Scientists have identified an unexpected process by which the genetic mutation linked to Huntington’s disease leads to the death of brain cells. These discoveries shift our view of this deadly neurodegenerative condition and hint at possible methods for delaying or even preventing its onset. For the past 30 years, it has been established that Huntington’s disease stems from a genetic mutation found in the Huntingtin (HTT) gene, but the exact mechanism by which this mutation causes brain cell death remained unclear. Recent research uncovers that the inherited mutation doesn’t immediately damage cells. Instead, it remains harmless for many years, before gradually transforming into a highly toxic version that then swiftly kills the cell.
Researchers from the Broad Institute of MIT and Harvard, Harvard Medical School, and McLean Hospital have unveiled a surprising mechanism by which a genetic mutation responsible for Huntington’s disease results in brain cell death. This study alters the existing narrative surrounding this fatal neurodegenerative disorder and points toward potential strategies for delaying or preventing its effects.
For over 30 years, scientists have recognized that Huntington’s disease is triggered by a hereditary mutation in the Huntingtin (HTT) gene, but the pathway leading to brain cell demise remained elusive. A new study published in Cell indicates that the inherited mutation itself does not harm brain cells. Instead, it remains benign for many years before slowly transforming into a toxic form that leads to rapid cell death.
The mutation associated with Huntington’s disease involves a segment of DNA in the HTT gene where a three-letter DNA sequence, “CAG,” is repeated 40 times or more—compared to the 15-35 repetitions found in individuals without the disease. The researchers discovered that tracts of DNA with 40 or more CAG repeats continue to grow, sometimes extending to hundreds of repeats. This phenomenon, known as “somatic expansion,” occurs exclusively in specific brain cells that ultimately succumb to Huntington’s disease. Cell death happens only after a cell reaches a critical threshold of approximately 150 CAG repeats, leading to the typical symptoms associated with the disease due to the cumulative death of these cells.
The study provides insight into why drugs aimed at reducing the HTT protein have faced challenges in clinical settings: only a small number of cells harbor the toxic form of the protein at any given moment, meaning these treatments may not have a beneficial effect on the majority of cells.
This research also suggests a new therapeutic approach: by preventing or slowing the expansion of CAG repeats in the HTT gene, it may be possible to delay toxicity across a broader range of cells, potentially postponing or even preventing the onset of the disease.
“These findings have transformed our understanding of Huntington’s disease progression,” stated Steve McCarroll, a geneticist and neuroscientist and co-senior author of the study. He is an institute member and director of genomic neurobiology at the Stanley Center for Psychiatric Research at Broad, as well as a professor at Harvard Medical School and an investigator with the Howard Hughes Medical Institute. “This offers a fundamentally new perspective on how mutations can lead to diseases, and we believe this may extend to other DNA-repeat disorders beyond Huntington’s.”
“Our ultimate goal is to alleviate the suffering caused by these diseases,” said co-senior author Sabina Berretta, an associate professor of psychiatry at Harvard Medical School and McLean Hospital, also affiliated with the Mass General Brigham healthcare system. She directs the Harvard Brain Tissue Resource Center (HBTRC), a NeuroBioBank center funded by NIH at McLean Hospital. “Our findings, along with related research, have the potential to significantly impact and enhance relief efforts in the near future.”
Bob Handsaker, a scientist, Seva Kashin, a senior principal software engineer, and former research associate Nora Reed from McCarroll’s team are co-first authors of this study.
Unanswered Questions
Huntington’s disease leads to the death of a type of cell called striatal projection neurons, which are found in the striatum, a brain region that plays critical roles in movement, cognition, and motivation. When a substantial number of these neurons perish, patients experience involuntary movements in their limbs and face, as well as cognitive difficulties. Symptoms generally emerge in mid-life and can progress over 10 to 20 years, leading to more serious cognitive impairments and challenges with movement or swallowing.
In 1993, it was discovered that the disease is caused by an expanded segment of CAG repeats in the HTT gene. People typically inherit versions of this gene with 15 to 35 consecutive CAGs, and they do not develop Huntington’s disease. However, those inheriting a version with 40 or more CAG repeats are highly likely to develop the disease later in life. Notably, the greater the number of repeats, the earlier symptoms tend to manifest. Additionally, the length of CAG repeats can expand over time, creating variability across different tissues.
Nonetheless, several biological questions lingered: What makes the HTT mutation harmful? Why does the HTT protein, found in nearly every cell, lead to the death of certain brain cells, while sparing others? And why do patients born with this mutation only begin exhibiting symptoms in middle age, after decades of seemingly good health?
Exploration of Repeat Expansion
To tackle these questions, the research team built on a technology called droplet single-cell RNA sequencing (Drop-seq), developed by McCarroll’s lab a decade ago. This technology enables scientists to analyze gene expression in thousands of single cells. To explore the effects of the CAG-repeat length, the researchers enhanced single-cell RNA sequencing capabilities to measure not only the gene expression and identities of individual cells but also the lengths of the DNA repeat segments within each one.
“It’s established that the repeats can expand within neurons,” noted Kashin. “However, to measure both the CAG length and the transcriptional profile in a specific cell has been a significant advancement that allows for robust analysis.”
The team examined brain tissue from 53 individuals with Huntington’s disease and 50 without, which was collected and preserved by the HBTRC. They analyzed over 500,000 single cells and noted that most cell types from individuals with the disease maintained the CAG repeat length they inherited. However, striatal projection neurons, the key type affected by the disease, exhibited significant growth in their CAG-repeat tracts. Past studies on human brain tissues focused on CAG repeats of fewer than 100, but this new research found some neurons had CAG expansions as vast as 800 CAGs, confirming earlier findings from Peggy Shelbourne at the University of Glasgow 20 years ago.
Interestingly, the team discovered that increasing the CAG repeat from 40 to 150 did not visibly harm neuron health. However, once the repeats surpassed 150 CAGs, the neurons demonstrated distorted gene expression, silencing vital genes and ultimately leading to cell death.
McCarroll’s team employed computer models to analyze the experimental data and estimate the rate and timing of CAG-repeat expansions in striatal projection neurons. They observed that CAG repeat tracts initially expanded slowly, growing at a rate of less than once per year during the first two decades of life. However, once a cell’s repeat length reached around 80 CAGs—usually after several decades—the pace of expansion accelerated rapidly.
The situation intensifies as the number of CAG repeats swiftly increases to 150 within just a few years. Following this, the neuron ultimately succumbs just months later. This indicates that a neuron spends over 95 percent of its existence with a harmless HTT gene. Additionally, since the CAG-repeat sections in various cells exceed this toxicity threshold at different intervals, the collective loss of these cells occurs gradually over an extended time, beginning roughly 20 years prior to the emergence of symptoms and accelerating once the symptoms start.
“Although there was already a considerable amount of knowledge regarding Huntington’s disease when we embarked on this research, there were still gaps and inconsistencies in our overall understanding,” Handsaker remarked. “We have successfully mapped out the entire progression of the disease as it develops over many years within individual neurons, which provides us with numerous potential timeframes for therapeutic intervention.”
Examining brain tissues contributed by individuals with Huntington’s was essential for this research. “We owe our deepest gratitude to the families who opted for such a challenging decision,” Berretta noted. “This study would not have been feasible without the selflessness of numerous brain donors, whose contributions will leave a lasting impact and benefit many others.”
Potential Therapeutic Approaches
The team led by McCarroll proposes that instead of focusing on the HTT protein, a potentially more effective therapeutic strategy could involve slowing or halting the expansion of DNA repeats, which may help postpone or even avert the onset of the disease.
Previous genetic research on Huntington’s, including work by Vanessa Wheeler and Ricardo Mouro Pinto at Massachusetts General Hospital, suggests possible methods for decelerating this expansion. These studies revealed that certain cellular proteins responsible for maintaining and repairing DNA may inadvertently compromise the stability of DNA-repeat segments. For instance, the MSH3 protein typically aids the cell in monitoring its DNA for potential mutations, but the loops in the DNA created by excess CAGs can mislead this protein into enlarging the CAG repeat. An international team of geneticists discovered that common genetic variations in the genes that code for these DNA-repair proteins can speed up or delay the onset of symptoms in Huntington’s patients—insights that McCarroll states have directly guided his team’s efforts to devise techniques for measuring the CAG repeat in individual cells. He further elaborates that molecular therapies designed to slow down specific DNA-maintenance processes might help decrease DNA-repeat expansion, as they would allow other, more reliable DNA-repair mechanisms to address these loops.
Currently, researchers are focused on understanding how DNA-repeat segments longer than 150 CAGs result in neuronal dysfunction and death, as well as why some neuron types experience more significant expansion of repeats than others. They are also employing a similar method of combining single-cell RNA sequencing with DNA-repeat profiling to explore the relationship between DNA-repeat expansion and cellular alterations in various other genetic disorders that feature DNA repeats and have late-onset symptoms. More than 50 human brain disorders, such as fragile X syndrome and myotonic dystrophy, are caused by the expansion of DNA repeats within different genes.
“It will require significant scientific efforts from many individuals to achieve treatments that can slow down DNA repeat expansion,” McCarroll stated. “However, we’re optimistic that recognizing this as the primary disease-driving mechanism will lead to focused research and new therapeutic options.”
Funding This research was funded by CHDI Foundation, Inc., the Department of Genetics in the Blavatnik Institute at Harvard Medical School, the Ludwig Neurodegenerative Disease Seed Grants Program at Harvard Medical School, and the National Human Genome Research Institute, part of the National Institutes of Health.
