Researchers Uncover Genetic Mechanisms Behind OTC Deficiency

A team of researchers at Northeastern University has made significant strides in understanding the biochemical mechanisms behind a rare genetic disorder known as ornithine transcarbamylase (OTC) deficiency. Using a novel machine learning tool, the researchers have identified how specific genetic mutations disrupt the function of the OTC enzyme, which is critical for the safe elimination of ammonia from the body. This discovery is a vital step towards developing more effective treatments for those affected by this potentially life-threatening condition.

OTC deficiency impairs the body’s ability to process ammonia, a byproduct of protein metabolism. When ammonia builds up, it can lead to serious health issues, including brain and liver damage, potentially resulting in death. The research team, led by professors of chemistry and chemical biology, Mary Jo Ondrechen and Penny Beuning, utilized their machine learning tool, named Partial Order Optimum Likelihood (POOL), in conjunction with biochemical laboratory experiments to analyze numerous mutations within the OTC gene.

The OTC gene encodes the OTC enzyme, which facilitates the conversion of nitrogen into urea, allowing the body to excrete it through urine. In their study, published in ACS Chemical Biology, the researchers demonstrated how certain mutations hinder the enzyme’s normal activity, contributing to the disorder.

“Professor Ondrechen’s machine learning method is extremely good at predicting the effects of mutations on the function of a protein,” Beuning stated. “This is the second time we have used this method to analyze hundreds of mutations in an enzyme associated with a disease, and the experimental analysis in both cases showed that the predictions were accurate.”

Every year, between 14,000 to 77,000 individuals are diagnosed with OTC deficiency. A severe form of the disorder typically affects newborns, particularly boys, shortly after birth. In contrast, a milder form may manifest later in childhood or adulthood, with symptoms that can include vomiting, fatigue, seizures, developmental delays, and psychiatric issues. In Massachusetts, newborns are routinely tested for inherited mutations, including OTC deficiency.

Current management strategies focus on controlling ammonia levels through dietary restrictions, medications that reduce nitrogen levels, and, in severe cases, liver transplants.

Insights into Genetic Mutations

According to the Human Gene Mutation Database, there are 486 known mutations in the OTC gene. Of these, 332 involve alterations in a single DNA building block, which can weaken or entirely disable the enzyme. Beuning noted that while some mutations are indeed harmful, others might appear in a person’s cells without leading to disease.

The research team’s experiments revealed that some mutations associated with the disorder performed normally in vitro but resulted in impaired enzyme function in living cells. By examining specific amino acids that can switch from positive to negative electrical charges, they assessed how these changes affect the enzyme’s ability to catalyze reactions. They calculated a measure known as μ4, which predicts the interactions of charged amino acids and their influence on the enzyme’s function.

“One of the benefits of the machine learning method is to narrow down the set of mutations to identify those most likely to change the activity of OTC,” Beuning explained.

POOL not only identifies damaging mutations but also accommodates instances where complete information is unavailable, predicting the potential impacts based on existing data.

Future Directions and Ongoing Research

The team focused on 17 mutations linked to disease and successfully predicted the effects of 18 mutations, with a high degree of accuracy. Notably, most mutations that did not impair the enzyme’s function in laboratory conditions did lead to dysfunction in cells. This finding suggests that the context of the cellular environment plays a crucial role in how mutations manifest.

“Understanding why certain mutations directly impair enzyme activity is only part of the challenge,” Ondrechen remarked. “We are also investigating why other mutations, which do not directly affect catalysis, result in disease.”

Beuning added that factors such as the amount of protein produced by the cell and its interactions with other proteins could contribute to the variability in enzyme activity. The research team is now focused on these additional elements to gain a comprehensive understanding of how different mutations impact enzyme function.

The insights gained from this study not only enhance the understanding of OTC deficiency but also pave the way for personalized treatment approaches in the future. As the research continues, the collaboration between computational methods and laboratory experimentation will remain central to advancing knowledge in the field of genetic disorders.

More information on this study can be found in the article by Emily Micheloni et al, titled “Biochemical Characterization of Disease-Associated Variants of Human Ornithine Transcarbamylase” in ACS Chemical Biology (2025).