Alzheimer’s risk genes linked to brain vasculature by new genetic atlas

Feb 23 2022

Nicholas Weiler

To understand what causes Alzheimer’s disease and other forms of brain degeneration, scientists may need to look beyond the brain’s computational units, the neurons and synapses, and explore the vast infrastructure that supports them.

Scientists have recognized for decades that the brains of people who die from advanced Alzheimer’s disease often exhibit severe damage to the network of blood vessels that feeds the energy-hungry brain. Some have speculated that age-related vascular failure could contribute to neurodegenerative disease — like a city grinding to a halt as its aging energy grid fails. But of course it’s also possible that the vascular damage and neurodegeneration both result from other, earlier causes, such as widespread inflammation.

Resolving this question has proved extremely challenging, in part because the endothelial cells that make up the brain's blood vessels are so tough and sticky that they resist analysis by many standard experimental procedures.

In a study published Feb 14, 2022, in Nature, researchers in the lab of Tony Wyss-Coray at the Wu Tsai Neurosciences Institute and colleagues have produced the first genetic atlas of the many cell types that make up brain’s intricate vasculature — as well as many support cells that mediate energy flow across the so-called blood brain barrier.

Their results — based on a new technique developed by the lab – revealed that an astonishing two thirds of the most common genetic risk factors for Alzheimer’s disease are expressed by these vascular associated cells. Additionally, some of these risk factors were seen only in human vascular cells — not in animal models of neurodegeneration.

We spoke with Wyss-Coray, who is D. H. Chen Professor in the Department of Neurology and Neurological Sciences and co-director of the Stanford Brain Rejuvenation Project, about the lab’s interest in exploring the role of the brain’s vasculature in Alzheimer’s disease, and the implications of the new findings for the search for better therapies.

Why were you interested in looking at the role of brain vasculature — the energy grid of the brain, so to speak — in Alzheimer's disease?

We’d noticed for a while now that when we look at the brains of aged mice and even more so in humans that there are a lot of molecular and cellular changes in the brain vasculature, but they have not really been characterized.

Similarly, when you look at population studies from people who die of old age and have cognitive impairment or Alzheimer's dementia, almost all of their brains have significant vascular damage. But, we realized that we don't know the molecular changes that occur with this damage. That's what we wanted to figure out.

Were you surprised to see just how many Alzheimer's associated genes are linked to blood vessel cell types in the brain?

Yes, that was indeed very surprising. The common knowledge that we have in the field is that they key players in the disease are the brain cells – neurons and microglia.

The autosomal dominant gene mutations that directly cause Alzheimer's disease in small numbers of people are mostly expressed in neurons, maybe a bit in glial cells. More recently, hundreds more gene variants have been identified as potential risk factors that slightly change your susceptibility to developing Alzheimer’s disease. Many of these risk genes turn out to be expressed in microglial cells, and many people have started to focus on trying to understand how expression of these genes might confer that lifetime risk of the disease.

But it was not really clear whether any of this growing number of risk genes were expressed in cells of the brain vasculature and whether they could potentially have a role in the disease.

What we found is that a majority of the top Alzheimer’s risk genes are significantly expressed in the vasculature — sometimes at much higher level than in other types of cells in the brain that have long been assumed to be the primary culprits.

Were these findings unique to human Alzheimer's patients?

Yes — we compared our results to existing maps of gene expression in the mouse brain and found that there are quite a few genes in mouse vascular cells that are not expressed to the same extent or at all in human vascular cells.

This suggests that there is a significant evolutionary shift in expression of some of these genes in the brain vasculature, which of course questions the use of mice in studying questions around brain vasculature in human diseases.

Why had it been so challenging to study these cells in the brain before?

This amazing new technology called single-cell nuclear RNA sequencing has led to a rapidly growing number of studies where people can isolate individual cells or cell nuclei from brain tissue to study the expression of genes across different cell types in the brain.

Interestingly, all these studies sort of missed the vasculature. It’s actually not surprising, because the vasculature has a lot of extracellular matrix around it which makes it quite stringy and tough so that when you use normal methods to grind up the tissue into individual cells, the stringy blood vessels often stay intact.

My student Andrew Yang, who is now at UCSF, compared it to pouring spaghetti through a sieve. On the other side you nicely get all the glial cells and the neurons and can pull out their nuclei to analyze their genetic material, but the stucky spaghetti-like vasculature stays in the strainer and typically gets thrown away. And along with it, you are throwing away cells that are associated with the vasculature, including structural cells like pericytes and smooth muscle cells, as well as cells like astrocytes, T cells, perivascular macrophages and fibroblasts, which all could play important roles in the development of Alzheimer’s.

To get around this problem, we collected these stringy vascular bits and, to switch metaphors, Andrew figured out how to squeeze the nuclei out of all the different cells like popping peas out of a pod, which let us sequence their gene expression for the first time. This new approach made a huge difference. We went from getting only a few dozen vascular cells among the thousands of single cells we were collecting to having half of the cells we collected coming from the vasculature.

What are the implications of all these new vasculature-associated risk genes for our understanding of Alzheimer’s disease? And how are you going to pursue that going forward?

That's the big question, of course. Right now we're basically generating a map and saying this is what we observe, but we don't yet know cause and effect. A gene variant may increase your risk of developing Alzheimer’s disease by, say, three fold, but right now we can't say whether that variant’s expression in endothelial cells is specifically responsible for the increased risk, even if its expressed there at high levels.

That needs to be tested experimentally, and it’s going to be difficult. We have to go back to model systems, such as patient-derived endothelial cell cultures or the blood brain barrier cultures that some people are generating. Or we could go back to model organisms and see whether a certain gene may be expressed in mice and could be studied in that context.

We’re really at the beginning at this point — but it’s exciting to be able to pursue these questions properly for the first time.

If it does turn out that damage to the brain vasculature occurs before the development of neurodegeneration in people who go on to develop Alzheimer’s disease, would that be promising for treatment and prevention of the disease?

It's hard to say, but I'm hopeful that it might be.

If you think about it, one of the biggest challenges of developing treatments for the brain is the blood brain barrier, which makes it really hard to get drugs into the brain. You can have an antibody that you would like to deliver to maybe clear up amyloid or to deliver a cargo but it's very difficult to get this from the bloodstream into the brain.

So what if the main target becomes the vasculature itself? That might be much easier to access. If the endothelial cells are damaged, you may be able to treat them with small molecule drugs and maybe you have a much easier way to have an impact on the disease.

So that's one hope that you could start targeting a more early-stage, proximal problem in the disease and you don't have to get into the much more protected areas of the brain.

Research Support:

This work was funded by the NOMIS Foundation, the National Institute on Aging, Nan Fung Life Sciences, the Bertarelli Brain Rejuvenation Sequencing Cluster (an initiative of the Stanford Wu Tsai Neurosciences Institute) and the Stanford Alzheimer’s Disease Research Center, as well as a grant from the Simons Foundation, a Siebel Scholarship, the CORSAAR study and the AHA–Allen Initiative in Brain Health and Cognitive Impairment.