A research team led by scientists at MIT and at the Mayo Clinic has identified what they say are remarkable overlaps at the cellular and molecular levels between the movement disorder amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD), which underlies the cognitive disorder frontotemporal dementia (FTD). The results of their study point to potential targets that could lead to the development of therapies applicable to both disorders.

One of the most prominent findings of the study was that the most vulnerable neurons were almost identical in the two diseases, both with respect to the genes that the cells express, and how expression of these genes changed in each disease. “These similarities were quite striking, suggesting that therapeutics for ALS may also apply to FTLD and vice versa,” said Myriam Heiman, PhD, associate professor in The Picower Institute for Learning and Memory and the Department of Brain and Cognitive Sciences at MIT. “Our study can help guide therapeutic programs that would likely be effective for both diseases.”

Heiman is lead corresponding author of the team’s published paper in Cell, titled “Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD.”

On the surface, ALS and FTLD manifest in very different ways. In addition, the two disorders are known to primarily affect very different regions of the brain. However, clinicians and scientists have noted several similarities over the years. “Although amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are considered two distinct diagnoses, they show overlapping clinical, pathological, and genetic characteristics, suggesting that they are part of the same disease spectrum,” the authors wrote.

Clinically 40–50% of patients diagnosed with either ALS or FTD will eventually develop symptoms of the other disease, and up to 15% of patients will be diagnosed with both disorders, the investigators continued. However, they noted, despite the shared features of both ALS and FTD  “… a detailed understanding of their associated transcriptional alterations across vulnerable cortical cell types is lacking,”

For their newly reported study Heiman and colleagues used single-nucleus RNA sequencing (snRNA-seq) technology to track RNA expression patterns in 620,000 cells spanning 44 different cell types across motor cortex (MCX) and dorsolateral prefrontal cortex (DLPFC) regions of the brain, from postmortem brain samples of 73 donors diagnosed with ALS, FTLD, and neurologically unaffected control individuals.

“Here, we report a high-resolution, comparative single-cell molecular atlas of the human primary motor and dorsolateral prefrontal cortices and their transcriptional alterations in sporadic and familial ALS and FTLD,” they wrote. “We use these to identify and characterize known and novel vulnerable populations, examine transcriptional alterations in neuronal, glial, and vascular cell types, identify convergent and divergent disease mechanisms and pathways across cell types, diseases, and brain regions, and implicate drivers of cell-type specific differential vulnerability.”

Co-senior author Manolis Kellis, PhD, a professor in the computer science and artificial intelligence laboratory at MIT, further explained, “We focused on two brain regions that we expected would be differentially affected between the two disorders. It turns out that at the molecular and cellular level, the changes we found were nearly identical in the two disorders, and affected nearly identical subsets of cell types between the two regions.”

Heiman and Kellis collaborated with co-senior author Veronique Belzil, PhD, then associate professor of neuroscience at the Mayo Clinic Florida, now director of the ALS Research Center at Vanderbilt University.

One key finding from the study was that brain donors with inherited vs. sporadic forms of the disorders showed similarly altered gene expression changes, even though these were previously thought to have different causes. The finding suggests that similar molecular processes could be going awry downstream of the diseases’ origins. “Our data demonstrate that cell-type-specific components of disease-induced gene dysregulation are conserved across ALS and FTLD and that there is an unequivocally high similarity of sporadic versus familial (C9) ALS/FTLD-induced gene expression changes,” the investigators stated.

“The molecular similarity between the familial (monogenic) form and the sporadic (polygenic) forms of these disorders suggests that convergence of diverse etiologies into common pathways,” Kellis added. “This has important implications for both understanding patient heterogeneity and understanding complex and rare disorders more broadly.”

This overlap between diseases was especially evident, the study found, when looking at the most affected cells. In ALS, known to cause progressive paralysis and ultimately death, the most endangered cells in the brain are upper motor neurons (UMN) in layer 5 of the motor cortex. Meanwhile in behavioral variant frontotemporal dementia (bvFTD), the most common type of FTLD that is characterized instead by changes to personality and behavior, the most vulnerable neurons are spindle neurons, or von Economo cells, found in layer 5 of more frontal brain regions.

“By integrating transcriptional and genetic information, we identify known and previously unidentified vulnerable populations in cortical layer 5 and show that ALS- and FTLD-implicated motor and spindle neurons possess a virtually indistinguishable molecular identity,” the scientists stated. “… we show that neuron loss in cortical layer 5 tracks more closely with transcriptional identity rather than cellular morphology and extends beyond previously reported vulnerable cell types.”

The new study shows that while the cells look different under the microscope, and make distinct connections in brain circuits, their gene expression in health and disease is nevertheless strikingly similar. “UMNs and spindle neurons look nothing alike and live in very different areas of the brain,” said Sebastian Pineda, lead author of the study and a graduate student jointly supervised by Heiman and Kellis. “It was remarkable to see that they appear practically indistinguishable at the molecular level and respond very similarly to disease.”

Stained motor cortex tissue from a donor with ALS (right) shows reduced amounts of the protein HLA-E (green) in the vasculature. HLA-E is thought to inhibit degradation of the Blood Brain Barrier by the immune system. Researchers found reduced expression of HLA-E in both ALS and FTLD.
Stained motor cortex tissue from a donor with ALS (right) shows reduced amounts of the protein HLA-E (green) in the vasculature. HLA-E is thought to inhibit degradation of the Blood Brain Barrier by the immune system. Researchers found reduced expression of HLA-E in both ALS and FTLD. [Heiman Lab/MIT Picower Institute]

The researchers found many of the genes involved in the two diseases implicated primary cilia, tiny antenna-like structures on the cell’s surface that sense chemical changes in the cell’s surrounding environment. Cilia are necessary for guiding the growth of axons, or long nerve fibers that neurons extend to connect with other neurons. Cells that are more dependent on this process, typically those with the longest projections, were found to be more vulnerable in each disease.


“Human ciliopathy disorders are characterized by developmental axonal malformations and axonal pathfinding abnormalities, and it is known that primary cilium-related genes have important developmental axonal functions,” the team stated. “The enrichment of these genes in the most vulnerable cell types suggests an unexplored determinant of cell-type-enhanced vulnerability.”

The analysis also found another type of neuron, which highly expresses the gene SCN4B and which was not previously associated with either disease, also shared many of these same characteristics and showed similar disruptions. “It may be that changes to this poorly characterized cell population underlie various clinically relevant disease phenomena,” Heiman said.

The study results indicated that the most vulnerable cells expressed genes known to be genetically associated with each disease, providing a potential mechanistic basis for some of these genetic associations. This pattern is not always the case in neurodegenerative conditions, Heiman said. For example, Huntington’s disease is caused by a well-known mutation in the huntingtin gene, but the most highly affected neurons don’t express huntingtin more than other cells, and the same is true for some genes associated with Alzheimer’s disease.

Looking beyond neurons, the study characterized gene expression differences in many other brain cell types. Notably, researchers saw several signs of trouble in the brain’s circulatory system. The blood-brain barrier (BBB), a filtering system that tightly regulates which molecules can go into or come out of the brain through blood vessels, is believed to be compromised in both disorders.

Building on their previous characterization of human brain vasculature and its changes in Huntington’s and Alzheimer’s disease by Heiman, Kellis, and collaborators including Picower Institute Director Li-Huei Tsai, PhD, the researchers found that proteins needed to maintain blood vessel integrity are reduced or misplaced in neurodegeneration. “Consistent with prior evidence of vascular leakage and tight junction loss, we found that components of tight and adherens junctions were downregulated.

in MCX endothelial cells of ALS, and to a lesser extent FTLD cases,” they stated. “Downregulation of proteins encoding tight and adherens junction components would be expected to affect blood-brain barrier (BBB) integrity.”

The scientists also found a reduction of HLA-E, a molecule thought to inhibit BBB degradation by the immune system. “HLA-E is an important regulator of natural killer (NK) cell function, specifically acting in endothelial cells as an inhibitory stimulus for NK-mediated cell lysis,” they wrote. “We observed reduced HLA-E protein expression in ALS MCX endothelial cells … loss of HLA-E from brain endothelium may represent a mechanism for NK-mediated BBB breakdown and/or NK cell parenchymal accumulation.”

Given the many molecular and mechanistic similarities in ALS and FTLD, Heiman and Kellis said they are curious why some patients present with ALS and others with FTLD, and others with both but in different orders.

While the present study examined upper motor neurons in the brain, Heiman and Kellis are now seeking to also characterize connected lower motor neurons in the spinal cord, also in collaboration with Belzil. “Our single-cell analyses have revealed many shared biological pathways across ALS, FTLD, Huntington’s, Alzheimer’s, vascular dementia, Lewy body dementia, and several other rare neurodegenerative disorders,” said Kellis. “These common hallmarks can pave the path for a new modular approach for precision and personalized therapeutic development, which can bring much-needed new insights and hope.”

Their approach could also have wider reaching applications, the team suggested in their discussion. “We identified differentially vulnerable cell populations and demonstrated the convergence of population-level genetic risk factors and transcriptional dysregulation using an approach that could be extended to other disorders where differentially vulnerable cell types are ill-defined or unknown,” they further pointed out.

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