Our Research

Genetic Variant Research

Our team has identified novel sequence variants in the regulatory regions of the N-acetylglutamate synthase (NAGS) and ornithine transcarbamylase (OTC) genes. Using comparative genomics and data mining, we discovered NAGS and OTC upstream regulatory elements and the transcription factors that bind them in the liver.

We analyzed and tested the functional impact of several non-coding, disease-causing variants found in patients with clinical and biochemical symptoms of NAGS or OTC deficiency—patients who had no pathogenic variants in coding regions or splice sites. This approach led to the discovery of two new NAGS regulatory elements: the -3 kb enhancer and an enhancer located in the first intron of the NAGS gene.

If you are a physician whose patient with a urea cycle disorder may have disease caused by non-coding sequence variants, please contact Ljubica Caldovic, PhD, or DNicholas AhMew, MD.

Expert Panel Membership

Members of the Caldovic Lab also serve on the Urea Cycle Disorders Variant Curation Expert Panel (UCD VCEP), which uses publicly available data to determine the clinical significance of sequence variants in urea cycle genes.

Further Reading

1. Predicting epistasis across proteins by structural logic
2. The functional impact of 1,570 individual amino acid substitutions in human OTC
3. Noncoding sequence variants define a novel regulatory element in the first intron of the N-acetylglutamate synthase gene
4. N-acetylglutamate synthase deficiency due to a recurrent sequence variant in the N-acetylglutamate synthase enhancer region
5. Disease-causing mutations in the promoter and enhancer of the ornithine transcarbamylase gene
6. Transcriptional regulation of N-acetylglutamate synthase
7. N-carbamylglutamate enhancement of ureagenesis leads to discovery of a novel deleterious mutation in a newly defined enhancer of the NAGS gene and to effective therapy

Regulation of Urea Cycle Gene Expression and Dietary Protein Intake

Genetic defects in urea cycle enzymes and transporters reduce the body’s ability to safely metabolize protein, leading to hyperammonemia, a dangerous buildup of ammonia in the blood. For more than four decades, the standard treatment for urea cycle disorders (UCDs) has relied on dietary protein restriction and acylating agents that remove ammonia through alternative disposal pathways. Unfortunately, these approaches often fail to prevent acute or chronic hyperammonemia, which can cause severe cognitive impairment or even death.

A promising solution is a therapy that enhances ureagenesis by increasing the abundance of partially active urea cycle enzymes. Such a drug would offer two major advantages. It works through the body’s natural catalytic pathway, rather than a stoichiometric process and it complements existing treatments without replacing them.

We discovered that AMP-dependent protein kinase (AMPK) regulates the expression of urea cycle enzymes. This finding makes the AMPK signaling pathway an attractive target for developing amplification therapies that boost enzyme levels and improve the body’s ability to convert ammonia into urea in patients with partial UCDs.

Further Reading

1. AMP-activated protein kinase signaling regulated expression of urea cycle enzymes in response to changes in dietary protein intake
2. Datamining approaches for examining the low prevalence of N-acetylglutamate synthase deficiency and understanding transcriptional regulation of urea cycle genes

Ammonia Toxicity to the Brain

Our lab is developing innovative treatments for hyperammonemia that aim to prevent irreversible brain injury caused by high ammonia levels. To identify and advance these therapies, we are screening chemicals and FDA-approved drugs for their ability to protect zebrafish from ammonia toxicity.

Evaluating these candidate drugs, and other treatments for urea cycle disorders (UCDs) requires reliable biomarkers to monitor brain injury caused by hyperammonemia. Currently, we are assessing the use of S100B, neuron-specific enolase (NSE), brain-derived neurotrophic factor (BDNF) and Tau as systemic biomarkers of ammonia-induced brain damage.

For the complete list of publication visit Dr. Caldovic's bibliography.

Visit bibliography