Timely intervention in HMG-CoA Lyase deficiency: The role of newborn screening, metabolic management, and genomic sequencing
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2025-12-01
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Abstract
3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase deficiency is a rare autosomal recessive metabolic disease caused by variants in the HMGCL gene leading to an impairment in leucine catabolism and ketone synthesis. In the United States, HMG-CoA lyase deficiency is listed on the recommended uniform screening panel as a core condition for newborn screening. A positive newborn screen will typically show an elevation of C5-hydroxylated species on the acylcarnitine profile using a dried-blood spot collected between 24 and 48 h of life. Initial follow-up testing generally includes a plasma acylcarnitine profile and a urine organic acid profile. Clinically, this metabolic alteration can lead to severe metabolic decompensation, presenting as hypoketotic hypoglycemia and, when left untreated, potential long-term neurological impairments. This report highlights the case of a 38-day-old male with an initial abnormal newborn screen. Follow-up testing showed moderate elevations of C5-hydroxylated and C6-dicarboxylated species on the plasma acylcarnitine profile and marked elevations of 3-hydroxy-3-methylglutaric acid, 3-methylglutaconic acid, 3-methylglutaric and 3-hydroxyisovaleric acid detected by urine organic acid analysis. These findings were consistent with a biochemical diagnosis of HMG-CoA lyase deficiency. Confirmatory molecular testing included targeted HMGCL sequencing including deletion/duplication analysis; the results of which were negative. Genome sequencing was then requested which identified a deep intronic complex variant of unknown significance within intron 1 of HGMCL. RNA sequencing studies were sent as follow-up which revealed that the level of expression of the HMGCL gene was negligible in comparison with tissue-matched controls, thus confirming the biochemical diagnosis of HMG-CoA lyase deficiency.
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Menkovic, I, N Makhijani, L Francescatto, S Pendyal, C Stanley, SP Young, DD Koeberl, D Niyazov, et al. (2025). Timely intervention in HMG-CoA Lyase deficiency: The role of newborn screening, metabolic management, and genomic sequencing. Molecular Genetics and Metabolism Reports, 45. pp. 101278–101278. 10.1016/j.ymgmr.2025.101278 Retrieved from https://hdl.handle.net/10161/33753.
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Scholars@Duke
Sarah Phyllis Young
As a clinical biochemical geneticist and a director of the Duke Biochemical Genetics laboratory, my research interests are focused on improving laboratory diagnostics for rare inherited disorders of metabolism. I am actively involved in the development of assays using mass spectrometry and other analytical techniques. My current research on biomarkers for lysosomal storage disorders, such as Fabry and Pompe disease and the mucopolysaccharidoses includes monitoring the response to novel therapies in patients. I also have an interest in neurometabolic disorders such as the creatine deficiency syndromes and sulfite oxidase and molybdenum cofactors. These disorders can be diagnosed using liquid chromatography-tandem mass spectrometric assays that measure biomarkers in urine. Guanidinoacetate methyltransferase deficiency is a disorder that can be detected in the newborn period and is amenable to dietary therapy, and is thus a good candidate for newborn screening.
Dwight D. Koeberl
As a physician-scientist practicing clinical and biochemical genetics, I am highly motivated to seek improved therapy for my patients with inherited disorders of metabolism. The focus of our research has been the development of gene therapy with adeno-associated virus (AAV) vectors, most recently by genome editing with CRISPR/Cas9. We have developed gene therapy for inherited disorders of metabolism, especially glycogen storage disease (GSD) and phenylketonuria (PKU).
1) GSD Ia: Glucose-6-phosphatase (G6Pase) deficient animals provide models for developing new therapy for GSD Ia, although early mortality complicates research with both the murine and canine models of GSD Ia. We have prolonged the survival and reversed the biochemical abnormalities in G6Pase-knockout mice and dogs with GSD type Ia, following the administration of AAV8-pseudotyped AAV vectors encoding human G6Pase. More recently, we have performed genome editing to integrate a therapeutic transgene in a safe harbor locus for mice with GSD Ia, permanently correcting G6Pase deficiency in the GSD Ia liver. Finally, we have identified reduced autophagy as an underlying hepatocellular defect that might be treated with pro-autophagic drugs in GSD Ia.
2) GSD II/Pompe disease: Pompe disease is caused by the deficiency of acid-alpha-glucosidase (GAA) in muscle, resulting in the massive accumulation of lysosomal glycogen in striated muscle with accompanying weakness. While enzyme replacement has shown promise in infantile-onset Pompe disease patients, no curative therapy is available. We demonstrated that AAV vector-mediated gene therapy will likely overcome limitations of enzyme replacement therapy, including formation of anti-GAA antibodies and the need for frequent infusions. We demonstrated that liver-restricted expression with an AAV vector prevented antibody responses in GAA-knockout mice by inducing immune tolerance to human GAA. Antibody responses have complicated enzyme replacement therapy for Pompe disease and emphasized a potential advantage of gene therapy for this disorder. The strategy of administering low-dose gene therapy prior to initiation of enzyme replacement therapy, termed immunomodulatory gene therapy, prevented antibody formation and increased efficacy in Pompe disease mice. We are currently conducting a Phase I clinical trial of immunomodulatory gene therapy in adult patients with Pompe disease. Furthermore, we have developed drug therapy to increase the receptor-mediated uptake of GAA in muscle cells, which provides adjunctive therapy to more definitively treat Pompe disease.
3) PKU: In collaboration with researchers at OHSU, we performed an early gene therapy experiment that demonstrated long-term biochemical correction of PKU in mice with an AAV8 vector. PKU is a very significant disorder detected by newborn screening and currently inadequately treated by dietary therapy. Phenylalanine levels in mice were corrected in the blood, and elevated phenylalanine causes mental retardation and birth defects in children born to affected women, and gene therapy for PKU would address an unmet need for therapy in this disorder.
Currently we are developing methods for genome editing that will stably correct the enzyme deficiency in GSD Ia and in Pompe disease. Our long-term goal is to develop efficacious genome editing for glycogen storage diseases, which will allow us to treat these conditions early in life with long-term benefits.
Dmitriy Niyazov
I see patients with Mitochondrial and Lysosomal Storage diseases, Developmental delay, Intellectual Disability, Chromosomal disorders, Congenital defects, Short stature, Failure to thrive and Adult genetic disorders. I use telemedicine extensively and apply the rapidly growing genetic knowledge to treat patients with a variety of medical problems which involve complex interaction of genetic and environmental factors, particularly since the Human Genome Project. I am interested in using the massive power of sequencing technology and artificial intelligence/machine learning to predict phenotypes from genotypes with increasing clinical relevance to human health.
Ashlee R. Stiles
Dr. Stiles is a fellow of the American College of Medical Genetics and Genomics trained in clinical biochemical genetics and molecular genetics. She is co-director of the Duke University Health System Biochemical Genetics Laboratory and external Referral Laboratory. In her work with the Biochemical Genetics laboratory, her research interests focus on improving and developing laboratory diagnostics for rare inborn errors of metabolism. In her role as director of the Referral laboratory, she works closely with hospital leadership on utilization management of genetic send-out tests.
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