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Lo RS, Cromie GA, Tang M, Teng K, Owens K, Sirr A, Kutz JN, Morizono H, Caldovic L, Ah Mew N, Gropman A, Dudley AM. The functional impact of 1,570 individual amino acid substitutions in human OTC. Am J Hum Genet 2023; 110:863-879. [PMID: 37146589 PMCID: PMC10183466 DOI: 10.1016/j.ajhg.2023.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/30/2023] [Indexed: 05/07/2023] Open
Abstract
Deleterious mutations in the X-linked gene encoding ornithine transcarbamylase (OTC) cause the most common urea cycle disorder, OTC deficiency. This rare but highly actionable disease can present with severe neonatal onset in males or with later onset in either sex. Individuals with neonatal onset appear normal at birth but rapidly develop hyperammonemia, which can progress to cerebral edema, coma, and death, outcomes ameliorated by rapid diagnosis and treatment. Here, we develop a high-throughput functional assay for human OTC and individually measure the impact of 1,570 variants, 84% of all SNV-accessible missense mutations. Comparison to existing clinical significance calls, demonstrated that our assay distinguishes known benign from pathogenic variants and variants with neonatal onset from late-onset disease presentation. This functional stratification allowed us to identify score ranges corresponding to clinically relevant levels of impairment of OTC activity. Examining the results of our assay in the context of protein structure further allowed us to identify a 13 amino acid domain, the SMG loop, whose function appears to be required in human cells but not in yeast. Finally, inclusion of our data as PS3 evidence under the current ACMG guidelines, in a pilot reclassification of 34 variants with complete loss of activity, would change the classification of 22 from variants of unknown significance to clinically actionable likely pathogenic variants. These results illustrate how large-scale functional assays are especially powerful when applied to rare genetic diseases.
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Affiliation(s)
- Russell S Lo
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Michelle Tang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Kevin Teng
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Katherine Owens
- Pacific Northwest Research Institute, Seattle, WA, USA; Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Amy Sirr
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - J Nathan Kutz
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | - Hiroki Morizono
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Nicholas Ah Mew
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Andrea Gropman
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA; Department of Neurology, Division of Neurogenetics and Neurodevelopmental Disabilities, Children's National Hospital, Washington, DC, USA; Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
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Serrano C, Lopes-Marques M, Amorim A, João Prata M, Azevedo L. A partial duplication of an X-linked gene exclusive of a primate lineage (Macaca). Gene 2023; 851:146997. [DOI: 10.1016/j.gene.2022.146997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022]
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Baker J, Hitchins L, Vucko E, Havens K, Becker K, Arduini K. Variable disease manifestations and metabolic management within a single family affected by ornithine transcarbamylase deficiency. Mol Genet Metab Rep 2022; 33:100906. [PMID: 36620388 PMCID: PMC9817479 DOI: 10.1016/j.ymgmr.2022.100906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 01/11/2023] Open
Abstract
We report on a family with ornithine transcarbamylase (OTC) deficiency, an X-linked urea cycle disorder, with variable disease severity and tailored management strategies based on each family member's biochemical profile and clinical presentation. Our primary patient is a female monozygotic twin who presented to medical care at 10 months of age with acute liver failure, gastrointestinal symptoms, altered mental status, hypoglycemia, and hyperammonemia. The patient's older brother, known to have hemizygous OTC deficiency, died at 8 months of age from cardiac arrest after complications secondary to his diagnosis. Despite her family history, manifestation of symptoms of heterozygous (partial) OTC deficiency went unrecognized by multiple providers based on misconceptions regarding a female's risk for X-linked disease. Despite barriers related to the family's low socioeconomic status, follow-up care by a multidisciplinary metabolic care team, including moderate protein restriction and nitrogen scavenger therapy, led to positive outcomes for the patient. Her twin sister and mother are also heterozygous for variants in OTC and remain controlled on moderate protein restriction. This case illustrates the importance of genotyping all individuals with genetic risk factors for OTC deficiency and the variability in disease manifestation that necessitates tailored treatment approaches for individuals with partial OTC deficiency.
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Key Words
- ALT, alanine aminotransferase
- AST, aspartate transaminase
- CVS, chorionic villus sampling
- DOL, day of life
- EAA, essential amino acid
- GPB, glycerol phenylbutyrate
- HC, head circumference
- IV, intravenous
- Late onset
- Manifesting heterozygote
- NBS, newborn screen
- NORD, National Organization for Rare Disorders
- NaPB, sodium phenylbutyrate
- OTC, ornithine transcarbamylase
- Ornithine transcarbamylase deficiency
- PO, per os, by mouth
- Partial ornithine transcarbamylase deficiency
- UCD, urea cycle disorder
- Urea cycle disorder
- X-linked
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Affiliation(s)
- Joshua Baker
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Ave, Chicago, IL 60611, USA
- Department of Pediatrics (Genetics, Birth Defects, and Metabolism), Northwestern University Feinberg School of Medicine, 420 E Superior St, Chicago, IL 60611, USA
- Corresponding author at: 225 E Chicago Ave, Chicago, IL 60611, USA.
| | - Lauren Hitchins
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Ave, Chicago, IL 60611, USA
| | - Erika Vucko
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Ave, Chicago, IL 60611, USA
| | - Kirsten Havens
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Ave, Chicago, IL 60611, USA
| | - Karen Becker
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Ave, Chicago, IL 60611, USA
| | - Katherine Arduini
- Division of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E Chicago Ave, Chicago, IL 60611, USA
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Lopes‐Marques M, Pacheco AR, Peixoto MJ, Cardoso AR, Serrano C, Amorim A, Prata MJ, Cooper DN, Azevedo L. Common polymorphic OTC variants can act as genetic modifiers of enzymatic activity. Hum Mutat 2021; 42:978-989. [PMID: 34015158 PMCID: PMC8362079 DOI: 10.1002/humu.24221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022]
Abstract
Understanding the role of common polymorphisms in modulating the clinical phenotype when they co‐occur with a disease‐causing lesion is of critical importance in medical genetics. We explored the impact of apparently neutral common polymorphisms, using the gene encoding the urea cycle enzyme, ornithine transcarbamylase (OTC), as a model system. Distinct combinations of genetic backgrounds embracing two missense polymorphisms were created in cis with the pathogenic p.Arg40His replacement. In vitro enzymatic assays revealed that the polymorphic variants were able to modulate OTC activity both in the presence or absence of the pathogenic lesion. First, we found that the combination of the minor alleles of polymorphisms p.Lys46Arg and p.Gln270Arg significantly enhanced enzymatic activity in the wild‐type protein. Second, enzymatic assays revealed that the minor allele of the p.Gln270Arg polymorphism was capable of ameliorating OTC activity when combined in cis with the pathogenic p.Arg40His replacement. Structural analysis predicted that the minor allele of the p.Gln270Arg polymorphism would serve to stabilize the OTC wild‐type protein, thereby corroborating the results of the experimental assays. Our findings demonstrate the potential importance of cis‐interactions between common polymorphic variants and pathogenic missense mutations and illustrate how standing genetic variation can modulate protein function.
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Affiliation(s)
- Mónica Lopes‐Marques
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Ana Rita Pacheco
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
| | - Maria João Peixoto
- ICVS‐ Life and Health Sciences Research Institute, School of MedicineUniversity of MinhoBragaPortugal
- ICVS/3B's‐PT Government Associate LaboratoryBragaGuimarãesPortugal
| | - Ana Rita Cardoso
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Catarina Serrano
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - António Amorim
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Maria João Prata
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - David N. Cooper
- Institute of Medical Genetics; School of MedicineCardiff UniversityCardiffUK
| | - Luísa Azevedo
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
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A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice. Nat Biotechnol 2016; 34:334-8. [PMID: 26829317 PMCID: PMC4786489 DOI: 10.1038/nbt.3469] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/30/2015] [Indexed: 02/05/2023]
Abstract
Many genetic liver diseases present in newborns with repeated, often lethal, metabolic crises. Gene therapy using non-integrating viruses such as AAV is not optimal in this setting because the non-integrating genome is lost as developing hepatocytes proliferate1,2. We reasoned that newborn liver may be an ideal setting for AAV-mediated gene correction using CRISPR/Cas9. Here we intravenously infuse two AAVs, one expressing Cas9 and the other expressing a guide RNA and the donor DNA, into newborn mice with a partial deficiency in the urea cycle disorder enzyme, ornithine transcarbamylase (OTC). This resulted in reversion of the mutation in 10% (6.7% – 20.1%) of hepatocytes and increased survival in mice challenged with a high-protein diet, which exacerbates disease. Gene correction in adult OTC-deficient mice was lower and accompanied by larger deletions that ablated residual expression from the endogenous OTC gene, leading to diminished protein tolerance and lethal hyperammonemia on a chow diet.
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Genotype-Phenotype Correlations in Ornithine Transcarbamylase Deficiency: A Mutation Update. J Genet Genomics 2015; 42:181-94. [PMID: 26059767 DOI: 10.1016/j.jgg.2015.04.003] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 12/31/2022]
Abstract
Ornithine transcarbamylase (OTC) deficiency is an X-linked trait that accounts for nearly half of all inherited disorders of the urea cycle. OTC is one of the enzymes common to both the urea cycle and the bacterial arginine biosynthesis pathway; however, the role of OTC has changed over evolution. For animals with a urea cycle, defects in OTC can trigger hyperammonemic episodes that can lead to brain damage and death. This is the fifth mutation update for human OTC with previous updates reported in 1993, 1995, 2002, and 2006. In the 2006 update, 341 mutations were reported. This current update contains 417 disease-causing mutations, and also is the first report of this series to incorporate information about natural variation of the OTC gene in the general population through examination of publicly available genomic data and examination of phenotype/genotype correlations from patients participating in the Urea Cycle Disorders Consortium Longitudinal Study and the first to evaluate the suitability of systematic computational approaches to predict severity of disease associated with different types of OTC mutations.
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Harada E, Nishiyori A, Tokunaga Y, Watanabe Y, Kuriya N, Kumashiro R, Kuno T, Kuromaru R, Hirose S, Ichikawa K, Yoshino M. Late-onset ornithine transcarbamylase deficiency in male patients: prognostic factors and characteristics of plasma amino acid profile. Pediatr Int 2006; 48:105-11. [PMID: 16635166 DOI: 10.1111/j.1442-200x.2006.02181.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The occurrence of male patients with ornithine transcarbamylase (OTC) deficiency during adolescence or in adulthood has now been recognized. The aim of this study was to determine the prognostic factors that affect the prognosis of life, to explore a basis for therapeutic strategy. METHODS In 10 patients, nine of whom carried the R40H mutation and the other one carrying the Y55D mutation in the OTC gene, 32 demographic and laboratory data were first compared between survivors and non-survivors, using the unpaired t-test. The factors with significant difference were then subjected to multiple regression analysis. RESULTS The factors that exhibited significant difference were: age at onset, concentration of plasma ammonium, blood pH, and concentrations of six amino acids in plasma. The multiple regression analysis then revealed concentrations of ammonium, leucine, lysine, isoleucine, phenylalanine, glutamine and proline to be significant prognostic factors. The amino acid profile in the 10 patients showed increases in glutamine, proline, lysine, valine and methionine, and decreases in serine, ornithine and arginine. There was an inverse correlation between the age at onset and the level of the residual hepatic OTC activity. CONCLUSION The results implied that: (i) the plasma amino acid profile was unique, in comparison to other liver diseases; (ii) the plasma concentration of each of the (mentioned above) six amino acids was a significant predictor of prognosis; and (iii) suppression of protein catabolism, as suggested by the higher concentrations in isoleucine and leucine in the non-survivors, prevention of glutamine-induced brain edema, correction of alkalosis, and supplementation with ornithine or arginine may improve the prognosis of life.
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Affiliation(s)
- Eimei Harada
- Department of Pediatrics and Child Health, Kurume University School of Medicine, Asahi-machi, Kurume, Japan
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Mavinakere M, Morizono H, Shi D, Allewell NM, Tuchman M. The clinically variable R40H mutant ornithine carbamoyltransferase shows cytosolic degradation of the precursor protein in CHO cells. J Inherit Metab Dis 2001; 24:614-22. [PMID: 11768581 DOI: 10.1023/a:1012726207870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Ornithine carbamoyltransferase (OCT) deficiency is now frequently found in adults with hyperammonaemia affected by mutations that cause partial deficiency of this urea cycle enzyme. One of these mutations (R40H) has occurred in several families and has been found also in asymptomatic relatives. To better understand the phenotypic heterogeneity of this recurrent mutation, we investigated the biological properties of the mutant protein. Using 35S labelling, the import and processing of the R40H mutant OCT protein was investigated in intact CHO cells and in isolated rat liver mitochondria and compared to the wild type and R141Q mutant that causes complete enzyme deficiency. The R40H OCT protein seems to be imported and processed by the mitochondria in a manner similar to that of wild type. However, it is consistently degraded to a smaller fragment in the intact cells, unlike the wild type and R141Q mutant. The mature form of the enzyme is not susceptible to degradation. These data, obtained in CHO cells, suggest that deficiency in OCT enzymatic function conferred by the R40H mutation is likely caused by enhanced degradation of the preprotein in the cytosol. We propose therefore that variation in the rate of OCT turnover is responsible for the heterogeneity of the clinical phenotype in these patients.
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Affiliation(s)
- M Mavinakere
- Children's Research Institute, Children's National Medical Center, The George Washington University, Washington DC 20010-2970, USA
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