction of microglia with the vasculature, as well as the downregulation of inflammatory and vascular genes. These changes provide novel insights and reproduce some prior observations. These studies highlight retinal changes in association with cSVD and serve as a precaution when interpreting vision-dependent cognitive testing of cSVD models.

Bridget Ashford

Post Doctoral Research Associate

University of Sheffield