Exploring the Brain with Spatial Biology

Spatial biology—analyzing the levels and locations of gene or protein expression within tissues—is boosting our understanding of many tissue types, but its application to the brain is especially revealing. With myriad cell types and innumerable cell-cell interactions, the brain’s mysteries are slowly unraveling as researchers apply spatial biology’s facility for tissue mapping and cell atlasing. The result is new insights into disease pathologies, and the mechanisms of neurodegenerative changes that occur in the brain. Here’s a look at how researchers are using spatial biology to study Alzheimer’s disease.

Staging neurodegeneration

Neurodegenerative diseases such as Alzheimer’s disease (AD) and multiple sclerosis (MS) typically present gradually and occur in stages. Researchers are using spatial transcriptomics, and the Visium platform from 10x Genomics, to study the progression of gene expression at different stages in AD and MS. “Specifically, it’s used to interrogate the cellular landscape around morphological disease markers and how alterations in gene expression patterns can drive various disease states,” says Jyoti Sheldon, Senior Marketing Manager at 10x Genomics. “For example, scientists at the University of Pittsburgh recently combined Visium with scRNAseq to identify unique transcriptional responses at amyloid plaque niches to study the mechanisms linking peripheral inflammation to AD pathology.”

For researchers who need to integrate spatial transcriptomics with histology workflows, Visium works with 10x Genomics’ CytAssist platform to pair morphological and spatial transcriptomics data. “This allows neuroscience researchers to access paraffin-embedded or archived tissues, along with the ability to use pre-sectioned tissues on standard glass slides,” says Sheldon. CyAssist enables researchers to pre-screen tissue sections to choose those best for analysis, which can be especially helpful when studying rare or precious samples.

In 2024, 10x Genomics will expand their higher-resolution toolbox with a Visium HD assay, adding to the current in situ Xenium platform. “As newer cell populations are being identified, researchers are now looking further into comparing transcriptomic profiles within these unique cell populations across various disease states,” says Sheldon.

AD and air pollution

In contrast to detecting RNA in spatial transcriptomics, another mode of spatial biology analyzes the proteins expressed across tissues, sometimes called spatial phenotyping. Researchers from Cedars Sinai used this method with the PhenoCycler^®-Fusion (PCF) system from Akoya Biosciences to study the effects of air pollution on the pathogenesis of Alzheimer’s disease in a mouse model. They found increased expression of markers for AD in mice exposed to particulate matter in the air. “The increase was region-specific and higher in the hippocampal area relative to the cerebral cortex, highlighting the need for whole-slide imaging technologies for spatial protein analysis,” says Dmytro Klymyshyn, Applications Scientist at Akoya Biosciences.

An important feature of the PCF system is its ability to analyze entire slides with unbiased spatial phenotyping. “It permits the simultaneous mapping of different cell types and their locations with the single-cell resolution that is especially important for analyzing smaller pathological features of Alzheimer's disease, like amyloid plaques,” says Klymyshyn.

A recent study from Stanford University used Akoya’s PhenoCycler technology and a 56-plex biomarker panel to characterize neuronal cell cultures from patient-derived induced pluripotent stem cells (iPSCs). Cultured iPSCs can be differentiated into various neuronal cell types, and are valuable in studying neuronal dysfunction and developing therapeutics. “Accurately capturing delicate neuronal cell processes using the PhenoCycler-Fusion can pave the way for AI-based cellular and morphological profiling of neuroinflammation,” says Aditya Pratapa, Senior Data Scientist at Akoya Biosciences. “It also furthers computational method development for spatial biomarker discoveries for precision medicine through spatial proteomic and transcriptomic data integration.”

Studying AD with single-cell gene expression

Gene expression studies can help us understand the physiological roles of distinct cell types, and pinpoint potential disease mechanisms. Vizgen’s MERSCOPE^® platform allows researchers to study single-cell gene expression in situ. It uses high-resolution spatial imaging along with spatial transcriptomics as measured by MERFISH (multiplexed error-robust fluorescence in situ hybridization) labeling and detection.

Researchers at the Allen Institute for Brain Science used MERSCOPE and single cell analysis to create a comprehensive, multimodal cell atlas of AD in the human brain. “They mapped the spatial distribution of different cell types in the human brain at different stages of AD, and characterized the proportional changes of specific cell supertypes as a function of disease severity,” says Jiang He, Scientific Co-Founder and Senior Director of Scientific Affairs at Vizgen. “Intriguingly, they found an early reduction of SST inhibitory neuronal subtypes, and a late decrease of supragranular IT excitatory neurons and Plvb+ inhibitory neurons, during disease progression.”

Brain tissue presents unique challenges in spatial biology, such as the complicating presence of lipofuscin, brownish pigment-containing granules often present in aging brains that can interfere with imaging by causing background autofluorescence. “To [help with this], Vizgen developed a MERSCOPE Photobleacher, and implemented a tissue clearing step during sample prep to reduce the background, enabling researchers to image human brain samples at different ages or disease stages.”

Spatial biology technologies like MERSCOPE continue to fuel cell atlasing efforts to create reference maps of the brain—and scientists will continue to rely on these maps to integrate multi-omics data into an understanding of brain function. “For example, combining multiplexed protein imaging with MERSCOPE imaging, researchers will be able to visualize plaques in AD patients’ brains, and characterize the cellular composition and states around the plaques,” he says. As spatial biology methods continue to advance, the further unlocking of brain mysteries will continue to intrigue us.