Combining Molecular and Spatial Information to Understand Alzheimer’s Disease

Exploration of cell types and disease states with the Rebus Esper

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Among the more than 50 million people in the world with dementia, Alzheimer’s disease is the most common cause. Despite the prevalence of this deadly disorder, scientists struggle to understand its precise mechanisms. With the Rebus Esper spatial omics platform, scientists can explore these details—understanding disease biology at every level, from broad distributions of cells across the tissue down to single transcripts in single cells.

Marcos Otero-Garcia, PhD, a neuroscientist by training, is now a senior scientist at Rebus Biosystems, where he is using spatial omics techniques to extend work he started while a postdoctoral researcher in the lab of Inma Cobos, MD, PhD, at Stanford University.

“We focus on selective cell vulnerability in Alzheimer’s disease,” Otero-Garcia says. “It’s well known that some brain regions are severely affected, like the hippocampus, while other areas are spared.” Similarly, some cells show pathological alterations, and others seem healthy.

“A key alteration closely associated with cognitive decline is the presence of neurofibrillary tangles (NFTs) inside some neurons—about 8% of all neurons in severe cases,” he continues. “We want to identify those vulnerable neurons and their molecular signatures so we can understand the disease mechanisms and facilitate targeted therapies.”

Single-cell analysis gives a clearer if incomplete picture

Otero-Garcia and his colleagues first approached the problem of selective vulnerability by using single-cell RNA sequencing on prefrontal cortex samples from Alzheimer’s patients. The goal was to identify the cell types vulnerable to NFTs and the associated gene expression signatures. So, the scientists marked cells containing NFTs prior to sequencing.

Left: Schematic representation of the dissected tissue area from prefrontal cortex (BA9) and different neuronal cell types present in the cortical layers, with some of the neurons displaying neurofibrillary tau tangles (NFTs). (Adapted from Right: Rebus Esper data showing the eight neuronal cell types identified by unsupervised clustering (Scanpy) of single-cell data with 15 genes, and a detail of the RNA plus phospho-tau (NFTs) co-detection.

Although the results revealed the neuronal types vulnerable to neurofibrilary tangles/NFTs and the associated molecular signatures, Otero-Garcia notes that tissue architecture and morphology are lost with single-cell RNA-sequencing. As he points out: “Getting that kind of spatial context is key to really unraveling the secrets of the disease.”

Validation and extension using spatial omics

After joining Rebus Biosystems, Otero-Garcia took the opportunity to validate his previous findings and bring in the important spatial information.

“Using the Rebus Esper spatial platform, we can validate our previous findings,” Otero-Garcia points out. “Reaching the same conclusions using a different platform will give us high confidence in our results. We hope to further extend those results by exploring changes in spatial distribution of cells and in the expression of disease-related genes in specific subcellular locations like the synapses, which is only possible with this platform.”

Otero-Garcia is now focused on what he can add to his previous results thanks to the Rebus Esper™ platform’s added layer of spatial data, which is visualizing RNA and protein with subcellular resolution. Now, scientists can ask: Where are the vulnerable cells located, what is their morphology, and who are their neighbors?

For example, the researchers can ask if vulnerable cells are surrounded by immune cells or are far away from them, see if anything looks different when there is a blood vessel nearby, and more. “Because we’re looking at cells in their native tissue context, there is a myriad of new questions we can explore,” Otero-Garcia explains.

For Otero-Garcia’s research, the Rebus Esper provides two key elements: high sensitivity and a large imaging area.

“Because we are able to detect each RNA transcript as a single spot, we can obtain truly quantitative data and measure subtle changes in gene expression,” he says. “The combination with a large imaging area allows us to find rare cell types or combine multiple samples in a single run to minimize batch effect, boosting statistical power.”

Otero-Garcia is excited about the power that the Rebus Esper brings to his research, and what it will bring to others.


* Marcos Otero-Garcia, et al. Single-soma transcriptomics of tangle-bearing neurons in Alzheimer’s disease reveals the signatures of tau-associated synaptic dysfunction. bioRxiv 2020.05.11.088591; doi:

For more information on the Rebus Esper, or to arrange a demo or pilot study, please contact us at [email protected]