A therapy candidate for fatal prion diseases turns off disease-causing gene

Good news!

"... a set of molecular tools that are delivered to the brain and adds a chemical tag to the gene for the prion protein to prevent the protein from being produced by cells. Unlike gene editing, this “epigenetic” editing does not modify the underlying DNA sequence, but it should switch the gene off permanently, which means that this could be a one-time treatment. ..."

From the editor's summary and abstract:

"Editor’s summary

Prion diseases are devastating neurodegenerative disorders that are invariably fatal, but removal of the prion protein from neurons can protect against disease progression. Neumann et al. developed a compact epigenetic silencer called CHARM that could efficiently shut off the prion gene throughout the mouse brain when delivered systemically by a viral vector without changing the underlying DNA sequence ... The epigenetic editor can also be programmed to turn itself off after silencing its target, thus limiting potential adverse effects from long-term expression. CHARM represents a therapeutic modality that could be applied to a range of other diseases caused by the toxic buildup of unwanted proteins. ...

Structured Abstract

INTRODUCTION

Prion diseases are fatal neurodegenerative disorders caused by misfolding of the prion protein in the brain. Cases can manifest spontaneously, be inherited genetically, or be acquired through transmission (e.g., mad cow disease). Although there are currently no effective treatments, reducing prion protein levels in the brain has been shown to halt disease progression in animal models with minimal adverse effects.  ...

RATIONALE

Genetic medicines hold great promise but are often difficult to translate to the clinic. Current CRISPR-based DNA-editing technologies are complex large molecules that are challenging to deliver and have been associated with unintended editing outcomes. We therefore favored an epigenetic editing approach to permanently turn off prion protein expression in the brain without altering the underlying DNA sequence or leading to continued expression of an altered mRNA and protein. This strategy uses DNA methylation to achieve long-term transcriptional silencing. However, current epigenetic editors are cytotoxic in some circumstances and are too large to fit in an adeno-associated virus (AAV) vector, the preferred delivery vehicle to the central nervous system.

RESULTS

To address these challenges, we engineered a compact, enzyme-free epigenetic editor termed CHARM (Coupled Histone tail for Autoinhibition Release of Methyltransferase). Through a direct fusion with the histone H3 tail and a noncatalytic Dnmt3l domain, CHARM is able to recruit and activate DNA methyltransferases endogenously expressed in the cell to methylate the target gene. CHARM can act independently of KRAB transcriptional repression domains and is compatible with multiple DNA-binding modalities, including CRISPR-Cas, transcription activator–like effectors, and zinc finger proteins. The small size of zinc finger proteins enables up to three DNA targeting elements to be accommodated in a single AAV with additional room for regulatory elements to confer cell-type specificity. When coupled to a prion protein–targeting zinc finger domain and delivered to the mouse brain through AAV, CHARM methylates the prion gene promoter and achieves up to 80% brainwide reduction in neuronal prion protein, far exceeding the minimal reduction required for therapeutic benefit. Furthermore, we developed self-silencing CHARMs that autonomously deactivate themselves after silencing their target. This approach temporally limits CHARM expression to circumvent potential antigenicity and off-target activity resulting from chronic expression in nondividing neurons.

CONCLUSION

This study represents the first demonstration of AAV-mediated delivery of an epigenetic editor that can programmably methylate DNA in the brain for durable, potent silencing of a target gene. CHARM avoids overexpression of potentially cytotoxic catalytic domains by harnessing the endogenous DNA methylation machinery. Its compact size enables modular self-silencing strategies, facilitates multiplexed targeting, and enhances compatibility with other delivery modalities, such as lipid nanoparticles. This work could enable an effective treatment for patients with prion disease as well as other neurodegenerative diseases involving the accumulation of toxic protein aggregates. More generally, CHARM represents the next generation of safe and easily deliverable epigenetic editors for therapeutic intervention and biological discovery."

A therapy candidate for fatal prion diseases turns off disease-causing gene | Broad Institute Whitehead and Broad scientists have developed a gene-silencing tool that could pave the way for a new class of genetic approaches to treat certain diseases.

Brainwide silencing of prion protein by AAV-mediated delivery of an engineered compact epigenetic editor (no public access)

Images of a mouse brain show the effect of a technology called CHARM in turning off the expression of a gene in the brain. Neurons were classified by software as either positive for prion protein expression (yellow) before treatment with CHARM (left panel), or negative (purple) after treatment (right panel).