When scientists discovered that mutations in the C9orf72 gene were the most common genetic cause of ALS and frontotemporal dementia (FTD), it was a game-changer. These repeat expansions (extra bits of DNA that shouldn’t be there) show up in up to 40% of inherited ALS cases and nearly 10% of sporadic ones, making them a prime target for therapy. But targeting C9orf72 has proven more complicated than anyone hoped.
From Hope to Hurdles: What We’ve Learned So Far
Back in 2016, Target ALS helped fund the first-ever clinical trial testing an antisense oligonucleotide (ASO) therapy aimed at silencing the toxic C9orf72 mutation. The mutation causes cells to produce abnormal RNA and proteins that clog up cellular machinery and lead to neurodegeneration.
In 2023, that ASO (called BIIB078) completed a large trial. The good news? It successfully reduced the abnormal RNA. The bad news? Patients didn’t get better. The clinical outcome suggests that the sense strand is not the key aspect of the pathology that is harmful.
This was a pivotal moment, not a failure, but a redirection. The clinical outcome provides evidence that scientists may have been targeting the wrong strand of RNA. This revelation opened new doors, and Target ALS stepped in again to accelerate the next wave of discoveries. At the same time, new preclinical research has demonstrated toxicity of the aberrant” antisense strand” and ability to alleviate toxicity with targeted ASOs.
| ALS 101: C9orf72: A gene where a repeat expansion mutation is the most common genetic cause of ALS and FTD. Antisense Oligonucleotide (ASO): A synthetic strand of DNA or RNA designed to silence harmful genes. TDP-43: A protein involved in RNA regulation. When it mislocalizes, it causes cellular dysfunction in ALS. Dipeptide Repeat Proteins (DPRs): Toxic proteins produced due to C9orf72 mutations.CRISPR: A gene-editing technology that can precisely modify DNA.Microglia: The immune cells of the brain and spinal cord. RNA Foci: Clumps of abnormal RNA that form in the nucleus and are a sign of cellular stress. |
The Antisense Awakening: A New Target Emerges
Now, a team well-positioned to deliver the first therapeutic against the AS strand, including Biogen, Ionis Pharmaceuticals, and Johns Hopkins University is focusing on the antisense RNA strand; the overlooked sibling of the one previously targeted. This work is motivated by the preclinical research mentioned above, which Target ALS helped to fund. Funding from Target ALS brings together the clinical and research expertise of the John Hopkins team with powerful biotech committed to treating motor neuron diseases.
Why the shift? Postmortem analyses showed that antisense RNA was more abundant in affected neurons and more closely associated with toxic TDP-43 protein buildup, a hallmark of ALS. In other words, this may be the true driver of disease.
In stem cell and mouse models, next-generation ASOs aimed at this antisense RNA have shown:
- Major reductions in toxic RNA foci in human motor neurons in a dish
- Restoration of normal gene activity tied to TDP-43
- Decreased levels of toxic dipeptide repeat proteins (DPRs), especially in key brain regions like the cortex and hippocampus in the mouse
- No major side effects, even with brain-wide delivery in the mouse
In postmortem human tissue, from 12 patients who died but had received treatment with BIIB078, found that the dose of BIIB078 given was effective at reducing sense foci, as anticipated. There was no inadvertent effect on the AS foci. Importantly, compared to the level of sense RNAs, the presence of AS RNAs was much more abundant and significantly correlated with motor neurons exhibiting pathological TDP43 accumulation.
With these strong pieces of clinical and preclinical evidence to support therapeutic targeting of the AS strand , the Target ALS grant continues to support advancement of lead therapeutic candidates. The team is now narrowing down on their lead therapeutic candidates, developing key assays needed to better detect the harmful AS-related proteins in preclinical models and in patient samples, and identify best dosing regimens using preclinical species.
💡 Key Insight: While early trials fell short, they laid the groundwork for smarter, more precise approaches. Targeting antisense RNA may offer the key to slowing, or even halting, ALS in people with C9orf72 mutations.
Rewriting the DNA Itself: Dr. Claire Clelland’s CRISPR Vision
Imagine not just blocking the harmful mutation, but removing it completely. That’s the bold vision of Dr. Claire Clelland at UCSF, who is engineering a precision CRISPR therapy for C9orf72-linked ALS.
Her lab has already shown that it’s possible to use custom tools to snip out the toxic repeat expansion in DNA from patient-derived neurons; proof that gene correction at the source is achievable.
Now, in collaboration with Denali Therapeutics, Dr. Clelland is working on a breakthrough delivery system: a non-viral, protein-based platform that uses the transferrin receptor (TfR) to shuttle CRISPR-based therapeutics into the brain safely via IV infusion. This could be the first time such gene-editing tech is delivered at scale in humans.
Her lab also developed a Precision Genome Therapy Toolkit to tailor CRISPR treatments to the subtle genetic differences found in C9 carriers, taking personalized medicine from theory to practice.
“Every day I think about the patients who are waiting on us. There’s not a second to waste.”
—Dr. Claire Clelland
💡 Key Insight: This project is blazing a trail toward personalized gene therapy for ALS, guided by deep genetic knowledge, smart design, and Target ALS’s foundational support. You can read more about it here.
Zooming Out: What the Immune System Can Tell Us
While much of ALS research has focused on neurons, Dr. Pegah Masrori is turning attention to a different player: the immune cells of the brain, known as microglia.
Her team, supported by the Target ALS research ecosystem, is using single-cell RNA sequencing to explore how microglia behave differently in C9-linked ALS compared to sporadic ALS.
Under normal conditions, the C9orf72 gene is highly expressed in myeloid cells, including microglia, and has been shown to play an important role in the brain’s innate immune system. Interestingly, Masrori finds that microglia from the spinal cord of patients carrying the C9 hexanucleotide repeat expansion mutation appear to show blunted changes in the gene expression of immune factors compared to the strong elevation in expression of immune factors seen in sporadic cases. This muted response may stem from lower expression of the C9orf72 gene in microglia, which seems to prevent them from activating fully in response to disease.
This suggests that some C9-linked patients may have an immune system that’s unable to mount a proper defense, potentially influencing how and when symptoms appear.
💡 Key Insight: ALS isn’t just a neuronal disease; it’s an immune and cellular ecosystem disorder. Understanding the impact of C9orf72 loss of function and gain of function in different cell types is critical to designing targeted, effective treatments.
Where We Go From Here
C9orf72 continues to be one of the most complex and urgent challenges in ALS research. But today, thanks to relentless collaboration across industry and academia, and strategic funding from Target ALS, researchers are:
- Rethinking RNA-targeted therapies
- Engineering DNA-level cures
- Mapping immune responses cell by cell
- And building tools that bring precision therapies within reach
Through thoughtful iteration and bold experimentation, researchers are beginning to chart a more defined course toward meaningful treatments.
