Investigators Profile FDA Drugs for Modulators of Nonsense-Mediated mRNA Decay

Sika Zheng

A team of investigators led by Sika Zheng, Division of Biomedical Sciences, School of Medicine, University of California, profiled drugs approved by the US Food and Drug Administration (FDA) to identify nonsense-mediated RNA decay (NMD) modulators. Hundreds of disorders are associated with NMD, and in the US, approximately 3 million individuals live with a genetic disease caused by nonsense mutations.

Nonsense-mediated RNA decay affects potentially defective messenger RNAs (mRNA). Investigators wrote that NMD selectively degrades mutant transcripts with a premature termination codon (PTC) to prevent translation of C-terminal, truncated proteins.

Subsequently, nonsense mutations can lead to neurological disease, immune diseases, cancers, and additional rare diseases, because the molecular disruption often causes a loss of functional proteins.

“For example, nonsense mutation is the leading cause of cystic fibrosis (CF) and Duchenne muscular dystrophy (DMD),” investigators wrote. “Since most nonsense mutation-associated disorders are rare diseases, therapeutic development is strategized toward targeting their commonalities (e.g., the underlying nonsense mutations and associated pathways) rather than individual symptoms.”

Implementing Advanced Methods

"We wanted to know whether the FDA-approved drugs can be repurposed to modulate NMD. So, we treated cells with each FDA-approved drug and tested whether cellular NMD activity was affected,” Zheng said in a statement.

A total of 704 FDA-approved drugs were profiled. The results showed 1 drug had a strong effect on NMD and 4 drugs had mild effects.

According to Zheng, without the method they designed to determine the effects each drug had on NMD, profiling 704 drugs to such a precision level would be unthinkable. Old methods are either too tedious or not precise enough.

The workflow of profiling each drug effect on NMD is detailed in the Results section of the study–drugs were divided into many treatment group batches.

Each batch included a negative control DMSO treatment and a positive control 0.2 μM thapsigargin (TG) treatment, which served as a benchmark as well as a quality control, investigators stated.

In order to increase the robustness of determining NMD-modulatory drugs, the analysis was assayed into three different endogenous NMD targets, Ptbp2, Hnrnpl, and Tra2b. Because of this, investigators expected a low false-positive rate.

Deciphering the Data

Investigators emphasized that the influence FDA-approved drugs have on nonsense-mediated RNA decay has not been closely analyzed in previous literature. Not only are disease causing mutations associated with NMD, but so are an increasing number of illnesses.

“For example, mutations in RNA splicing factors leading to the appearance of PTC-containing transcripts have been shown as the most common mechanism in myelodysplastic syndromes, investigators wrote. “In other cases, NMD activity eliminates potentially functional products and leads to a more severe phenotype.”

Through this study, it was discovered that most FDA drugs act minimally on NMD, which is valuable information for multiple reasons. The most concerning is that patients who have underlying nonsense mutations may be affected by approved drugs unknowingly. As a result, investigators issued an urgent recommendation to further examine the relationship between FDA-approved drugs and cellular NMD activity.

“Therefore," investigators wrote, “systematic profiling for chemical modulators among existing drugs is an immediate path to identify and distinguish drugs that can ameliorate versus worsen NMD-associated diseases."

The study, "Molecular profiling of individual FDA-approved clinical drugs indentifies modulators of nonsense-mediated mRNA decay", was published in Molecular Therapy Nucleic Acids.