The Brains Behind the Breakthroughs: Representation in Clinical Trials

The level of diversity that exists globally has not been documented in large-scale clinical trials for Alzheimer’s disease (AD). This under-represesentation limits our understanding of disease progression and exacerbates health inequalities, especially in light of the fact that many populations that are understudied in AD research are at increased risk of disease.

94.7 percent. A recent investigation digging into the percentage of White participants in clinical trials for Alzhiemer’s disease found that in 101 studies profiled between 2001 and 2019, the average percentage of White participants was 94.7%. 

African Americans are 1.4 times more likely than European Americans to carry the apolipoprotein E (APOE) ε4 risk factor for AD. Despite this increased risk, studies tracking the neural correlates of cognitive decline and disease progression in African Americans have been limited. Efforts including the Healthy Aging in Neighborhoods of Diversity across the Life Span cohort study (https://clinicaltrials.gov/ct2/show/NCT01323322) have provided crucial insights between the relationships between race, APOE genotype, and cognition; however, these studies often recruit a limited number of participants and require additional funding, attention, and recruitment.

Take for example the events that happen in African Americans with progressive chronic and end stage kidney disease. There are two African-specific risk variants (i.e. changes) in a gene called APOL1 that lead to a 7- to 10-fold increased risk for kidney disease. It is studies like this one that highlight why African Americans have a higher incidence of end stage kidney disease than European Americans. Of interest, these variants occur at higher frequency in individuals of West African descent because they are protective against sleeping sickness caused by an insidious protozoa. What other clues into the origin of disease are we missing by not taking into account the local adaptations in the genetic architecture of complex diseases?

The National Human Genome Research Institute catalogs the results of genome wide association studies with the goal of using genetic evidence to enhance the success of drug target identification. The question remains: drug target identification for which patient populations? In a call to arms to increase diversity in clinical trials published in the prestigious journal Cell in 2019, researchers from the University of Pennsylvania reported that the number of individuals included in GWAS studies based on ethnicity has the following ancestry distributions: 78% European, 10% Asian, 2% African, 1% Hispanic, and all other ethnicities represent < 1% of GWAS (https://www.ebi.ac.uk/gwas/home). 

Genetic variation among diverse populations can affect how likely a drug will work and also how likely it might be to cause adverse side-effects. 

What can the Alzheimer’s disease research field learn from cancer research? The Count Me In project, for example, successfully accomplished the goal of generating a database of patient-reported data with the possibility of providing a benefit for every person affected by cancer, especially individuals from marginalized communities who have historically been excluded from research, no matter whether they live close to a major research institution. The success of Count Me In depends on patients across all backgrounds and experiences being able to share saliva samples, medical records, and survey responses without leaving home. The data is then de-identified and shared with researchers all over the world to accelerate progress against all forms of cancer. 

The Alzheimer’s disease research community has its own grassroots, patient-driven efforts to learn more about disease progression in the form of the Brain Donor Project. The Brain Donor Project’s core mission is the following: to increase the recruitment of underrepresented Americans for brain donation registration. 

Built on the legacy of Gene Armentrout who understood that his brain could be valuable for other patients who also suffered from Lewy Bodies Dementia, the Brain Donor Project seeks to increase brain donation for research by connecting patients to the NeuroBio Bank, part of the National Institute of Health. Importantly, the BDP understands that science benefits when patients from every background are included and is seeking to bridge the knowledge gap by partnering with patients from every community. The research community is seeking to remedy exclusionary practices of the past by including minority populations in biobank initiatives. The BDP encourages donations of healthy brains (for controls) and also those with neurologic disorders, and more information can be found on their website: braindonorproject.org. The Brain Donor Project states their mission best: you can be the brain behind the breakthrough.

The regulation of genes by non-coding regions of DNA impacts Alzheimer’s Disease risk: Rethinking So-Called "Junk DNA

            The term “junk DNA” is thought to date back to the discovery of DNA’s double helical structure when Dr. Francis Crick described the genetic gibberish surrounding the small pieces of DNA that coded for proteins (called exons) as “little better than junk.” In 2000, scientists of the Human Genome Project suggested that 97% of the human sequence had no apparent function. It wasn’t until 2012 that scientists began to appreciate that there were hidden switches and regulatory regions embedded in this so-called junk DNA. New research provides even more compelling evidence that “junk DNA” might be involved in regulating risk of Alzheimer’s disease.

The majority of human DNA is non-coding DNA – regions of the genome that do not directly translate into proteins. In addition, most of the disease-risk genetic variants are located in non-coding regions of the genome. As a result, non-coding regions of the DNA are increasingly being recognized as important for Alzheimer’s disease risk since these areas of the genome contain enhancers – short-regions of DNA that can change the odds that a specific protein is made.

In research published in Science under the direction of Dr. Christopher Glass, M.D., Ph.D at the Salk Institute of the University of California, San Diego, it was shown that disease risk for neurodegeneration is often linked to specific enhancer regions in specific cell types – in this case, in the immune cells of the brain called microglia. This paper adds an added layer of complexity to how genetic variants in one cell type influence disease risk.

  In this study, tissue was obtained from six patients in order to isolate four different kinds of cell types in different brain regions. In this case, the brain cell types included neurons, microglia, oligodendrocytes, and astrocytes. Investigating different cell types revealed that variants in transcriptional enhancers in neurons were more commonly associated with psychiatric disorders. Alzheimer’s disease risk variants, for late-onset forms of the disease, were almost exclusively confined to microglia enhancers.

“In an interview with Science, Dr. Glass explained: “We show preferential enrichment in disease risk variants in enhancers that are selectively active in microglia. This finding substantially extends prior studies linking microglia to late-onset Alzheimer’s disease.””

— https://www.eurekalert.org/pub_releases/2019-11/uoc--gvi111419.php

The research went a step further by creating a map between the enhancers and the genes they regulate. This provided novel insights into the differences seen across different cell types in the brain. While the sample size was limited, this paper suggests that creating a cell type-specific promoter-enhaner interactome has the potential to help interpret risk alleles associated with neurological and psychiatric diseases.

A Blueprint for the Brain

Zeroing in on the characteristics of female cells that make them more vulnerable to Alzheimer’s disease

MIT scientists Manolis Kellis and Li-Huei Tsai are combining bioinformatics and molecular biology to understand the brain in an entirely new way.

 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 powerhouse 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 different properties and behaviors of different cells and tissue both in health and disease. 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 a 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 study published in Nature took 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 that has previously been largely over-looked in Alzheimer’s disease. Oligodendrocytes are a type of brain cell that 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. What they found was 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.

Dr. Li Huei Tsai in discussing the research 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. So far, 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.

Largest Genetic Dataset Confirms 29 Risk Genes for Alzheimer’s Disease… and Counting

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94,437 individuals who had been diagnosed with late-onset Alzheimer’s disease participated in a genome-wide association study that identified variants in five new genes that put people at risk for Alzheimer’s disease. The data also confirmed 20 other genes that had been previously implicated in Alzheimer’s disease.

The last large-scale genome-wide association study (GWAS) was published five years ago and included approximately 75,000 individuals. This study identified 20 genetic risk loci. At the time, 11 of the newly identified loci had never before been implicated in conferring risk for Alzheimer’s disease. In January of 2019, an international team of scientists published an updated Alzheimer’s disease GWAS that was published in Nature Genetics. This time the study included genetic data from over 635,000 individuals. This dramatic increase in the number of subjects allowed for the identification of nine novel Alzheimer’s disease risk loci.

In some ways, this latest GWAS study allowed for the confirmation of the involvement of genes identified in the previous study in Alzheimer’s disease while also identifying novel targets and de-emphasizing some of the suggested hits from the previous paper. An interesting, newly identified risk gene for Alzheimer’s disease is APH1B. Along with presenilins, APH1B makes up the gamma-secretase complex which is responsible for cleaving amyloid precursor protein to form a smaller protein, amyloid b, that is more toxic due to its propensity to form plaques in the brain.

Genome-wide association studies are useful in identifying gene variants that turn up often in patients with a specific disease. What is harder to identify are the rare gene variants. The international team of scientists increased their sample size to genomic data from more than 94,000 individuals in order to identify these rare genetic variants in five additional genes: IQCK, ACE, ADAM10, ADAMTS1, and WWOX that are associated with late onset Alzheimer’s disease.

Another huge advance from this paper is the identification of the groups of genes that work together to influence risk and disease progression. Many of the genes identified play a role in the formation of beta-amyloid plaques, tau accumulation, and the immune system.

By themselves, each of these newly discovered variants contribute only a small amount of increased risk. That being said, this study advances the biological pathways that are involved in the onset and progression of the disease.

A huge component of this study to keep in mind is the dramatic similarity between genes implicated in early-onset and late-onset Alzheimer’s disease. This aspect of the study suggests that treatments developed for people with the early onset form might also help those with the more common late-onset of the disease.

This new research paper is ground breaking for those interested in finding a way to predict who will get Alzheimer’s disease later in life. The goal of this research is to understand how the complex biological, environmental, and lifestyle factors interact to contribute to Alzheimer’s.