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,” said Steve McCarroll, a 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.