Posted October 6, 2019

MIT scientists Manolis Kellis and Li-Huei Tsai are combining complex biological data with molecular biology to gain a new and unique understanding the brain. This research was published in NATURE and funded in part by Cure Alzheimer’s Fund.

This desire to leave no stone-unturned in Alzheimer’s disease research led Dr. Tsai, a molecular neurobiologist, to venture across the street at MIT for a collaboration with Dr. Manolis Kellis and his team of computational biologists. Dr. Tsai and the many scientists that make up the Picower Institute are primarily interested in studying how experience changes the brain. Dr. Kellis is motivated to use computational tools to bring powerful insights to human biology. A collaboration between these two accomplished scientists has resulted in the first single-cell transcriptome for Alzheimer’s disease – a map and blueprint for the molecular changes that differentiate healthy aging from neurodegeneration.

In humans, nearly every cell in the body contains the same genes, but different cells show different patterns of gene expression. These differences in expression are responsible for the many properties and behaviors of healthy and diseased cells and tissue. A kidney cell is very different from a brain cell in large part due to which genes are turned on or off in the cell at a given time; a transcriptome is a collection of all of the gene readouts present in a cell at that given time. By comparing the transcriptome of different cells, the researchers determined what profile makes up a specific cell type and how changes in the normal level of that gene’s activity could contribute to disease. The transcriptome provides insights into what genes are active in which cells.

The research involved brain tissue from 48 individuals with varying severity of Alzheimer’s disease pathology. Research in the past has relied on a technique called “bulk sequencing” which evaluates changes in gene expression that are reflected across the entire brain in aggregate. Single-cell sequencing, on the other hand, enables scientists to examine changes in gene expression in different brain cell types. This allows for more details to be pulled out from the brain on a truly unprecedented scale with far more specificity and resolution.

Thousands of cells – 80,660 to be precise – from the brains of individuals at different stages of Alzheimer’s disease were analyzed to offer new clues into what goes wrong at the molecular level and why women and men present differently with the disease. The study identified a new role for a type of brain cell called an oligodendrocyte; these cells  provide support and insulation to axons in the central nervous system. Additionally, the study has shown that women have much higher levels of Alzheimer’s associated cell populations.

The study began by performing a type of analysis referred to as a cell-type annotation cluster. Essentially, the researchers created a profile of gene expression that characterized different players in the brain ranging from excitatory neurons to the circulating immune cells called microglia. The analysis revealed that there are subpopulations of neurons within the brain that are most closely associated with disease pathology.

The ability to characterize the collection of genes upregulated and downregulated across different cell types was once only discussed in the realms of science fiction. The researchers have taken advantage of advances in data processing to examine tens of thousands of individual cells from the human brain. The scientists have given each cell type its own signature. They discovered that birds of a feather do in fact tend to flock together: excitatory neurons have a similar profile as other excitatory neurons while inhibitory neurons resemble other inhibitory neurons.

The next crucial step in the study was to identify the changes that occur at early stages of Alzheimer’s disease and those that occur later in the disease. Interestingly, in early stages, neurons tend to show a decrease in expression of certain key genes while microglia tend to show a dramatic increase in expression of key genes.

At later stages of Alzheimer’s disease, there was less diversity in the types of gene expression changes: across the major cell types in the brain, the genes affected tended to be involved in only a handful of key pathways related to cellular stress, cell death, and protein folding.

When discussing the research with Cure Alzheimer’s Fund, Dr. Li Huei Tsai stated: “We wanted to know if we could distinguish whether each cell type has differential gene expression patterns between healthy and diseased brain tissue. This is the power of single-cell-level analysis: you have the resolution to see the differences among the different cell types in the brain.”

One of the most dramatic findings of the paper is that brain cells from male and female Alzheimer’s patients are very different. In fact, despite the fact that female patients had similar levels of cognitive impairments and amyloid plaque build-up, the excitatory neurons in the female brain had far more pronounced gene expression changes than the brain cells from male patients. More research is required to understand why this discrepancy exists; however, it is an important finding that supports the fact that the therapeutic strategies that work for men may work differently for women.