Scientists discover new mechanism behind Huntington’s disease brain cell death

Scientists at the Broad Institute of MIT and Harvard, Harvard Medical School, and McLean Hospital have discovered a surprising mechanism by which the inherited genetic mutation known to cause Huntington’s disease leads to the death of brain cells. The findings change the understanding of the fatal neurodegenerative disorder and suggest potential ways to delay or even prevent it.

For 30 years, researchers have known that Huntington’s is caused by an inherited mutation in the Huntingtin (HTT) gene, but they didn’t know how the mutation causes brain cell death. A new study published today in Cell reveals that the inherited mutation doesn’t itself harm cells. Rather, the mutation is innocuous for decades but slowly morphs into a highly toxic form that then quickly kills the cell.

The Huntington’s mutation involves a stretch of DNA in the HTT gene in which a three-letter sequence of DNA, “CAG,” is repeated at least 40 times, as opposed to the 15-35 repeats inherited by people without the disease. The researchers found that DNA tracts with 40 or more CAG repeats grow until they are hundreds of repeats long. This type of “somatic expansion” occurs in only the specific types of brain cells that later die in Huntington’s disease. Only once a cell’s DNA expansion reaches a threshold number of CAGs – roughly 150 – does the cell sicken and then die. The cumulative death of many such cells leads to the symptoms of Huntington’s disease.

The study offers a potential explanation as to why candidate Huntington’s drugs that aim to reduce expression of the HTT protein have struggled in clinical trials: Very few cells have the toxic version of the protein at any given time, so the treatments may not be having a therapeutic effect in most cells.

The research also elevates a different therapeutic strategy: Stopping or slowing the CAG-repeat expansion in the HTT gene might postpone toxicity in a far larger number of cells, delaying or even preventing the onset of the disease.

These experiments have changed how we think about how Huntington’s develops.”

Steve McCarroll, geneticist and neuroscientist and co-senior author of the study

McCarroll is an institute member and director of genomic neurobiology at the Stanley Center for Psychiatric Research at the Broad, the Dorothy and Milton Flier Professor of Biomedical Science and Genetics at Harvard Medical School, and an investigator of the Howard Hughes Medical Institute. “This is a really different way of thinking about how a mutation brings about a disease, and we think that it will apply in DNA-repeat disorders beyond Huntington’s disease.”

“The point of our work – what we all do – is relieving suffering caused by disease,” said co-senior author Sabina Berretta, associate professor of psychiatry at Harvard Medical School and McLean Hospital, a member of the Mass General Brigham healthcare system. She is also the director of the Harvard Brain Tissue Resource Center (HBTRC), an NIH NeuroBioBank center at McLean Hospital. “This study and the work it informs could be impactful and make a major difference in relieving suffering in the short term.”

Bob Handsaker, a staff scientist, Seva Kashin, a senior principal software engineer, and former research associate Nora Reed, all from McCarroll’s group, are co-first authors on the work.

Open questions

Huntington’s disease kills a population of cells called striatal projection neurons, which are located in the striatum, a structure deep in the brain responsible for movement, many cognitive functions, and motivation. When large numbers of these cells die, patients develop involuntary movements in the arms, legs, and face, and many patients also develop cognitive problems. These symptoms typically begin in mid-life and then progress over 10 to 20 years to more severe cognitive problems and difficulty moving or swallowing.

In 1993, researchers discovered that the disease is caused by an expanded stretch of CAGs in the HTT gene. Most people inherit versions of the gene with 15 to 35 consecutive CAGs and never develop Huntington’s, but those who inherit a version with 40 or more consecutive CAGs almost always develop the illness later in life. The longer the stretch of repeats, the younger a person tends to be when symptoms first appear. The tract of repeated CAGs has also been shown to expand over time, resulting in a variety of lengths in different tissues.

But underlying biological questions had always lingered: How is the HTT mutation toxic? Why would the HTT protein – which appears in almost every cell in the body – kill only some brain cells and not others? And why do patients, who are born with the mutation and express the protein throughout life, develop symptoms only in middle age, after decades of apparent good health?

Repeat expansion

To answer these questions, the research team built upon a technology the McCarroll lab developed a decade ago called droplet single-cell RNA-sequencing (Drop-seq), which allows researchers to analyze gene expression in thousands of single cells. Seeking to understand the direct biological effects of CAG-repeat length, the researchers adapted single-cell RNA-sequencing to help them determine not only gene expression and the identity of single cells, but also the length of DNA repeat tracts inside each cell.

“It’s been known that these repeats expand in neurons,” said Kashin. “But the ability to take a particular cell and measure both the CAG length and the transcriptional profile – that’s a really important underpinning that’s allowed for really powerful analysis.”

The researchers studied brain tissue donated by 53 people with Huntington’s and 50 without the disease, collected and preserved by the HBTRC. They analyzed more than 500,000 single cells and found that most cell types from people with the disease had essentially the same CAG repeat that they had inherited. But striatal projection neurons – the primary striatal cells that die in the disease – had greatly expanded their CAG-repeat tracts. Most previous research on human brain tissue had focused on CAG-repeat tracts of fewer than 100 repeats, but the new study showed that some neurons had as many as 800 CAGs, confirming a discovery made 20 years ago by Peggy Shelbourne at the University of Glasgow.

Most surprisingly, the research team found that expansion of the DNA repeat from 40 to 150 CAGs had no apparent effect on the neurons’ health. But neurons whose repeats exceeded 150 CAGs showed greatly distorted gene expression, losing expression of critical genes and then dying.

McCarroll’s team also used computer modeling of the experimental data to estimate the rate and timing of CAG-repeat expansion in striatal projection neurons. They found that CAG-repeat tracts initially grow slowly, expanding less than once a year during the first two decades of life. But when a cell’s repeat tract reaches about 80 CAGs – usually after several decades – its rate of expansion accelerates dramatically and it expands to 150 CAGs in only a few more years. The cell then dies just months later. This means that a neuron spends more than 95 percent of its life with an innocuous HTT gene. Moreover, because the CAG-repeat tracts in different cells cross this toxicity threshold at different times, the cells, as a group, disappear slowly over a long period, starting about 20 years before symptoms appear and more quickly as symptoms commence.

“A lot was known about Huntington’s disease before we started this work, but there were gaps and inconsistencies in our collective understanding,” Handsaker said. “We’ve been able to piece together the full trajectory of the pathology as it unfolds over decades in individual neurons, and that gives us potentially many different time points at which we can intervene therapeutically.”

Analyzing brain tissue contributed by Huntington’s patients was critical for the work. “Our gratitude is with the families that chose to do something that is very difficult to do,” Berretta said. “This would not have been possible without the altruism of many brain donors who have left a legacy of knowledge that will last and benefit many other people.”

Therapeutic possibilities

McCarroll’s team suggests that rather than targeting the HTT protein, a complementary or potentially better therapeutic approach could be to slow or stop the DNA-repeat expansion, which could help delay or even prevent the disease.

Previous genetic studies of Huntington’s, including studies by Vanessa Wheeler and Ricardo Mouro Pinto at Massachusetts General Hospital, hint at possible ways to slow this expansion. The studies showed that cellular proteins involved in maintaining and repairing DNA sometimes undermine the stability of DNA-repeat tracts. For example, the MSH3 protein normally helps the cell monitor its DNA for potential mutations, but loops in the DNA formed by extra CAGs can confuse this protein into expanding the CAG repeat. An international team of human geneticists found that common genetic variations in the genes encoding these DNA-repair proteins can hasten or delay onset of symptoms in Huntington’s patients – findings that McCarroll says directly inspired his team’s focus on developing ways to measure the CAG repeat in single cells. He adds that slowing down certain DNA-maintenance processes with a molecular therapy might slow down DNA-repeat expansion by allowing other less error-prone DNA-repair mechanisms to resolve these loops.

In the meantime, the researchers are working to understand how DNA-repeat tracts longer than 150 CAGs lead to neuronal impairment and death, and why repeats expand more in some kinds of neurons than in others. They are also using a similar combination of single-cell RNA sequencing alongside DNA-repeat profiling to understand the connection between DNA-repeat expansion and cellular changes in other genetic disorders involving DNA repeats and late onset in patients. More than 50 human brain disorders, including fragile X syndrome and myotonic dystrophy, are caused by expansions of DNA repeats in various genes.

“It’s going to take much scientific work by many people to get to treatments that slow the expansion of DNA repeats,” McCarroll said. “But we’re hopeful that understanding this as the central disease-driving process leads to deep focus and new options.”

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