HD research is continuously evolving, as creative scientists develop and apply novel techniques to the study of cells, models, human tissue, and big data. In collaboration with HDBuzz and the Huntington’s Disease Foundation (HDF), five post-doctoral fellows share here the cutting-edge techniques they’re bringing to their work, and why these innovations matter for accelerating discovery and moving the field closer to meaningful treatments.
How Big is Your Repeat?
Carlos Chillon-Marinas and Sonia Vazquez-Sanchez, University of California, San Diego
Huntington’s disease (HD) is caused by an expansion of a short DNA sequence — the letters C-A-G — located in the first exon of the HTT gene. Everyone carries this repeat. The difference is how long it is. If the repeat is under 35 copies, people do not develop HD. Above 40, the disease is fully penetrant.
The story does not end with the inherited mutation. Over time, this repeat continues to expand within vulnerable brain cells, a phenomenon known as somatic repeat expansion. This process is now a major focus of HD research, as it appears to be a key driver of disease onset and progression. Ultra-long expansions are strongly linked to cell damage.
This means HD is not only about the repeat a person inherits; it’s also about how much that repeat grows inside their brain.
So how do you measure something that long?
Traditionally, repeat length has been measured using PCR-based techniques. These methods copy DNA and estimate repeat size from the resulting fragments. They work well for diagnosis and moderate expansions, but they struggle with very long repeats. Once repeats exceed roughly 100 copies, short-read DNA sequencing becomes unreliable. The longest expansions — the ones that may matter most biologically — are often missed.
For years, scientists suspected somatic expansion was important, but our tools could not fully capture its scale.
This is where PureTarget’s targeted long-read sequencing changes the game. PureTarget isolates high molecular weight DNA and selectively enriches the entire repeat region, molecule by molecule, without breaking it into tiny fragments. These intact DNA molecules are then sequenced end-to-end using high-fidelity long-read platforms, allowing entire repeat tracts — together with their surrounding genomic context — to be read in a single continuous molecule. Importantly, each molecule is sequenced multiple times, resulting in highly accurate repeat-length measurements.
The outcome is a much clearer view of repeat biology: exact repeat length, repeat interruptions, insertions or deletions, and allele-to-allele variability are measured directly rather than inferred. This matters because two cells with the same inherited mutation can accumulate very different repeat lengths over a lifetime, differences that may underlie selective neuronal vulnerability.
In a disease where DNA length drives biology, measuring the true size of the expansion is more than a detail. It’s a new window into how HD unfolds — and how we might one day slow it.
Multimodal Spatial Transcriptomics: Looking at Huntington’s Like Never Before
Carlos Chillon-Marinas and Sonia Vazquez-Sanchez, University of California, San Diego
One of the first questions scientists ask about HD is why the mutation harms brain cells but spares most other tissues in the body, even though every cell carries the same CAG expansion. Even within the brain, not all neurons are affected equally. Some populations, such as those in the striatum, are remarkably vulnerable, while others remain resilient. For decades, researchers have been trying to understand why.
Traditional tools could only show fragments of the story.
We could examine huntingtin protein aggregates, measure gene expression, or estimate the length of the CAG repeat tract —but each experiment had to be done separately, often in different pieces of tissue. That meant we could only correlate results indirectly. We had no way to see all of these features at once inside the same cells, and we usually had to destroy the tissue’s natural structure in the process.
Multimodal spatial transcriptomics changes that.
This new approach is imaging-based and enables a look inside individual cells while preserving intact tissue. It relies on advanced microscopy, combined with a sophisticated fluidic system allowing the measurement of RNA expression across thousands of genes, CAG repeat length, huntingtin aggregates, and signals of DNA damage, stress, and neuronal identity — all in the same experiment, and in the same cells, while maintaining their spatial context.
In essence, this technology lets us watch HD unfold at cellular resolution.
What makes this especially powerful is that it connects molecular events to the fate of individual neurons. We can identify which cells are most vulnerable and begin to understand why: is it the size of the CAG expansion, the presence of protein aggregates, or DNA damage? Early findings suggest that neurons with the largest repeat expansions are at greatest risk of loss, while huntingtin aggregates appear more closely linked to shifts in gene activity. These relationships were previously invisible because no single method could capture all these dimensions together.
Beyond solving long-standing biological puzzles, multimodal spatial transcriptomics may help guide future therapies. By revealing which DNA repair pathways are active in vulnerable neurons, or which cell types show the earliest signs of stress, researchers can make more informed decisions about therapeutic targets. As the technology continues to evolve, it promises an increasingly detailed view of how HD progresses within living neural circuits — and how we might intervene.
A High-Resolution Map of Cells
Devon Pendlebury, University of California, Irvine
Cryo-electron tomography (cryo-ET) is an imaging technique which allows us to generate 3D pictures of important features inside cells. The cells are flash-frozen quickly, helping to preserve their insides to give us a more accurate picture of how the cells look in real life. Once frozen, an electron microscope is used to image inside the cells. Electron microscopes can see much more detail than traditional light microscopes. The frozen sample is tilted at multiple angles and a 2D image is taken at each angle. These images can then be combined to create a 3D reconstruction which allows us to see compartments and proteins in the cell.
In HD, cryo-ET has been applied to see what aggregates of the Huntingtin protein look like in cells, and also to study how mitochondria are impacted by mutant Huntingtin. A study by the laboratories of Wah Chiu (Stanford University) and Leslie Thompson (University of California, Irvine) utilized cryo-ET to look at mitochondria, the energy factories of the cell, in HD neurons. They found that HD mitochondria had distorted shapes and contained granules that were not found in healthy mitochondria. This technique can also be used to determine how treatments affect mitochondria health. The fine details available using cryo-ET allow scientists to identify changes in HD that would not be detectable through other methods.
The Force is Strong with This Protein: Laser Tweezers vs. Huntingtin
Do you remember Star Wars, Star Trek, or Ghostbusters, where light traps and manipulates ships and monsters? That technology was awarded the Nobel Prize in Physics in 2018. Optical tweezers are a single molecule “force microscope” that uses a tightly focused laser beam to trap tiny plastic beads. The beads act like handles: if a protein is attached between two beads using molecular linkers, the instrument can gently pull on that one protein molecule by moving the laser traps. While pulling, it measures both the force applied and how far the protein extends, with nanometer precision. These forces are extremely small — typically a few to tens of piconewtons (billionths of a newton) — similar to what proteins experience inside cells.
This is particularly helpful for huntingtin because the region containing the polyglutamine (polyQ) tract is disordered, shifts between forms, and is prone to aggregation. Most structural methods work best when a protein is stable, uniform, and long-lived, but they report an average over huge populations of molecules. That averaging can blur distinct shapes together and hide rare, short-lived conformations that may still be biologically important — especially at polyQ lengths linked to HD.
Single-molecule optical tweezer experiments avoid this averaging by mechanically unfolding one huntingtin molecule at a time. By analyzing force-extension curves and unfolding/refolding event timing, researchers can map the protein’s energy landscape and conformations. They can determine whether the single protein (monomer) behaves like a random coil or forms a transient structure, whether intermediate structures exist, how stable they are, and how quickly the molecule switches between them. Because many individual molecules are measured, heterogeneity can be directly quantified rather than inferred from an average across millions of proteins.
Optical tweezers can help solve a long-standing question in the HD field: how does the mutation render the huntingtin protein toxic? Researchers are using this technique to compare huntingtin with different polyQ lengths and identify early structural changes that may trigger toxicity. They are also testing how post-translational modifications, chaperones, antibodies, and candidate drugs reshape huntingtin’s conformation. This single-molecule approach may reveal new therapeutic strategies, such as stabilizing a non-toxic huntingtin conformation. It may also provide mechanistic readouts for screening treatments and help connect molecular events to clinically relevant outcomes — showing how sci-fi technology can solve real biological problems.
Let’s Sort It Out
Chris Kay, Centre for Brain Research, University of Auckland
Your brain contains billions of specialized cells called neurons. There are hundreds or even thousands of types of neurons in the brain, each of which do different things, but strangely only a few specific types of neurons die in HD. Scientists would like to know what it is about these specific neurons that makes them so vulnerable to the disease, so we might understand how to stop them from dying in the first place. However, it’s very hard to study those specific vulnerable neurons when they are surrounded by so many other kinds of unaffected cells in human brain tissue. If only we could sort out the vulnerable ones to look at them on their own!
This is exactly the idea behind a new technique being used by leading HD researchers to study what makes specific neurons different in HD that may reveal what makes them more susceptible to the disease. Fluorescence-activated nuclei sorting (or FANS for short) involves attaching a small fluorescent tag to a desired neuron type from a brain tissue sample, then passing all the cells from that brain sample through a small tube with a camera. Whenever the camera detects a cell that is glowing with the fluorescent tag, it gets pushed into a separate tube for collection, whereas the non-glowing cells are allowed to pass straight through. After this procedure is done, the collected neurons that are sorted out with the fluorescent tag can be looked at separately from all other brain cell types.
Using these sorted neurons as starting material, scientists who study HD have already applied many cutting-edge technologies to examine what makes these specific neurons different in HD. That’s what makes this novel FANS technique for sorting out neurons so powerful — after sorting, the neurons can be analyzed in many different ways by scientists with different approaches and tools. For example, some of these approaches have already shown that the specific neurons affected in HD have more somatic CAG expansion, of interest to many drug companies that are trying to block somatic expansion for the treatment of HD.
