Allele-agnostic approaches for the treatment of ataxia-telangiectasia

The National Institute of Neurological Disorders and Stroke, part of the Department of Health and Human Services National Institutes of Health, awarded The Broad Institute, Inc. $123,890 on August 6, 2026, under the Extramural Research Programs in the Neurosciences and Neurological Disorders program (CFDA 93.853).

The award funds research into allele-agnostic approaches for treating ataxia-telangiectasia, a childhood-onset neurodegenerative disorder caused by loss-of-function mutations in the ATM gene. The research will develop prime editing-mediated readthrough of premature termination codons (PERT), a genome editing strategy that installs optimized suppressor transfer RNAs directly into the genome to restore translation across multiple nonsense alleles simultaneously. During the K99 phase, the investigator will use directed evolution to identify synergistic combinations of mutations that maximize engineered suppressor transfer RNA efficiency and stability, then validate their ability to restore ATM expression and DNA damage response in patient-derived ataxia-telangiectasia cell lines. Twin prime editing will be used to install full-length engineered suppressor transfer RNAs at safe harbor loci for stable expression. The R00 phase will reprogram transfer RNA introns into circularized small RNAs, including splice-skipping antisense oligonucleotides, to enable permanent correction of ATM splice-site mutations.

The period of performance extends through July 31, 2028. Work is performed in Cambridge, Massachusetts.

Abstract

Ataxia-telangiectasia (a-T) is a devastating childhood-onset neurodegenerative disorder caused by loss-of-function mutations in the ATM gene, leading to progressive ataxia, immunodeficiency, and cancer predisposition. Approximately 40% of a-T patients harbor nonsense or splice-site mutations that eliminate ATM expression, yet no therapies restore protein function. Current interventions remain purely supportive, and the size of ATM (~13 KB) precludes conventional gene replacement. To overcome these barriers, I have developed prime editing-mediated readthrough of premature termination codons (PERT), a genome editing strategy that installs optimized suppressor TRNAS (SUP-TRNAS) directly into the genome. SUP-TRNAS restore translation across multiple nonsense alleles simultaneously, providing a durable, allele- agnostic therapy that circumvents the need for repeated dosing. Unlike viral or RNA delivery, PERT leverages endogenous trna loci to achieve lifelong expression while maintaining normal stop codon fidelity. In the K99 phase, I will use directed evolution to identify synergistic combinations of mutations that maximize the efficiency and stability of engineered SUP-TRNAS and validate their ability to restore ATM expression and DNA damage response in patient-derived a-T cell lines. I will then use twin prime editing (TWINPE), an advanced editing platform capable of seamless, large-fragment integration, to install full- length engineered SUP-TRNAS at safe harbor loci for stable expression. These studies will establish a durable framework for treating nonsense mutations in ATM and related genes. In the R00 phase, I will expand this platform to reprogram trna introns into circularized small rnas, such as splice-skipping antisense oligonucleotides (ASOS), enabling permanent correction of ATM splice-site mutations. This strategy exploits the natural processing and stability of trna introns to produce genome-encoded small RNA therapeutics. Together, these approaches create a unified and scalable RNA therapeutic platform that addresses two major classes of pathogenic variants (nonsense and splicing mutations) through stable, genome- encoded solutions. This work will (1) establish the first durable, allele-agnostic therapy for a-T, (2) demonstrate prime editing-installed SUP-trna rescue of ATM function in patient cells and mouse models, and (3) define a new paradigm for engineering trna-based therapeutics to treat a broad spectrum of genetic diseases.