Huntington’s is one of the large devastating monogenic diseases for which disease-modifying therapies have yet to materialize. This is about to change as a combination of big data sciences (single cell sequencing and GWAS) together with good old molecular biology is unraveling the detailed mechanisms of this neurodegenerative disorder. This provides an understanding for when and how to intervene. New therapeutic modalities, in particular sequence-specific therapeutics like oligonucleotides and genome editing that have emerged in recent years will play an important role in this endeavor.
In this blog entry, I will try to summarize the research findings and how individual steps along the pathogenic pathway may be targeted. Hold on, it will be an exciting one.
Somatic repeat expansion
Huntington’s Disease is linked to the expansion of the CAG triplet repeats found in exon 1 of the huntingtin gene. If you inherit a copy of huntingtin from either parent that carries 40 repeats of CAG or more you will almost certainly develop symptoms of HD (manifest HD). Symptoms intially involve emotional instability and cognitive deficits, progressing to include the famous movement abnormalities, ultimately culminating in life-shortening problems with basic physiological processes such as feeding and breathing. These follow neurodegenerative processes which can be observed decades before symptom onset (Scahill et al, 2025), most notably severe striatal atrophy. If you start with a number that is closer to 40 at birth, symptom onset may be in the early 60s, but if it is 50 or so, it will be more like at age 30.
Newer findings (Handsaker et al, 2025), show that having a huntingtin copy with 40 CAG repeats per se is not toxic to a given cell. But having 36 (incomplete disease penetrance), and especially 40 repeats or more is essential for stage 1 of pathogenesis: somatic repeat expansion. Genome-wide association studies (GWAS) have highlighted the critical role of the mismatch DNA repair (MMR) in facilitating such repeat expansion, also in post-mitotic cells in the CNS (Gem-HD, 2015). It is possible that as the transcription bubble in the triplet repeat DNA is formed during huntingtin mRNA transcription, chances of the DNA bubble collapsing out of register increases exponentially with repeat length. The consequently misaligned DNA strands would then be recognized by MMR and haphazardly resolved, in most cases by adding a CAG triplet on both strands.
The reason why symptom onset can differ by decades depending on starting CAG numbers is because repeat expansion itself is length-dependent and the initial expansion is quite slow until it picks up steam later (Handsaker et al, 2025). It is when repeat numbers reach ~150 in a given striatal projection neuron (aka medium spiny neuron), toxic substance X (see discussion below) gets produced and the cell starts to suffer.
The exact timing of manifest HD for a given CAG repeat number, however, also varies substantially and depends on additional factors, many of them genetic. Genome-wide association studies (GWAS) looking at those differences have clearly shown that proteins in the mismatch DNA repair pathway mediate repeat expansion (MSH3, FAN1, MLH1 etc) and have critically contributed to the mechanistic model of somatic repeat expansion outlined above (Gem-HD, 2015; Gem-HD, 2019).
An obvious therapeutic strategy therefore would be to inhibit repeat expansion by targeting DNA repair or by cutting down its size, if not get it below the 36 risk threshold using CRISPR genome editing (e.g. by twin prime editing). A number of companies among them Ionis, Biogen, Rgenta, Atalanta, LoQus23, Prime Medicine are attempting just that. Just binding DNA with zinc fingers has also been shown to inhibit expansion (Mathews et al, 2024). This strategy would also be able to simultaneously reduce the generation of toxic factor X.
DNA repair could in theory be targeted by small molecules. There is, however, perhaps unsurprisingly ample evidence that doing so indiscriminately throughout the body may be too risky a strategy. For example, early research of somatic repeat expansion in HD showed that knockout mice of the MMR protein MSH2 develop cancer (Wheeler et al, 2003), and while having heterzygous mutations in MMR genes slows HTT repeat expansion, it causes Lynch Syndrome, the most common genetic predisposition for cancer (Skarping et al, 2024).
More targeted approaches are therefore called for. These may include delivery specifically to the cells most affected by repeat expansion (i.e. the striatal projection neurons) or at least limit delivery to the post-mitotic and therefore less cancer-prone CNS using oligonucleotides, mRNA and/or DNA (by AAV, LNP). Alternatively, one could identify and copy rare missense or exon-skipping genetic modifier mutations in the human population that are protective against repeat expansion without predisposing to cancer. This could involve CRISPR prime or base editing, or non genome-editing ADAR RNA editing.
Toxic Factor X
Somatically expanded CAG repeats in the huntingtin gene DNA per se, however, is not what causes cellular toxicity. This is illustrated by GWAS hits that disentangle somatic expansion from age of disease onset and disease duration (GEM-HD, 2019). Furthermore, while CAG repeat length at birth strongly correlates with age at onset of disease and death, other genetic factors determine the duration between onset of disease and death (Keum et al, 2016). Finally, while the MSH2 knockout mice mentioned earlier (Wheeler et al, 2003) did not exhibit CAG expansion, they still showed some striatal-specific huntingtin inclusions characteristic of HD, albeit at much reduced levels compared to wild-type mice.
Historically, HD was thought of as a 'polyglutamine' disease, meaning that it is extended polyglutamine stretch that is toxic to a cell, either by forming inclusions causing cellular stress or by inappropriately interacting with other proteins. In fact, polyglutamine inclusions are characteristic of disease pathology as they are found in the cells most affected by HTT. Interestingly, these inclusions are best detected by antibodies directed at the N-terminus of HTT encoded by exon 1.
However, this polyglutamine-only model is seriously challenged by the observation that other CAG expansion diseases carry extensions in untranslated UTR elements and by the fact that mutations in HTT exon 1 itself that extend the stretch of glutamine by non-CAG synonymous codons do not increase inherent toxicity and may in fact delay disease onset and death.
In addition to protein, differences in HTT expansion should affect RNA structure and RNA polymerase II transcription. Toxic RNA is thought to be at the root of other repeat expansion diseases such as type I myotonic dystrophy as they by sequester important RNA-binding proteins away from their normal functions. Intriguingly, HTT RNA clusters in a repeat length-dependent manner around the huntingtin gene locus and these clusters appear to be seeded by exon 1 RNA (Ly et al, 2022).
Exon 1 mRNA
In the 90s it was found that merely expressing a fragment of the human huntingtin in mice comprising exon 1 makes for a good mouse model of HD (Mangiarini et al, 1996). The R6/2 line is widely used to this day, also because it models highly aggressive disease pathogenesis. Little did the authors of that paper probably suspect that the highly toxic exon 1-only huntingtin is not only generated in a length-dependent manner in mice (Sathasivam et al, 2013)...it is also expressed in patients (Neueder et al, 2017). In fact, there is (yet to be published) talk (Huntington's Study Group 2024, Wexler Symposium 2024) that exon 1 mRNA production is tied to somatic repeat expansion.
If you now consider that exon 1 is extremely toxic on its own, gets generated in a repeat number-dependent manner, and that the characteristic N-terminal huntingtin inclusions may not represent cleavage fragments of full-length huntingtin and that exon 1 mRNA may seed huntingtin RNA clusters, a compelling model emerges whereby once CAG somatic repeat expansion has reached a certain length, highly toxic exon 1 mRNA/protein gets produced and triggers manifest HD. This would also explain why the duration of manifest HD is independent of the original repeat length.
Mechanistically, it is possible that the expanded CAGs can impact the dynamics at which RNA polymerase II moves along the huntingtin gene which may allow for cryptic polyadenylation sites in huntingtin intron 1 to be recognized. The formation of complex R-loop structures between nascent RNA with extended CAGs and equally CAG-extended DNA may play a role here.
Therapeutic Strategies Aimed at Toxic RNA/Protein
There are a number of obvious modalities you could deploy to target the toxic agent in HD. These include RNaseH antisense, RNAi and genome editing for HTT knockdown, steric blocking antisense oligonucleotides to inhibit intron 1 polyadenylation site usage. Genome editing and ADAR RNA editing may also be used to interrupt the stretch of CAGs. Disrupting even just 10% or so of 150 CAG repeats in a given RNA or protein could have a huge impact on its toxic property.
While many of such agents are in preclinical development, some have reached the clinic already. Unfortunately, straightforward lowering of total, full-length huntingtin by RNaseH antisense (ASO) by Ionis and Roche failed to show benefit in a pivotal clinical trial (McColgan NEJM, 2023). In fact, the trial with tominersen was stopped early for toxicity as it may have done more harm than good as the therapy seemed to drive ventricular expansion along with striatal atrophy. While some argue that this shows the perils of lowering wild-type along with mutant huntingtin, this not only is inconsistent with human genetics showing no such effect in people with heterozygous null mutations in the huntingtin gene. If HD was caused by huntingtin insufficiency, there would be many more mutations aside from CAG repeat expansions that associated with HD. More likely, toxicity stemming from the heavily phosphorothioated oligonucleotide backbone led to increased death of already stressed striatal cells.
But sure, there should be no harm in targeting exclusively or predominantly mutant huntingtin as does Wave Life Sciences with their RNaseH antisense oligos targeting naturally occurring variations (SNPs) in the HTT gene correlating with the mutation.
Both strategies, however, fail to address highly toxic exon 1-only mRNA/protein as they are targeted downstream of exon 1. This is where UniQure’s DNA-directed RNAi and Alnylam’s synthetic oligonucleotide RNAi that target huntingtin in exon 1 itself come in.
In fact, the clinically more advanced of the two (Alnylam's ALN-HTT02 has just entered phase I), UniQure's AMT-130 has generated data suggesting almost disease stabilization as measured on the widely used cUHDRS scale along with stabilization, if not lowering of neurofilament, a biomarker for CNS injury over time. The data was so compelling when compared to external control in a propensity weighted manner that the FDA and UniQure are now working on expeditiously bringing the intrastriatally administered AAV therapy to the market possibly in 2026 already.
At this stage, I should disclose that I have started to invest in UniQure. Being first-to-market with a disease-modifying drug for HD would obviously be enormously lucrative for a well-financed company with an $800M market cap. While their intrastriatal approach makes it difficult to tell how much huntingtin knockdown is achieved, also on a single cellular level, and how much is therapeutically impactful, the increasingly promising clinical evidence and them probably pursuing the most impactful target increases my confidence in their success. Alignment with the FDA on the statistical analysis of their ongoing study which would form the basis for an accelerated approval along with upcoming 3-year follow-up data in the next 6 months will be key.
Please let me know in the comments below, if you come across evidence disproving the exon 1 hypothesis. I will keep looking, but have yet to find it.
Longer-term, I am excited by the prospect of exon 1-targeting therapeutics with agents slowing somatic repeat expansion, an area seeing significant investment. Since somatic expansion is a stochastic, asynchronous process and overlap generation of toxic RNA/protein, combining the two mechanisms will likely be most impactful.
