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Bonfim‐Freitas PE, Andrade RS, Ribeiro‐dos‐Santos ÂK, Silva LCS. Molecular characterization of phenylketonuria patients from the North Region of Brazil: State of Pará. Mol Genet Genomic Med 2023; 11:e2224. [PMID: 37421234 PMCID: PMC10568386 DOI: 10.1002/mgg3.2224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/23/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Phenylketonuria (PKU) is an autosomal recessive disease resulting from a deficiency of the enzyme phenylalanine hydroxylase (PAH). Hyperphenylalaninemias (HPA) due to PAH deficiency are accompanied by a wide variety of clinical, biochemical, and molecular features. To identify and characterize pathogenic variants in the PAH gene and establish a correlation between genotype and biochemical phenotype in patients with PKU from state of Pará in the North Region of Brazil. METHODS All 13 exons of the PAH gene from 32 patients (21 PKU and 11 non-PKU HPA) were amplified by PCR and submitted to DNA sequencing (Sanger). Biochemical data were obtained from the patients' medical records. RESULTS Molecular analysis identified 17 pathogenic variants and 3 nonpathogenic variants. The most frequent pathogenic variants were IVS10-11G>A (7.9%), p. Arg261Gln (7.9%), p. Val388Met (6.3%) and p. Ile65Thr (4.7%). Was observed correlations and inconsistencies between genotype and biochemical phenotype. CONCLUSION In PKU patients from state of Pará, North Region of Brazil, a heterogeneous mutation spectrum was revealed, in which the most frequent mutations are variants commonly observed in other Brazilian studies and in the region of the Iberian Peninsula.
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Affiliation(s)
- Pedro E. Bonfim‐Freitas
- Laboratory of Inborn Errors of MetabolismInstitute of Biological Sciences, Federal University of ParáBelémBrazil
- Present address:
Hepatology DepartmentEvandro Chagas InstituteBelémPABrazil
| | - Roseani S. Andrade
- Faculty of NutritionInstitute of Health Sciences, Federal University of ParáBelémBrazil
| | | | - Luiz C. Santana‐da Silva
- Laboratory of Inborn Errors of MetabolismInstitute of Biological Sciences, Federal University of ParáBelémBrazil
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2
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Paulson OB, Schousboe A, Hultborn H. The history of Danish neuroscience. Eur J Neurosci 2023; 58:2893-2960. [PMID: 37477973 DOI: 10.1111/ejn.16062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/04/2023] [Accepted: 05/29/2023] [Indexed: 07/22/2023]
Abstract
The history of Danish neuroscience starts with an account of impressive contributions made at the 17th century. Thomas Bartholin was the first Danish neuroscientist, and his disciple Nicolaus Steno became internationally one of the most prominent neuroscientists in this period. From the start, Danish neuroscience was linked to clinical disciplines. This continued in the 19th and first half of the 20th centuries with new initiatives linking basic neuroscience to clinical neurology and psychiatry in the same scientific environment. Subsequently, from the middle of the 20th century, basic neuroscience was developing rapidly within the preclinical university sector. Clinical neuroscience continued and was even reinforced during this period with important translational research and a close co-operation between basic and clinical neuroscience. To distinguish 'history' from 'present time' is not easy, as many historical events continue in present time. Therefore, we decided to consider 'History' as new major scientific developments in Denmark, which were launched before the end of the 20th century. With this aim, scientists mentioned will have been born, with a few exceptions, no later than the early 1960s. However, we often refer to more recent publications in documenting the developments of initiatives launched before the end of the last century. In addition, several scientists have moved to Denmark after the beginning of the present century, and they certainly are contributing to the present status of Danish neuroscience-but, again, this is not the History of Danish neuroscience.
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Affiliation(s)
- Olaf B Paulson
- Neurobiology Research Unit, Department of Neurology, Rigshospitalet, 9 Blegdamsvej, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Arne Schousboe
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans Hultborn
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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The pathogenicity classification of PAH gene variants in the Iranian population. Comput Biol Chem 2022; 98:107665. [PMID: 35339094 DOI: 10.1016/j.compbiolchem.2022.107665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 12/29/2022]
Abstract
Till now not many studies have been conducted to classify PAH gene variants according to American College of Medical Genetics and Genomics (ACMG-AMP) guidelines. The aim of this study was to collect all PAH gene variants reported among Iranian population and investigate their pathogenicity based on ACMG-AMP guidelines. Systematic collection of PAH gene variants, verification of variants, in silico analysis, and application of ACMG-AMP guidelines were the main steps in performing the present study. A total of 267 unique variants were identified; according to ACMG-AMP guidelines, 90, 40, 71, 14, and 52 variants were classified as pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), and benign (B), respectively. The need to pay more attention to synonymous and missense variants with low or no impact on protein function as well as intronic variants, whether they are deep or are close to intron/exon boundaries, was a highlight of this study. Due to the fact that few functional studies are performed on these variants, it is suggested that they be analyzed first using bioinformatics tools, and if positive results are obtained, then functional studies can be designed.
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4
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Makukh HV, Chorna LB, Tyrkus MY, Akopyan HR, Shuvarska VI, Malakhova AY, Poliakova YO. Analysis of the PAH Gene Mutations in the Ukrainian Population: A Report from the West Ukrainian Region. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721050066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Rothgangl T, Dennis MK, Lin PJC, Oka R, Witzigmann D, Villiger L, Qi W, Hruzova M, Kissling L, Lenggenhager D, Borrelli C, Egli S, Frey N, Bakker N, Walker JA, Kadina AP, Victorov DV, Pacesa M, Kreutzer S, Kontarakis Z, Moor A, Jinek M, Weissman D, Stoffel M, van Boxtel R, Holden K, Pardi N, Thöny B, Häberle J, Tam YK, Semple SC, Schwank G. In vivo adenine base editing of PCSK9 in macaques reduces LDL cholesterol levels. Nat Biotechnol 2021; 39:949-957. [PMID: 34012094 PMCID: PMC8352781 DOI: 10.1038/s41587-021-00933-4] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/23/2021] [Indexed: 02/02/2023]
Abstract
Most known pathogenic point mutations in humans are C•G to T•A substitutions, which can be directly repaired by adenine base editors (ABEs). In this study, we investigated the efficacy and safety of ABEs in the livers of mice and cynomolgus macaques for the reduction of blood low-density lipoprotein (LDL) levels. Lipid nanoparticle-based delivery of mRNA encoding an ABE and a single-guide RNA targeting PCSK9, a negative regulator of LDL, induced up to 67% editing (on average, 61%) in mice and up to 34% editing (on average, 26%) in macaques. Plasma PCSK9 and LDL levels were stably reduced by 95% and 58% in mice and by 32% and 14% in macaques, respectively. ABE mRNA was cleared rapidly, and no off-target mutations in genomic DNA were found. Re-dosing in macaques did not increase editing, possibly owing to the detected humoral immune response to ABE upon treatment. These findings support further investigation of ABEs to treat patients with monogenic liver diseases.
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Affiliation(s)
- Tanja Rothgangl
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Dominik Witzigmann
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Lukas Villiger
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Martina Hruzova
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Daniela Lenggenhager
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Sabina Egli
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | - Nina Frey
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Noëlle Bakker
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland
| | | | | | | | - Martin Pacesa
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Zacharias Kontarakis
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Laboratory, ETH Zurich, Zurich, Switzerland
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | | | - Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Beat Thöny
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ying K Tam
- Acuitas Therapeutics Inc., Vancouver, BC, Canada
| | | | - Gerald Schwank
- University of Zurich, Institute for Pharmacology and Toxicology, Zurich, Switzerland.
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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6
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Odagiri S, Kabata D, Tomita S, Kudo S, Sakaguchi T, Nakano N, Yamamoto K, Shintaku H, Hamazaki T. Clinical and Genetic Characteristics of Patients with Mild Hyperphenylalaninemia Identified by Newborn Screening Program in Japan. Int J Neonatal Screen 2021; 7:ijns7010017. [PMID: 33803550 PMCID: PMC8006226 DOI: 10.3390/ijns7010017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 11/22/2022] Open
Abstract
Phenylketonuria (PKU) and hyperphenylalaninemia (HPA), both identified in newborn screening, are attributable to variants in PAH. Reportedly, the p.R53H(c.158G>A) variant is common in patients with HPA in East Asia. Here, we aimed to define the association between p.R53H and HPA phenotype, and study the long-term outcome of patients with HPA carrying p.R53H. We retrospectively reviewed the genotype in 370 patients detected by newborn screening, and identified the phenotype in 280 (117, HPA; 163, PKU). p.R413P(c.1238G>C) was the most frequently found (n = 117, 31.6%) variant, followed by p.R53H (n = 89, 24.1%). The odds ratio for heterozygous p.R53H to cause HPA was 48.3 (95% CI 19.410-120.004). Furthermore, we assessed the non-linear association between the phenylalanine (Phe) value and elapsed time using the follow-up data of the blood Phe levels of 73 patients with HPA carrying p.R53H. The predicted levels peaked at 161.9 μmol (95% CI 152.088-172.343) at 50-60 months of age and did not exceed 360 μmol/L during the 210-month long observation period. The findings suggest that patients with HPA, carrying p.R53H, do not need frequent Phe monitoring as against those with PKU. Our study provides convincing evidence to determine clinical management of patients detected through newborn screening in Japan.
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Affiliation(s)
- Shino Odagiri
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (S.O.); (S.K.); (T.S.); (N.N.)
| | - Daijiro Kabata
- Department of Medical Statistics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (D.K.); (S.T.)
| | - Shogo Tomita
- Department of Medical Statistics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (D.K.); (S.T.)
| | - Satoshi Kudo
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (S.O.); (S.K.); (T.S.); (N.N.)
| | - Tomoko Sakaguchi
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (S.O.); (S.K.); (T.S.); (N.N.)
| | - Noriko Nakano
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (S.O.); (S.K.); (T.S.); (N.N.)
| | - Kouji Yamamoto
- Department of Biostatistics, Yokohama City University School of Medicine, Yokohama 236-0004, Japan;
| | - Haruo Shintaku
- Donated Course “Disability Medicine and Regenerative Medicine”, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan;
| | - Takashi Hamazaki
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; (S.O.); (S.K.); (T.S.); (N.N.)
- Correspondence: ; Tel.: +81-6-6645-3815
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7
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Villiger L, Rothgangl T, Witzigmann D, Oka R, Lin PJC, Qi W, Janjuha S, Berk C, Ringnalda F, Beattie MB, Stoffel M, Thöny B, Hall J, Rehrauer H, van Boxtel R, Tam YK, Schwank G. In vivo cytidine base editing of hepatocytes without detectable off-target mutations in RNA and DNA. Nat Biomed Eng 2021; 5:179-189. [PMID: 33495639 PMCID: PMC7610981 DOI: 10.1038/s41551-020-00671-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/02/2020] [Indexed: 12/26/2022]
Abstract
Base editors are RNA-programmable deaminases that enable precise single-base conversions in genomic DNA. However, off-target activity is a concern in the potential use of base editors to treat genetic diseases. Here, we report unbiased analyses of transcriptome-wide and genome-wide off-target modifications effected by cytidine base editors in the liver of mice with phenylketonuria. The intravenous delivery of intein-split cytidine base editors by dual adeno-associated viruses led to the repair of the disease-causing mutation without generating off-target mutations in the RNA and DNA of the hepatocytes. Moreover, the transient expression of a cytidine base editor mRNA and a relevant single-guide RNA intravenously delivered by lipid nanoparticles led to ~21% on-target editing and to the reversal of the disease phenotype; there were also no detectable transcriptome-wide and genome-wide off-target edits. Our findings support the feasibility of therapeutic cytidine base editing to treat genetic liver diseases.
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Affiliation(s)
- Lukas Villiger
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Tanja Rothgangl
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Dominik Witzigmann
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Rurika Oka
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Paulo J C Lin
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Sharan Janjuha
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Christian Berk
- Institute for Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Femke Ringnalda
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Markus Stoffel
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Beat Thöny
- Zurich Center for Integrative Human Physiology, Zurich, Switzerland
- Neuroscience Center Zurich, Zurich, Switzerland
- Division of Metabolism, University Children's Hospital Zurich and Children's Research Centre, Zurich, Switzerland
| | - Jonathan Hall
- Institute for Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Ruben van Boxtel
- Oncode Institute, Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ying K Tam
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald Schwank
- Department of Biology, Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
- Institute for Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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8
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Phenylketonuria Diagnosis by Massive Parallel Sequencing and Genotype-Phenotype Association in Brazilian Patients. Genes (Basel) 2020; 12:genes12010020. [PMID: 33375644 PMCID: PMC7824641 DOI: 10.3390/genes12010020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/04/2022] Open
Abstract
Phenylketonuria (PKU) is a common inborn error of amino acid metabolism in which the enzyme phenylalanine hydroxylase, which converts phenylalanine to tyrosine, is functionally impaired due to pathogenic variants in the PAH gene. Thirty-four Brazilian patients with a biochemical diagnosis of PKU, from 33 unrelated families, were analyzed through next-generation sequencing in the Ion Torrent PGM™ platform. Phenotype–genotype correlations were made based on the BioPKU database. Three patients required additional Sanger sequencing analyses. Twenty-six different pathogenic variants were identified. The most frequent variants were c.1315+1G>A (n = 8/66), c.473G>A (n = 6/66), and c.1162G>A (n = 6/66). One novel variant, c.524C>G (p.Pro175Arg), was found in one allele and was predicted as likely pathogenic by the American College of Medical Genetics and Genomics (ACMG) criteria. The molecular modeling of p.Pro175Arg indicated that this substitution can affect monomers binding in the PAH tetramer, which could lead to a change in the stability and activity of this enzyme. Next-generation sequencing was a fast and effective method for diagnosing PKU and is useful for patient phenotype prediction and genetic counseling.
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9
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McCague AF, Raraigh KS, Pellicore MJ, Davis-Marcisak EF, Evans TA, Han ST, Lu Z, Joynt AT, Sharma N, Castellani C, Collaco JM, Corey M, Lewis MH, Penland CM, Rommens JM, Stephenson AL, Sosnay PR, Cutting GR. Correlating Cystic Fibrosis Transmembrane Conductance Regulator Function with Clinical Features to Inform Precision Treatment of Cystic Fibrosis. Am J Respir Crit Care Med 2020; 199:1116-1126. [PMID: 30888834 DOI: 10.1164/rccm.201901-0145oc] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: The advent of precision treatment for cystic fibrosis using small-molecule therapeutics has created a need to estimate potential clinical improvements attributable to increases in cystic fibrosis transmembrane conductance regulator (CFTR) function. Objectives: To derive CFTR function of a variety of CFTR genotypes and correlate with key clinical features (sweat chloride concentration, pancreatic exocrine status, and lung function) to develop benchmarks for assessing response to CFTR modulators. Methods: CFTR function assigned to 226 unique CFTR genotypes was correlated with the clinical data of 54,671 individuals enrolled in the Clinical and Functional Translation of CFTR (CFTR2) project. Cross-sectional FEV1% predicted measurements were plotted by age at which measurement was obtained. Shifts in sweat chloride concentration and lung function reported in CFTR modulator trials were compared with function-phenotype correlations to assess potential efficacy of therapies. Measurements and Main Results: CFTR genotype function exhibited a logarithmic relationship with each clinical feature. Modest increases in CFTR function related to differing genotypes were associated with clinically relevant improvements in cross-sectional FEV1% predicted over a range of ages (6-82 yr). Therapeutic responses to modulators corresponded closely to predictions from the CFTR2-derived relationship between CFTR genotype function and phenotype. Conclusions: Increasing CFTR function in individuals with severe disease will have a proportionally greater effect on outcomes than similar increases in CFTR function in individuals with mild disease and should reverse a substantial fraction of the disease process. This study provides reference standards for clinical outcomes that may be achieved by increasing CFTR function.
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Affiliation(s)
- Allison F McCague
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Karen S Raraigh
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | | | | | - Taylor A Evans
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Sangwoo T Han
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Zhongzhou Lu
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Anya T Joynt
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Neeraj Sharma
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Carlo Castellani
- 2 Cystic Fibrosis Center, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Joseph M Collaco
- 3 Eudowood Division of Pediatric Respiratory Sciences, School of Medicine
| | | | | | | | - Johanna M Rommens
- 7 Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anne L Stephenson
- 8 Department of Respirology, Adult Cystic Fibrosis Program, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Patrick R Sosnay
- 9 Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Garry R Cutting
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
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10
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Rajabi F, Rohr F, Wessel A, Martell L, Dobrowolski SF, Guldberg P, Güttler F, Levy HL. Phenylalanine hydroxylase genotype-phenotype associations in the United States: A single center study. Mol Genet Metab 2019; 128:415-421. [PMID: 31623983 DOI: 10.1016/j.ymgme.2019.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 11/28/2022]
Abstract
Phenylketonuria (PKU) is an autosomal recessive inborn error of metabolism caused by pathogenic variants in the phenylalanine hydroxylase gene (PAH). The correlation between genotype and phenotype can be complex and sometimes variable but often very useful for categorizing and predicting dietary tolerance and potential outcome. We reviewed medical records for 367 patients diagnosed with PKU or persistent mild hyperphenylalaninemia (MHP) between 1950 and 2015 who had PAH genotyping. In 351 we had the full PAH genotype as well as phenotypic characteristics such as phenylalanine (Phe) concentrations (at newborn screening, confirmation, and highest known), and dietary Phe tolerance. On 716 mutant chromosomes, including 14 in genotypes with only one identified variant, we identified 114 different pathogenic variants. The most frequent, p.R408W, was present in 15.4% of the alleles; other frequent variants were c.1315 + 1G > A (6.1%), p.I65T (5.7%), and p.R261Q (5.7%). Three variants, c.142 T > G (p.L48 V), c.615G > C (p.E205D), and c.1342_1345delCTCC, were novel. We used the phenotypic parameters of variants paired with null alleles (functional hemizygotes) to assign the variants as classic PKU, moderate PKU, mild PKU, MHP-gray zone, or MHP. We also included the phenotype association(s) for all of the full genotypes. In 103 patients, we also could assign sapropterin dihydrochloride responsiveness, which is a synthetic form of the tetrahydrobiopterin (BH4) PAH cofactor. This compilation from a single metabolic center provides further information on PAH variants in the United States and the correlations between genotype and phenotype.
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Affiliation(s)
- Farrah Rajabi
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Frances Rohr
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Ann Wessel
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Leslie Martell
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Harvey L Levy
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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11
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Kanavy DM, McNulty SM, Jairath MK, Brnich SE, Bizon C, Powell BC, Berg JS. Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. Genome Med 2019; 11:77. [PMID: 31783775 PMCID: PMC6884856 DOI: 10.1186/s13073-019-0683-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The 2015 American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that "well-established" functional studies can be used as evidence in variant classification. These guidelines articulated key attributes of functional data, including that assays should reflect the biological environment and be analytically sound; however, details of how to evaluate these attributes were left to expert judgment. The Clinical Genome Resource (ClinGen) designates Variant Curation Expert Panels (VCEPs) in specific disease areas to make gene-centric specifications to the ACMG/AMP guidelines, including more specific definitions of appropriate functional assays. We set out to evaluate the existing VCEP guidelines for functional assays. METHODS We evaluated the functional criteria (PS3/BS3) of six VCEPs (CDH1, Hearing Loss, Inherited Cardiomyopathy-MYH7, PAH, PTEN, RASopathy). We then established criteria for evaluating functional studies based on disease mechanism, general class of assay, and the characteristics of specific assay instances described in the primary literature. Using these criteria, we extensively curated assay instances cited by each VCEP in their pilot variant classification to analyze VCEP recommendations and their use in the interpretation of functional studies. RESULTS Unsurprisingly, our analysis highlighted the breadth of VCEP-approved assays, reflecting the diversity of disease mechanisms among VCEPs. We also noted substantial variability between VCEPs in the method used to select these assays and in the approach used to specify strength modifications, as well as differences in suggested validation parameters. Importantly, we observed discrepancies between the parameters VCEPs specified as required for approved assay instances and the fulfillment of these requirements in the individual assays cited in pilot variant interpretation. CONCLUSIONS Interpretation of the intricacies of functional assays often requires expert-level knowledge of the gene and disease, and current VCEP recommendations for functional assay evidence are a useful tool to improve the accessibility of functional data by providing a starting point for curators to identify approved functional assays and key metrics. However, our analysis suggests that further guidance is needed to standardize this process and ensure consistency in the application of functional evidence.
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Affiliation(s)
- Dona M Kanavy
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shannon M McNulty
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meera K Jairath
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bradford C Powell
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Zastrow DB, Baudet H, Shen W, Thomas A, Si Y, Weaver MA, Lager AM, Liu J, Mangels R, Dwight SS, Wright MW, Dobrowolski SF, Eilbeck K, Enns GM, Feigenbaum A, Lichter-Konecki U, Lyon E, Pasquali M, Watson M, Blau N, Steiner RD, Craigen WJ, Mao R. Unique aspects of sequence variant interpretation for inborn errors of metabolism (IEM): The ClinGen IEM Working Group and the Phenylalanine Hydroxylase Gene. Hum Mutat 2019; 39:1569-1580. [PMID: 30311390 DOI: 10.1002/humu.23649] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/28/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022]
Abstract
The ClinGen Inborn Errors of Metabolism Working Group was tasked with creating a comprehensive, standardized knowledge base of genes and variants for metabolic diseases. Phenylalanine hydroxylase (PAH) deficiency was chosen to pilot development of the Working Group's standards and guidelines. A PAH variant curation expert panel (VCEP) was created to facilitate this process. Following ACMG-AMP variant interpretation guidelines, we present the development of these standards in the context of PAH variant curation and interpretation. Existing ACMG-AMP rules were adjusted based on disease (6) or strength (5) or both (2). Disease adjustments include allele frequency thresholds, functional assay thresholds, and phenotype-specific guidelines. Our validation of PAH-specific variant interpretation guidelines is presented using 85 variants. The PAH VCEP interpretations were concordant with existing interpretations in ClinVar for 69 variants (81%). Development of biocurator tools and standards are also described. Using the PAH-specific ACMG-AMP guidelines, 714 PAH variants have been curated and will be submitted to ClinVar. We also discuss strategies and challenges in applying ACMG-AMP guidelines to autosomal recessive metabolic disease, and the curation of variants in these genes.
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Affiliation(s)
- Diane B Zastrow
- Palo Alto Medical Foundation, Palo Alto, California.,Stanford University, Stanford, California
| | - Heather Baudet
- University of North Carolina, Chapel Hill, North Carolina
| | - Wei Shen
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Amanda Thomas
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Yue Si
- GeneDx, Gaithersburg, Maryland
| | - Meredith A Weaver
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Angela M Lager
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Jixia Liu
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | | | | | | | | | | | | | - Annette Feigenbaum
- Rady Children's Hospital and University of California, San Diego, California
| | - Uta Lichter-Konecki
- Children's Hospital of Pittsburg of UPMC, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elaine Lyon
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Marzia Pasquali
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
| | - Michael Watson
- American College of Medical Genetics and Genomics, Bethesda, Maryland
| | - Nenad Blau
- Dietmar-Hopp Metabolic Center, University Children's Hospital, Department of General Pediatrics, Heidelberg, Germany
| | - Robert D Steiner
- Marshfield Clinic Research Institute, Marshfield, Wisconsin.,University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | - Rong Mao
- ARUP Laboratories, Salt Lake City, Utah.,University of Utah, Salt Lake City, Utah
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13
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Asano Y. Screening and development of enzymes for determination and transformation of amino acids. Biosci Biotechnol Biochem 2019; 83:1402-1416. [PMID: 30621552 DOI: 10.1080/09168451.2018.1559027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.
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Affiliation(s)
- Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Toyama , Japan
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14
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Himmelreich N, Shen N, Okun JG, Thiel C, Hoffmann GF, Blau N. Relationship between genotype, phenylalanine hydroxylase expression and in vitro activity and metabolic phenotype in phenylketonuria. Mol Genet Metab 2018; 125:86-95. [PMID: 30037505 DOI: 10.1016/j.ymgme.2018.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 01/22/2023]
Abstract
Residual phenylalanine hydroxylase (PAH) activity is the main determinant of the metabolic phenotype in phenylketonuria (PKU). The genotypic heterogeneity of PKU, involving >1000 PAH variants and over 2500 different genotypes, makes genotype-based phenotype prediction challenging. While a relationship between PAH variants and the metabolic phenotype is well established, we questioned the importance of PAH expression and residual in vitro activity for the metabolic phenotype. Thirty-four PAH variants (p.F39 L, p.A47V, p.D59Y, p.I65S, p.R68G, p.R68S, p.E76G, p.A104D, p.D143G, p.R155H, p.R176L, p.V190A, p.G218 V, p.R241C, p.R243Q, p.P244L, p.R252W, p.R261Q, p.E280K, p.R297H, p.A300S, p.I306V, p.A309V, p.L311P, p.A313T, p.L348 V, p.V388 M, A403V, p.R408Q, p.R408W, p.R413P, p.D415N, p.Y417H, and p.A434D) were transiently transfected into COS-7 cells, and expression of PAH was investigated. Expression patterns were compared with in vitro PAH activity and allelic phenotype values (APVs). In vitro PAH activity was significantly higher (p < .01) in variants associated with mild hyperphenylalaninemia (PAH activity = 52.1 ± 8.5%; APV = 6.7-10.0) than that in classic PKU variants (PAH activity = 21.1 ± 7.0%; APV = 0-2.7). Mild PKU variants (PAH activity = 40.2 ± 7.6%; APV = 2.8-6.6) were not significantly different from mild hyperphenylalaninemia, but there was a difference (p < .048) compared with classic PKU phenotypes.
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Affiliation(s)
- Nastassja Himmelreich
- Center for Child and Adolescent Medicine, and Dietmar-Hopp Metabolic Center, University of Heidelberg, Heidelberg, Germany
| | - Nan Shen
- Center for Child and Adolescent Medicine, and Dietmar-Hopp Metabolic Center, University of Heidelberg, Heidelberg, Germany; Department of Rehabilitation Medicine, Xin Hua Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jürgen G Okun
- Center for Child and Adolescent Medicine, and Dietmar-Hopp Metabolic Center, University of Heidelberg, Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, and Dietmar-Hopp Metabolic Center, University of Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Center for Child and Adolescent Medicine, and Dietmar-Hopp Metabolic Center, University of Heidelberg, Heidelberg, Germany
| | - Nenad Blau
- Center for Child and Adolescent Medicine, and Dietmar-Hopp Metabolic Center, University of Heidelberg, Heidelberg, Germany.
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15
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Li N, He C, Li J, Tao J, Liu Z, Zhang C, Yuan Y, Jiang H, Zhu J, Deng Y, Guo Y, Li Q, Yu P, Wang Y. Analysis of the genotype-phenotype correlation in patients with phenylketonuria in mainland China. Sci Rep 2018; 8:11251. [PMID: 30050108 PMCID: PMC6062512 DOI: 10.1038/s41598-018-29640-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/13/2018] [Indexed: 11/22/2022] Open
Abstract
Mutations in the gene encoding phenylalanine hydroxylase (PAH) are associated with various degrees of phenylketonuria (PKU). The aim of our study was to define the genotype-phenotype correlations of mutations in the PAH gene that cause phenylketonuria (PKU) among the Chinese mainland population. Mutations in the PAH gene were analysed by next-generation sequencing, and a genotype-phenotype correlation analysis was performed in 1079 patients. Fifteen “null + null” genotypes, including four homoallelic and eleven heteroallelic genotypes, were clearly associated with classic PKU. Five functionally hemizygous (p.E280K, p.R252Q, p.E56D, p.S310F and p.T372R) and four compound heterozygous (p.T278I/p.S359L, p.R408W/p.R243Q, p.F161S/p.R243Q and p.F161S/p.R413P) genotypes were clearly associated with classic PKU. Ten functionally hemizygous genotypes, p.G257V, p.R158W, p.L255S, p.G247V, p.F161S, p.R158Q, p.V388M, p.I65T, p.I324N and p.R400K, were frequently associated with classic PKU. Three functionally hemizygous genotypes, p.P147L, p.I95del and p.F331S, and four compound heterozygous genotypes, p.G257V/p.R408Q, p.A434D/p.R413P, p.R243Q/p.A47E and p.R241C/p.G239D, were consistently correlated with mild PKU. Three functionally hemizygous genotypes, p.H107R, p.Q419R and p.F392I, and nine compound heterozygous genotypes (p.G312V/p.R241C, p.R243Q/p.V230I, p.R243Q/p.A403V, p.R243Q/p.Q419R, p.R243Q/p.R53H, p.R243Q/p.H107R, p.R241C/p.R408Q, p.R241C/p.H220P and p.R53H/p.R400K) were consistent with mild hyperphenylalaninaemia (MHP). Our study provides further support for the hypothesis that the PAH genotype is the main factor that determines the phenotype of PKU.
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Affiliation(s)
- Nana Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Chunhua He
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jing Li
- Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jing Tao
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhen Liu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Chunyan Zhang
- Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, 518103, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ying Deng
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yixiong Guo
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Qintong Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ping Yu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Yanping Wang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
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16
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Garbade SF, Shen N, Himmelreich N, Haas D, Trefz FK, Hoffmann GF, Burgard P, Blau N. Allelic phenotype values: a model for genotype-based phenotype prediction in phenylketonuria. Genet Med 2018; 21:580-590. [DOI: 10.1038/s41436-018-0081-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/31/2018] [Indexed: 02/08/2023] Open
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17
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Lilleväli H, Reinson K, Muru K, Simenson K, Murumets Ü, Möls T, Õunap K. Hyperphenylalaninaemias in Estonia: Genotype-Phenotype Correlation and Comparative Overview of the Patient Cohort Before and After Nation-Wide Neonatal Screening. JIMD Rep 2017; 40:39-45. [PMID: 28956315 PMCID: PMC6122019 DOI: 10.1007/8904_2017_61] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 02/11/2023] Open
Abstract
The present study provides a retrospective overview of the cohort of phenylketonuria (PKU) patients in Estonia. Based on the available data, the patients clearly cluster into two distinct groups: the patients with late diagnosis and start of therapy (N = 46), who were born before 1993 when the national newborn screening programme was launched, and the screened babies (N = 48) getting their diagnoses at least in a couple of weeks after birth.Altogether 153 independent phenylalanine hydroxylase (PAH) alleles from 92 patients were analysed in the study, wherein 80% of them were carrying the p.Arg408Trp variation, making the relative frequency of this particular variation one of the highest known. Additionally, 15 other different variations in the PAH gene were identified, each with very low incidence, providing ground for phenotypic variability and potential response to BH4 therapy. Genealogical analysis revealed some "hotspots" of the origin of the p.Arg408Trp variation, with especially high density in South-East Estonia. According to our data, the incidence of PKU in Estonia is estimated as 1 in 6,700 newborns.
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Affiliation(s)
- Hardo Lilleväli
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia. .,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.
| | - Karit Reinson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia ,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kai Muru
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Kristi Simenson
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Ülle Murumets
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Tõnu Möls
- Centre for Limnology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia ,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
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18
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Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WY, Chen W, Shah H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A, Diaz GA, Edelmann L, Schadt EE, Friend SH. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nat Biotechnol 2016; 34:531-8. [PMID: 27065010 DOI: 10.1038/nbt.3514] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/12/2016] [Indexed: 12/21/2022]
Abstract
Genetic studies of human disease have traditionally focused on the detection of disease-causing mutations in afflicted individuals. Here we describe a complementary approach that seeks to identify healthy individuals resilient to highly penetrant forms of genetic childhood disorders. A comprehensive screen of 874 genes in 589,306 genomes led to the identification of 13 adults harboring mutations for 8 severe Mendelian conditions, with no reported clinical manifestation of the indicated disease. Our findings demonstrate the promise of broadening genetic studies to systematically search for well individuals who are buffering the effects of rare, highly penetrant, deleterious mutations. They also indicate that incomplete penetrance for Mendelian diseases is likely more common than previously believed. The identification of resilient individuals may provide a first step toward uncovering protective genetic variants that could help elucidate the mechanisms of Mendelian diseases and new therapeutic strategies.
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Affiliation(s)
- Rong Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jörg Hakenberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Pamela Sklar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Om Prakash
- Department of Clinical Sciences, Diabetes &Endocrinology, Lund University Diabetes Center, Skåne University Hospital, Lund University, Malmö, Sweden
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Patrick Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wei-Yi Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Menachem Fromer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Matthew A Deardorff
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jason R Bobe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Elissa Levin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Leif Groop
- Department of Clinical Sciences, Diabetes &Endocrinology, Lund University Diabetes Center, Skåne University Hospital, Lund University, Malmö, Sweden
| | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen H Friend
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sage Bionetworks, Seattle, Washington, USA
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19
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Schiff M, Haberberger B, Xia C, Mohsen AW, Goetzman ES, Wang Y, Uppala R, Zhang Y, Karunanidhi A, Prabhu D, Alharbi H, Prochownik EV, Haack T, Häberle J, Munnich A, Rötig A, Taylor RW, Nicholls RD, Kim JJ, Prokisch H, Vockley J. Complex I assembly function and fatty acid oxidation enzyme activity of ACAD9 both contribute to disease severity in ACAD9 deficiency. Hum Mol Genet 2015; 24:3238-47. [PMID: 25721401 DOI: 10.1093/hmg/ddv074] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/23/2015] [Indexed: 01/05/2023] Open
Abstract
Acyl-CoA dehydrogenase 9 (ACAD9) is an assembly factor for mitochondrial respiratory chain Complex I (CI), and ACAD9 mutations are recognized as a frequent cause of CI deficiency. ACAD9 also retains enzyme ACAD activity for long-chain fatty acids in vitro, but the biological relevance of this function remains controversial partly because of the tissue specificity of ACAD9 expression: high in liver and neurons and minimal in skin fibroblasts. In this study, we hypothesized that this enzymatic ACAD activity is required for full fatty acid oxidation capacity in cells expressing high levels of ACAD9 and that loss of this function is important in determining phenotype in ACAD9-deficient patients. First, we confirmed that HEK293 cells express ACAD9 abundantly. Then, we showed that ACAD9 knockout in HEK293 cells affected long-chain fatty acid oxidation along with Cl, both of which were rescued by wild type ACAD9. Further, we evaluated whether the loss of ACAD9 enzymatic fatty acid oxidation affects clinical severity in patients with ACAD9 mutations. The effects on ACAD activity of 16 ACAD9 mutations identified in 24 patients were evaluated using a prokaryotic expression system. We showed that there was a significant inverse correlation between residual enzyme ACAD activity and phenotypic severity of ACAD9-deficient patients. These results provide evidence that in cells where it is strongly expressed, ACAD9 plays a physiological role in fatty acid oxidation, which contributes to the severity of the phenotype in ACAD9-deficient patients. Accordingly, treatment of ACAD9 patients should aim at counteracting both CI and fatty acid oxidation dysfunctions.
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Affiliation(s)
- Manuel Schiff
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Reference Center for Inborn Errors of Metabolism, Hôpital Robert Debré, APHP, INSERM U1141 and Université Paris-Diderot, Sorbonne Paris Cité, Paris, France
| | - Birgit Haberberger
- Institute of Human Genetics, Technische Universität München, Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Chuanwu Xia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Eric S Goetzman
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Yudong Wang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Radha Uppala
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Yuxun Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Dolly Prabhu
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Hana Alharbi
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Edward V Prochownik
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | - Tobias Haack
- Institute of Human Genetics, Technische Universität München, Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Johannes Häberle
- Division of Metabolism, University Children's Hospital Zurich, Zurich, Switzerland
| | - Arnold Munnich
- Institut Imagine and INSERM U781, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Université Paris-Descartes, Paris, France
| | - Agnes Rötig
- Institut Imagine and INSERM U781, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Université Paris-Descartes, Paris, France
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK and
| | - Robert D Nicholls
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jung-Ja Kim
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich, Germany Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15224, USA
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Burgard P, Mönch E, Zschocke J, Wendel U, Langenbeck U. Development of Metabolic Phenotype in Phenylketonuria: Evaluation of the Blaskovics Protein Loading Test at 5 Years of Age. JIMD Rep 2015; 29:77-84. [DOI: 10.1007/8904_2015_508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 09/16/2015] [Accepted: 10/02/2015] [Indexed: 10/22/2022] Open
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Mato JM, Martínez-Chantar ML, Lu SC. Systems biology for hepatologists. Hepatology 2014; 60:736-43. [PMID: 24449428 PMCID: PMC4105331 DOI: 10.1002/hep.27023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/17/2013] [Accepted: 01/15/2014] [Indexed: 12/17/2022]
Abstract
Medicine is expected to benefit from combining usual cellular and molecular studies with high-throughput methods (genomics, transcriptomics, proteomics, and metabolomics). These methods, collectively known as omics, permit the determination of thousands of molecules (variations within genes, RNAs, proteins, metabolites) within a tissue, cell, or biological fluid. The use of these methods is very demanding in terms of the design of the study, acquisition, storage, analysis, and interpretation of the data. When carried out properly, these studies can reveal new etiological pathways, help to identify patients at risk for disease, and predict the response to specific treatments. Here we review these omics methods and mention several applications in hepatology research.
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Affiliation(s)
- José M Mato
- CIC bioGUNE, Ciberehd, Parque Tecnológico de Bizkaia, Bizkaia, Spain
| | | | - Shelly C Lu
- Division of Gastroenterology and Liver Diseases, USC Research Center for Liver Diseases, The Southern California Research Center for Alcoholic and Pancreatic Diseases & Cirrhosis, Keck School of Medicine USC, Los Angeles, California
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22
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Camp KM, Parisi MA, Acosta PB, Berry GT, Bilder DA, Blau N, Bodamer OA, Brosco JP, Brown CS, Burlina AB, Burton BK, Chang CS, Coates PM, Cunningham AC, Dobrowolski SF, Ferguson JH, Franklin TD, Frazier DM, Grange DK, Greene CL, Groft SC, Harding CO, Howell RR, Huntington KL, Hyatt-Knorr HD, Jevaji IP, Levy HL, Lichter-Konecki U, Lindegren ML, Lloyd-Puryear MA, Matalon K, MacDonald A, McPheeters ML, Mitchell JJ, Mofidi S, Moseley KD, Mueller CM, Mulberg AE, Nerurkar LS, Ogata BN, Pariser AR, Prasad S, Pridjian G, Rasmussen SA, Reddy UM, Rohr FJ, Singh RH, Sirrs SM, Stremer SE, Tagle DA, Thompson SM, Urv TK, Utz JR, van Spronsen F, Vockley J, Waisbren SE, Weglicki LS, White DA, Whitley CB, Wilfond BS, Yannicelli S, Young JM. Phenylketonuria Scientific Review Conference: state of the science and future research needs. Mol Genet Metab 2014; 112:87-122. [PMID: 24667081 DOI: 10.1016/j.ymgme.2014.02.013] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/25/2014] [Accepted: 02/26/2014] [Indexed: 01/17/2023]
Abstract
New developments in the treatment and management of phenylketonuria (PKU) as well as advances in molecular testing have emerged since the National Institutes of Health 2000 PKU Consensus Statement was released. An NIH State-of-the-Science Conference was convened in 2012 to address new findings, particularly the use of the medication sapropterin to treat some individuals with PKU, and to develop a research agenda. Prior to the 2012 conference, five working groups of experts and public members met over a 1-year period. The working groups addressed the following: long-term outcomes and management across the lifespan; PKU and pregnancy; diet control and management; pharmacologic interventions; and molecular testing, new technologies, and epidemiologic considerations. In a parallel and independent activity, an Evidence-based Practice Center supported by the Agency for Healthcare Research and Quality conducted a systematic review of adjuvant treatments for PKU; its conclusions were presented at the conference. The conference included the findings of the working groups, panel discussions from industry and international perspectives, and presentations on topics such as emerging treatments for PKU, transitioning to adult care, and the U.S. Food and Drug Administration regulatory perspective. Over 85 experts participated in the conference through information gathering and/or as presenters during the conference, and they reached several important conclusions. The most serious neurological impairments in PKU are preventable with current dietary treatment approaches. However, a variety of more subtle physical, cognitive, and behavioral consequences of even well-controlled PKU are now recognized. The best outcomes in maternal PKU occur when blood phenylalanine (Phe) concentrations are maintained between 120 and 360 μmol/L before and during pregnancy. The dietary management treatment goal for individuals with PKU is a blood Phe concentration between 120 and 360 μmol/L. The use of genotype information in the newborn period may yield valuable insights about the severity of the condition for infants diagnosed before maximal Phe levels are achieved. While emerging and established genotype-phenotype correlations may transform our understanding of PKU, establishing correlations with intellectual outcomes is more challenging. Regarding the use of sapropterin in PKU, there are significant gaps in predicting response to treatment; at least half of those with PKU will have either minimal or no response. A coordinated approach to PKU treatment improves long-term outcomes for those with PKU and facilitates the conduct of research to improve diagnosis and treatment. New drugs that are safe, efficacious, and impact a larger proportion of individuals with PKU are needed. However, it is imperative that treatment guidelines and the decision processes for determining access to treatments be tied to a solid evidence base with rigorous standards for robust and consistent data collection. The process that preceded the PKU State-of-the-Science Conference, the conference itself, and the identification of a research agenda have facilitated the development of clinical practice guidelines by professional organizations and serve as a model for other inborn errors of metabolism.
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Affiliation(s)
- Kathryn M Camp
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD 20982, USA.
| | - Melissa A Parisi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | - Gerard T Berry
- Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Deborah A Bilder
- Department of Psychiatry, University of Utah, Salt Lake City, UT 84108, USA.
| | - Nenad Blau
- University Children's Hospital, Heidelberg, Germany; University Children's Hospital, Zürich, Switzerland.
| | - Olaf A Bodamer
- University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Jeffrey P Brosco
- University of Miami Mailman Center for Child Development, Miami, FL 33101, USA.
| | | | | | - Barbara K Burton
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.
| | - Christine S Chang
- Agency for Healthcare Research and Quality, Rockville, MD 20850, USA.
| | - Paul M Coates
- Office of Dietary Supplements, National Institutes of Health, Bethesda, MD 20982, USA.
| | - Amy C Cunningham
- Tulane University Medical School, Hayward Genetics Center, New Orleans, LA 70112, USA.
| | | | - John H Ferguson
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20982, USA.
| | | | | | - Dorothy K Grange
- Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO 63110, USA.
| | - Carol L Greene
- University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Stephen C Groft
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20982, USA.
| | - Cary O Harding
- Oregon Health & Science University, Portland, OR 97239, USA.
| | - R Rodney Howell
- University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | | | - Henrietta D Hyatt-Knorr
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20982, USA.
| | - Indira P Jevaji
- Office of Research on Women's Health, National Institutes of Health, Bethesda, MD 20817, USA.
| | - Harvey L Levy
- Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Uta Lichter-Konecki
- George Washington University, Children's National Medical Center, Washington, DC 20010, USA.
| | | | | | | | | | - Melissa L McPheeters
- Vanderbilt Evidence-based Practice Center, Institute for Medicine and Public Health, Nashville, TN 37203, USA.
| | - John J Mitchell
- McGill University Health Center, Montreal, Quebec H3H 1P3, Canada.
| | - Shideh Mofidi
- Maria Fareri Children's Hospital of Westchester Medical Center, Valhalla, NY 10595, USA.
| | - Kathryn D Moseley
- University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
| | - Christine M Mueller
- Office of Orphan Products Development, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Andrew E Mulberg
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Lata S Nerurkar
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20982, USA.
| | - Beth N Ogata
- University of Washington, Seattle, WA 98195, USA.
| | - Anne R Pariser
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA.
| | - Suyash Prasad
- BioMarin Pharmaceutical Inc., San Rafael, CA 94901, USA.
| | - Gabriella Pridjian
- Tulane University Medical School, Hayward Genetics Center, New Orleans, LA 70112, USA.
| | | | - Uma M Reddy
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | | - Sandra M Sirrs
- Vancouver General Hospital, University of British Columbia, Vancouver V5Z 1M9, Canada.
| | | | - Danilo A Tagle
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Susan M Thompson
- The Children's Hospital at Westmead, Sydney, NSW 2145, Australia.
| | - Tiina K Urv
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Jeanine R Utz
- University of Minnesota, Minneapolis, MN 55455, USA.
| | - Francjan van Spronsen
- University of Groningen, University Medical Center of Groningen, Beatrix Children's Hospital, Netherlands.
| | - Jerry Vockley
- University of Pittsburgh, Pittsburgh, PA 15224, USA.
| | - Susan E Waisbren
- Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Linda S Weglicki
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Desirée A White
- Department of Psychology, Washington University, St. Louis, MO 63130, USA.
| | | | - Benjamin S Wilfond
- Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA.
| | | | - Justin M Young
- The Young Face, Facial Plastic and Reconstructive Surgery, Cumming, GA 30041, USA.
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The mutation spectrum of the phenylalanine hydroxylase (PAH) gene and associated haplotypes reveal ethnic heterogeneity in the Taiwanese population. J Hum Genet 2014; 59:145-52. [PMID: 24401910 DOI: 10.1038/jhg.2013.136] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/29/2013] [Accepted: 12/05/2013] [Indexed: 02/01/2023]
Abstract
Phenylalanine hydroxylase (PAH) deficiency is responsible for most cases of phenylketonuria (PKU). In this study of the PAH mutation spectrum in the Taiwanese population, 139 alleles were identified including 34 different mutations. The V190G, Q267R and F392I mutations are first reported in this study. The most common mutations, R241C, R408Q and Ex6-96A>G, account for 23.2%, 12.0% and 9.2%, of the mutant alleles, respectively. Haplotype analysis shows that R241C and Ex6-96A>G are exclusively associated with haplotype 4.3 to suggest founder effects. On the other hand, R408Q is found on two distinct haplotypes suggesting recurrent mutations. The spectrum of PAH mutations in Taiwan shows various links to those of other Asian regions, yet remarkable differences exist. Notably, R408Q, E286K and -4173_-407del, accounting for 21% of all mutant alleles in Taiwan, are very rare or are undetected among PKU cohorts of other Asian regions to suggest local founder effects. Moreover, the low homozygosity value of 0.092 hints at a high degree of ethnic heterogeneity within the Taiwanese population. Our study of PAH mutation spectrum and the associated haplotypes is useful for subsequent study on the origin and migration pattern via Taiwan, an island at the historical crossroad of migration of ancient populations.
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Intra-familiar discordant PKU phenotype explained by mutation analysis in three pedigrees. Clin Biochem 2013; 47:233-5. [PMID: 24296287 DOI: 10.1016/j.clinbiochem.2013.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/16/2013] [Accepted: 11/19/2013] [Indexed: 11/23/2022]
Abstract
Classical phenylketonuria (PKU) and mild hyperphenylalaninemia (MHP) are two phenotypes of phenylalanine hydroxylase (PAH) deficiency with different degrees of severity. We have analyzed three families in which classical PKU, MHP and a normal phenotype occurred within each family due to the different combinations of three mutations segregating within the family. Indeed, sequence PAH analysis revealed three different alleles segregating in each family. This report suggests that when discordant phenotypes occur in a family, complete analysis of the PAH gene may be performed in order to support the diagnosis and assist in accurate genetic counseling and patient management. We further support the marked heterogeneity of hyperphenylalaninemia primarily due to allelic heterogeneity at the PAH locus.
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Zhu T, Ye J, Han L, Qiu W, Zhang H, Liang L, Gu X. Variations in genotype–phenotype correlations in phenylalanine hydroxylase deficiency in Chinese Han population. Gene 2013; 529:80-7. [DOI: 10.1016/j.gene.2013.07.079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/16/2022]
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Mutation spectrum of phenylketonuria in Syrian population: Genotype–phenotype correlation. Gene 2013; 528:241-7. [DOI: 10.1016/j.gene.2013.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/24/2013] [Accepted: 07/01/2013] [Indexed: 11/24/2022]
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Mo XM, Li Y, Tang AG, Ren YP. Simultaneous determination of phenylalanine and tyrosine in peripheral capillary blood by HPLC with ultraviolet detection. Clin Biochem 2013; 46:1074-1078. [DOI: 10.1016/j.clinbiochem.2013.05.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/22/2013] [Accepted: 05/15/2013] [Indexed: 10/26/2022]
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Karam PE, Alhamra RS, Nemer G, Usta J. Spectrum of mutations in Lebanese patients with phenylalanine hydroxylase deficiency. Gene 2012; 515:117-22. [PMID: 23220018 DOI: 10.1016/j.gene.2012.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 11/24/2022]
Abstract
Phenylketonuria is an autosomal recessive inborn error of metabolism resulting from phenylalanine hydroxylase deficiency. Genetic basis of phenylalanine hydroxylase deficiency has been reported in various European and Asian countries with few reports available in Arab populations of the Mediterranean region. This is the first pilot study describing phenotype and genotype of 23 Lebanese patients with phenylketonuria. 48% of the patients presented mainly with neurological signs at a mean age of 2 years 9 months, as newborn screening is not yet a nationwide policy. 56.5% of the patients had classical phenylketonuria. Thirteen different mutations were identified: splice site 52%, frameshift 31%, and missense 17% with no nonsense mutations. IVS10-11G>A was found mainly in Christians at high relative frequency whereas Muslims carried the G352fs and R261Q mutations. A rare splice mutation IVS7+1G>T, not described before, was identified in the homozygous state in one family with moderate phenylketonuria phenotype. Genotype-phenotype correlation using Guldberg arbitrary value method showed high consistency between predicted and observed phenotypes. Calculated homozygosity rate was 0.07 indicating the genetic heterogeneity in our patients. Our findings underline the admixture of different ethnicities and religions in Lebanon that might help tracing back the PAH gene flux history across the Mediterranean region.
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Affiliation(s)
- Pascale E Karam
- Department of Pediatrics and Adolescent, American University Medical Center, Faculty of Medicine, Beirut, Lebanon
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Baturina OA, Bondar AA, Tupikin AE, Zhabin SG, Morozov IV. Analysis of phenylalanine hydroxylase gene mutations in phenylketonuria patients from Kemerovo oblast and the Sakha Republic. CYTOL GENET+ 2012. [DOI: 10.3103/s0095452712040032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Heintz C, Troxler H, Martinez A, Thöny B, Blau N. Quantification of phenylalanine hydroxylase activity by isotope-dilution liquid chromatography-electrospray ionization tandem mass spectrometry. Mol Genet Metab 2012; 105:559-65. [PMID: 22300847 DOI: 10.1016/j.ymgme.2011.12.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/30/2011] [Accepted: 12/30/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND Residual phenylalanine hydroxylase (PAH) activity is the key determinant for the phenotype severity in phenylketonuria (PKU) patients and correlates with the patient's genotype. Activity of in vitro expressed mutant PAH may predict the patient's phenotype and response to tetrahydrobiopterin (BH(4)), the cofactor of PAH. METHODS A robust LC-ESI-MSMS PAH assay for the quantification of phenylalanine and tyrosine was developed. We measured PAH activity a) of the PAH mutations p.Y417C, p.I65T, p.R261Q, p.E280A, p.R158Q, p.R408W, and p.E390G expressed in eukaryotic COS-1 cells; b) in different cell lines (e.g. Huh-7, Hep3B); and c) in liver, brain, and kidney tissue from wild-type and PKU mice. RESULTS The PAH assay was linear for phenylalanine and tyrosine (r(2)≥0.99), with a detection limit of 105 nmol/L for Phe and 398 nmol/L for Tyr. Intra-assay and inter-assay coefficients of variation were <5.3% and <6.2%, respectively, for the p.R158Q variant in lower tyrosine range. Recovery of tyrosine was 100%. Compared to the wild-type enzyme, the highest PAH activity at standard conditions (1 mmol/L L-Phe; 200 μmol/L BH(4)) was found for the mutant p.Y417C (76%), followed by p.E390G (54%), p.R261Q (43%), p.I65T (33%), p.E280A (15%), p.R158Q (5%), and p.R408W (2%). A relative high PAH activity was found in kidney (33% of the liver activity), but none in brain. CONCLUSIONS This novel method is highly sensitive, specific, reproducible, and efficient, allowing the quantification of PAH activity in different cells or tissue extracts using minimum amounts of samples under standardized conditions.
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Affiliation(s)
- Caroline Heintz
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital, Zürich, Switzerland
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Sarkissian CN, Gamez A, Scott P, Dauvillier J, Dorenbaum A, Scriver CR, Stevens RC. Chaperone-like therapy with tetrahydrobiopterin in clinical trials for phenylketonuria: is genotype a predictor of response? JIMD Rep 2011; 5:59-70. [PMID: 23430918 DOI: 10.1007/8904_2011_96] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 08/04/2011] [Accepted: 09/20/2011] [Indexed: 12/24/2022] Open
Abstract
Prospectively enrolled phenylketonuria patients (n=485) participated in an international Phase II clinical trial to identify the prevalence of a therapeutic response to daily doses of sapropterin dihydrochloride (sapropterin, KUVAN(®)). Responsive patients were then enrolled in two subsequent Phase III clinical trials to examine safety, ability to reduce blood Phenylalanine levels, dosage (5-20 mg/kg/day) and response, and bioavailability of sapropterin. We combined phenotypic findings in the Phase II and III clinical trials to classify study-related responsiveness associated with specific alleles and genotypes identified in the patients. We found that 17% of patients showed a response to sapropterin. The patients harbored 245 different genotypes derived from 122 different alleles, among which ten alleles were newly discovered. Only 16.3% of the genotypes clearly conferred a sapropterin-responsive phenotype. Among the different PAH alleles, only 5% conferred a responsive phenotype. The responsive alleles were largely but not solely missense mutations known to or likely to cause misfolding of the PAH subunit. However, the metabolic response was not robustly predictable from the PAH genotypes, based on the study design adopted for these clinical trials, and accordingly it seems prudent to test each person for this phenotype with a standardized protocol.
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Affiliation(s)
- Christineh N Sarkissian
- Departments of Biology, Human Genetics and Pediatrics, McGill University, Montreal, QC, Canada
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Blau N, Hennermann JB, Langenbeck U, Lichter-Konecki U. Diagnosis, classification, and genetics of phenylketonuria and tetrahydrobiopterin (BH4) deficiencies. Mol Genet Metab 2011; 104 Suppl:S2-9. [PMID: 21937252 DOI: 10.1016/j.ymgme.2011.08.017] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/17/2011] [Accepted: 08/17/2011] [Indexed: 11/29/2022]
Abstract
This article summarizes the present knowledge, recent developments, and common pitfalls in the diagnosis, classification, and genetics of hyperphenylalaninemia, including tetrahydrobiopterin (BH4) deficiency. It is a product of the recent workshop organized by the European Phenylketonuria Group in March 2011 in Lisbon, Portugal. Results of the workshop demonstrate that following newborn screening for phenylketonuria (PKU), using tandem mass-spectrometry, every newborn with even slightly elevated blood phenylalanine (Phe) levels needs to be screened for BH4 deficiency. Dried blood spots are the best sample for the simultaneous measurement of amino acids (phenylalanine and tyrosine), pterins (neopterin and biopterin), and dihydropteridine reductase activity from a single specimen. Following diagnosis, the patient's phenotype and individually tailored treatment should be established as soon as possible. Not only blood Phe levels, but also daily tolerance for dietary Phe and potential responsiveness to BH4 are part of the investigations. Efficiency testing with synthetic BH4 (sapropterin dihydrochloride) over several weeks should follow the initial 24-48-hour screening test with 20mg/kg/day BH4. The specific genotype, i.e. the combination of both PAH alleles of the patient, helps or facilitates to determine both the biochemical phenotype (severity of PKU) and the responsiveness to BH4. The rate of Phe metabolic disposal after Phe challenge may be an additional useful tool in the interpretation of phenotype-genotype correlation.
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Affiliation(s)
- Nenad Blau
- University Children's Hospital, Zürich, Switzerland.
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Okano Y, Kudo S, Nishi Y, Sakaguchi T, Aso K. Molecular characterization of phenylketonuria and tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency in Japan. J Hum Genet 2011; 56:306-12. [PMID: 21307867 DOI: 10.1038/jhg.2011.10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phenylketonuria (PKU) is a heterogeneous metabolic disorder caused by a deficiency in hepatic phenylalanine hydroxylase (PAH). On the basis of phenotype/genotype correlations, determination of phenylketonuric genotype is important for classification of the clinical phenotype and treatment of PKU, including tetrahydrobiopterin therapy. We characterized the genotypes of 203 Japanese patients with PKU and hyperphenylalaninemia using the following systems: (1) denaturing high-performance liquid chromatography with a GC-clamped primer; (2) direct sequencing; and, (3) multiplex ligation-dependent probe amplification. Of 406 mutant alleles, 390 (96%) were genotyped; 65 mutations were identified, including 22 new mutations. R413P, R241C, IVS4-1g>a, R111X and R243Q were prevalent mutations. Mutations prevalent in the Japanese cohort are also common in Korean and Northern Chinese populations, suggesting same origin. The spectrum of prevalent mutations was not significantly different among six Japanese districts, indicating that Japan comprises a relatively homogeneous ethnic group. We classified the mutations by clinical phenotypes and in vivo PAH activity and estimated the mutations with potential tetrahydrobiopterin (BH(4)) responsiveness. The frequency of BH(4) responsiveness based on the genotype was 29.1% in Japanese PKU patients. A catalog of PKU genotypes would be useful for predicting clinical phenotype, deciding on the subsequent treatment of PKU including BH(4) therapy, and genetic counseling in East Asia.
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Affiliation(s)
- Yoshiyuki Okano
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka, Japan.
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Boonyapiwat B, Mitchell SC, Steventon GB. Recombinant heteromeric phenylalanine monooxygenase and the oxygenation of carbon and sulfur substrates. J Pharm Pharmacol 2011; 63:558-64. [DOI: 10.1111/j.2042-7158.2010.01242.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abstract
Objectives
The aim of this investigation was to provide in-vitro enzyme kinetic data to support the hypothesis that the in-vivo heterozygous dominant phenotype for phenylalanine monooxygenase (hPAH) was responsible for the S-oxidation polymorphism in the metabolism of S-carboxymethyl-l-cysteine reported in humans. Using a dual-vector expression strategy for the co-production of wild-type and mutant human hPAH subunits we report for the first time the kinetic parameters (Km, Vmax, CLE) for the C-oxidation of l-phenylalanine and the S-oxidation of S-carboxymethyl-l-cysteine in homomeric wild-type, heteromeric mutant and homomeric mutant hPAH proteins in vitro.
Methods
A PROTM dual-vector bacterial expression system was used to produce the required hPAH proteins. Enzyme activity was determined by HPLC with fluorescence detection.
Key findings
The heteromeric hPAH proteins (I65T, R68S, R158Q, I174T, R261Q, V338M, R408W and Y414C) all showed significantly decreased Vmax and CLE values when compared to the homomeric wild-type hPAH enzyme. For both substrates, all calculated Km values were significantly higher than homomeric wild-type hPAH enzyme, with the exception of I65T, R68S and Y414C heteromeric hPAH proteins employing l-phenylalanine as substrate.
Conclusions
The net outcome for the heteromeric mutant hPAH proteins was a decrease significantly more dramatic for S-carboxymethyl-l-cysteine S-oxidation (1.0–18.8% of homomeric wild-type hPAH activity) when compared to l-phenylalanine C-oxidation (25.9–52.9% of homomeric wild-type hPAH activity) as a substrate. Heteromeric hPAH enzyme may be related to the variation in S-carboxymethyl-l-cysteine S-oxidation capacity observed in humans.
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Affiliation(s)
- Boontarika Boonyapiwat
- Bureau of Drug and Narcotic, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Stephen C Mitchell
- Imperial College London, Biomolecular Medicine, Division of Surgery, Faculty of Medicine, South Kensington, London, UK
| | - Glyn B Steventon
- University of Surrey, Clinical Medicine Division, Postgraduate Medical School, Daphne Jackson Road, Manor Park, Guildford, Surrey, UK
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Kand'ár R, Záková P. Determination of phenylalanine and tyrosine in plasma and dried blood samples using HPLC with fluorescence detection. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:3926-9. [PMID: 19836316 DOI: 10.1016/j.jchromb.2009.09.045] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 07/30/2009] [Accepted: 09/29/2009] [Indexed: 11/29/2022]
Abstract
The determination of phenylalanine and tyrosine is presently the most reliable direct approach to the diagnosis of phenylketonuria. An HPLC method for the simultaneous measurement of phenylalanine and tyrosine in samples of dried blood spots and plasma has been developed and evaluated. We have used an inherent fluorescence of both phenylalanine and tyrosine. For the separation, a reverse-phase column LiChroCart 125-4, Purospher RP-18e, 5microm, was used. The mixture of ethanol and deionized water (5:95, v/v) was used as a mobile phase. Analytical performance of this method is satisfactory for both phenylalanine and tyrosine: the intra-assay and inter-assay coefficients of variation were below 10%. Quantitative recoveries from spiked plasma and blood samples were between 92.0 and 102.9%. The limit of detection was 10.0 and 5.0micromol/L, respectively. The preliminary reference ranges of phenylalanine and tyrosine in a group of newborns are 69.3+/-13.1 and 42.7+/-12.9micromol/L, in a group of blood donors are 68.4+/-9.9 and 52.1+/-10.9micromol/L. The presented method is inexpensive and suitable for diagnosis of phenylketonuria.
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Affiliation(s)
- Roman Kand'ár
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Strossova 239, 530 03 Pardubice, Czech Republic.
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Molecular Diagnosis of Phenylketonuria: From Defective Protein to Disease-Causing Gene Mutation. J Med Biochem 2009. [DOI: 10.2478/v10011-009-0021-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular Diagnosis of Phenylketonuria: From Defective Protein to Disease-Causing Gene MutationPhenylketonuria (PKU) is the most common inborn error of amino acid metabolism, with an average incidence of 1/10000 in Caucasians. PKU is caused by more than 500 mutations in the phenylalanine hydroxylase gene (PAH) which result in phenylalanine hydroxylase (PAH) enzyme deficiency. Two approaches, in vitro expression analysis of mutant PAH and genotype-phenotype correlation study, are used for the assessment of severity ofPAHmutations. It has been shown that there is a significant correlation between mutantPAHgenotypes and PKU phenotypes. As a result, the molecular diagnosis is completely shifted toward the detection of mutations in the phenylalanine hydroxylase gene. The study of the molecular basis of PKU in Serbia included identification of the spectrum and frequency ofPAHmutations in Serbian PKU patients and genotype-phenotype correlation analysis. By using both PCR-RFLP and »broad range« DGGE/DNA sequencing analysis, the mutation detection rate reached 97%. Thus, the base for molecular diagnosis, genetic counseling and selection of BH4-responsive PKU patients in Serbia was created.
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Langenbeck U, Burgard P, Wendel U, Lindner M, Zschocke J. Metabolic phenotypes of phenylketonuria. Kinetic and molecular evaluation of the Blaskovics protein loading test. J Inherit Metab Dis 2009; 32:506-13. [PMID: 19609714 DOI: 10.1007/s10545-009-1152-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 04/30/2009] [Accepted: 05/19/2009] [Indexed: 11/28/2022]
Abstract
BACKGROUND As part of the German Collaborative Study of Children Treated for Phenylketonuria (PKU), a three-day protein loading test was applied to children at 6 months of age. This load elicits three principal types of blood phenylalanine (Phe) response, with types I and III clinically corresponding to classic PKU and mild hyperphenylalaninaemia not requiring diet (MHP), respectively. An intermediate type II, clinically corresponding to mild PKU, is characterized by early decline of blood Phe from above 1200 micromol/L down to levels between 600 and 1200 micromol/L at 72 h. AIMS Unbiased classification and kinetic and molecular characterization of the intermediate Phe response; estimation of phenotypic variability of Phe disposal. METHOD A kinetic model with zero-order protein synthesis and first-order rate of metabolic disposal of Phe is applied to 157 tests. RESULTS A model of exponentially saturated activation describes the acceleration of Phe disposal from day 1 to 3 in the intermediate type of response. Eleven of 14 p.Y414C functional hemizygotes and two of three p.R261Q homozygotes manifested this kinetic type. The rate estimates of Phe metabolic disposal differ widely in patients with identical PAH genotype, yet are highly correlated with the Phe level at 72 h.
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Affiliation(s)
- U Langenbeck
- Institute of Human Genetics, Frankfurt University Hospital, Frankfurt/Main, Germany.
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Daniele A, Scala I, Cardillo G, Pennino C, Ungaro C, Sibilio M, Parenti G, Esposito L, Zagari A, Andria G, Salvatore F. Functional and structural characterization of novel mutations and genotype-phenotype correlation in 51 phenylalanine hydroxylase deficient families from Southern Italy. FEBS J 2009; 276:2048-59. [DOI: 10.1111/j.1742-4658.2009.06940.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kand'ár R, Žáková P, Jirošová J, Sladká M. Determination of branched chain amino acids, methionine, phenylalanine, tyrosine and α-keto acids in plasma and dried blood samples using HPLC with fluorescence detection. Clin Chem Lab Med 2009; 47:565-72. [DOI: 10.1515/cclm.2009.123] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Bercovich D, Elimelech A, Zlotogora J, Korem S, Yardeni T, Gal N, Goldstein N, Vilensky B, Segev R, Avraham S, Loewenthal R, Schwartz G, Anikster Y. Genotype-phenotype correlations analysis of mutations in the phenylalanine hydroxylase (PAH) gene. J Hum Genet 2008; 53:407-418. [PMID: 18299955 DOI: 10.1007/s10038-008-0264-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
Abstract
The aims of our research were to define the genotype-phenotype correlations of mutations in the phenylalanine hydroxylase (PAH) gene that cause phenylketonuria (PKU) among the Israeli population. The mutation spectrum of the PAH gene in PKU patients in Israel is described, along with a discussion on genotype-phenotype correlations. By using polymerase chain reaction/denaturing high-performance liquid chromatography (PCR/dHPLC) and DNA sequencing, we screened all exons of the PAH gene in 180 unrelated patients with four different PKU phenotypes [classic PKU, moderate PKU, mild PKU, and mild hyperphenylalaninemia (MHP)]. In 63.2% of patient genotypes, the metabolic phenotype could be predicted, though evidence is also found for both phenotypic inconsistencies among subjects with more than one type of mutation in the PAH gene. Data analysis revealed that about 25% of patients could participate in the future in (6R)-L: -erythro-5, 6, 7, 8-tetrahydrobiopterin (BH4) treatment trials according to their mutation genotypes. This study enables us to construct a national database in Israel that will serve as a valuable tool for genetic counseling and a prognostic evaluation of future cases of PKU.
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Affiliation(s)
- Dani Bercovich
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel. .,Tel-Hai Academic College, Upper Galilee, Israel.
| | - Arava Elimelech
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel
| | - Joel Zlotogora
- Department of Genetic Community, Public Health Services, Health Ministry and Hebrew University, Jerusalem, Israel
| | - Sigal Korem
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel.,Tel-Hai Academic College, Upper Galilee, Israel
| | - Tal Yardeni
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel
| | - Nurit Gal
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Nurit Goldstein
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Bela Vilensky
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Roni Segev
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Smadar Avraham
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ron Loewenthal
- Tissue Typing Unit and Safra Children Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gerard Schwartz
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yair Anikster
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Okano Y, Takatori K, Kudo S, Sakaguchi T, Asada M, Kajiwara M, Yamano T. Effects of tetrahydrobiopterin and phenylalanine on in vivo human phenylalanine hydroxylase by phenylalanine breath test. Mol Genet Metab 2007; 92:308-14. [PMID: 17884650 DOI: 10.1016/j.ymgme.2007.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 07/30/2007] [Accepted: 07/30/2007] [Indexed: 11/23/2022]
Abstract
BH(4) administration results in the reduction of blood phenylalanine level in patients with tetrahydrobiopterin (BH(4))-responsive phenylalanine hydroxylase (PAH) deficiency. The mechanism underlying BH(4) response remains unknown. Here, we studied the effects of BH(4) and phenylalanine on in vivo PAH activity of normal controls using the phenylalanine breath test (PBT) by converting l-[1-(13)C] phenylalanine to (13)CO(2). Phenylalanine oxidation rates were expressed as Delta(13)C ((13)CO(2)/(12+13)CO(2), per thousand) and cumulative recovery rates over 120min (CRR(120), %; total amount of (13)CO(2)/the administered dose of (13)C-phenylalanine). Under physiological conditions of blood phenylalanine, BH(4) administration reduced the Delta(13)C peak from 40.8 per thousand to 21.6 per thousand and CRR(120) from 16.9% to 10.2%. Under high blood phenylalanine conditions, administration of BH(4) increased the Delta(13)C peak from 30.7 per thousand to 46.0 per thousand, while the CRR(120) was similar between phenylalanine (19.9%) and phenylalanine+BH(4) (21.1%) groups. Corrected Delta(13)C and CRR(120) were calculated against serum phenylalanine levels to remove the effects of phenylalanine loading. After BH(4) administration, the corrected Delta(13)C peak increased from 82.7 per thousand to 112.6 per thousand, while the corrected CRR(120) was similar (47.6% and 45.6%). These results indicate that phenylalanine worked as a regulator of in vivo PAH by serving as both a substrate and an activator for the enzyme. Excessive dosages of BH(4) inhibited PAH under normal phenylalanine conditions and activated PAH under conditions of high phenylalanine. The regulation system is therefore designed to maintain phenylalanine levels in the human body. Appropriate BH(4) supplementation must be reviewed in patients with BH(4)-responsive PAH deficiency.
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Affiliation(s)
- Yoshiyuki Okano
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan.
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Abstract
"Inborn errors of metabolism," first recognized 100 years ago by Garrod, were seen as transforming evidence for chemical and biological individuality. Phenylketonuria (PKU), a Mendelian autosomal recessive phenotype, was identified in 1934 by Asbjörn Fölling. It is a disease with impaired postnatal cognitive development resulting from a neurotoxic effect of hyperphenylalaninemia (HPA). Its metabolic phenotype is accountable to multifactorial origins both in nurture, where the normal nutritional experience introduces L-phenylalanine, and in nature, where mutations (>500 alleles) occur in the phenylalanine hydroxylase gene (PAH) on chromosome 12q23.2 encoding the L-phenylalanine hydroxylase enzyme (EC 1.14.16.1). The PAH enzyme converts phenylalanine to tyrosine in the presence of molecular oxygen and catalytic amounts of tetrahydrobiopterin (BH4), its nonprotein cofactor. PKU is among the first of the human genetic diseases to enter, through newborn screening, the domain of public health, and to show a treatment effect. This effect caused a paradigm shift in attitudes about genetic disease. The PKU story contains many messages, including: a framework on which to appreciate the complexity of PKU in which phenotype reflects both locus-specific and genomic components; what the human PAH gene tells us about human population genetics and evolution of modern humans; and how our interest in PKU is served by a locus-specific mutation database (http://www.pahdb.mcgill.ca; last accessed 20 March 2007). The individual Mendelian PKU phenotype has no "simple" or single explanation; every patient has her/his own complex PKU phenotype and will be treated accordingly. Knowledge about PKU reveals genomic components of both disease and health.
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Affiliation(s)
- Charles R Scriver
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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Yalaz K, Vanli L, Yilmaz E, Tokatli A, Anlar B. Phenylketonuria in pediatric neurology practice: a series of 146 cases. J Child Neurol 2006; 21:987-90. [PMID: 17092471 DOI: 10.1177/08830738060210111401] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The neurologic manifestations of patients with phenylketonuria treated at different ages are illustrated in this series of 146 cases, including 9 sib pairs. In addition to well-known findings such as mental retardation, autistic features, microcephaly, and tremor, motor retardation was common and responded promptly to dietary treatment. Hypotonia and diminished reflexes were more frequent findings than hypertonia. Four sib pairs showed divergent features, such as the later-treated sibling having higher function than the early-treated one. Because siblings have a similar genotype and similar environmental and dietary conditions, this observation can be explained by differences in phenylalanine transport to the brain or additional metabolic or perinatal factors influencing the neurologic outcome.
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Leandro J, Nascimento C, de Almeida IT, Leandro P. Co-expression of different subunits of human phenylalanine hydroxylase: evidence of negative interallelic complementation. Biochim Biophys Acta Mol Basis Dis 2006; 1762:544-50. [PMID: 16545551 DOI: 10.1016/j.bbadis.2006.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Revised: 02/01/2006] [Accepted: 02/03/2006] [Indexed: 11/30/2022]
Abstract
To study the interaction between two different subunits of the heteromeric human phenylalanine hydroxylase (hPAH), present in hyperphenylalaninemic (HPA) compound heterozygous patients, heteroallelic hPAH enzymes were produced. A dual vector expression system was used (PRO Bacterial Expression System) in which each mutant subunit was expressed from a separate compatible vector, with different epitope tags, in a single bacterial host. Experimental conditions were selected in order that each plasmid produced equivalent levels of mutant subunits. In this study, we demonstrated that both subunits were expressed and that the purified heteroallelic enzymes, were catalytically active. As expected, the produced proteins displayed enzymatic activities levels lower than the predicted catalytic activity, calculated by averaging in vitro PAH activities from both alleles, and were strongly dependent on the proteins subunit composition. The obtained data suggest that interactions between the studied hPAH subunits, namely the I65T, R261Q, R270K and V388M, and the wild-type protein occurred. As postulated, this phenomenon could be a source of phenotypic variation in genetic diseases involving multimeric proteins.
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Affiliation(s)
- João Leandro
- Unidade de Biologia Molecular e Biopatologia Experimental, Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Okano Y, Hase Y, Kawajiri M, Nishi Y, Inui K, Sakai N, Tanaka Y, Takatori K, Kajiwara M, Yamano T. In vivo studies of phenylalanine hydroxylase by phenylalanine breath test: diagnosis of tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency. Pediatr Res 2004; 56:714-9. [PMID: 15319459 DOI: 10.1203/01.pdr.0000141520.06524.51] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tetrahydrobiopterin (BH4)-responsive phenylalanine hydroxylase (PAH) deficiency is characterized by reduction of blood phenylalanine level after a BH4-loading test. Most cases of BH4-responsive PAH deficiency include mild phenylketonuria (PKU) or mild hyperphenylalaninemia (HPA), but not all patients with mild PKU respond to BH4. We performed the phenylalanine breath test as reliable method to determine the BH4 responsiveness. Phenylalanine breath test quantitatively measures the conversion of L-[1-13C] phenylalanine to 13CO2 and is a noninvasive and rapid test. Twenty Japanese patients with HPA were examined with a dose of 10 mg/kg of 13C-phenylalanine with or without a dose of 10 mg . kg(-1) . d(-1) of BH4 for 3 d. The phenylalanine breath test [cumulative recovery rate (CRR)] could distinguish control subjects (15.4 +/- 1.5%); heterozygotes (10.3 +/- 1.0%); and mild HPA (2.74%), mild PKU (1.13 +/- 0.14%), and classical PKU patients (0.29 +/- 0.14%). The genotypes in mild PKU cases were compound heterozygotes with mild (L52S, R241C, R408Q) and severe mutations, whereas a mild HPA case was homozygote of R241C. CRR correlated inversely with pretreatment phenylalanine levels, indicating the gene dosage effects on PKU. BH4 loading increased CRR from 1.13 +/- 0.14 to 2.95 +/- 1.14% (2.6-fold) in mild PKU and from 2.74 to 7.22% (2.6-fold) in mild HPA. A CRR of 5 to 6% reflected maintenance of appropriate serum phenylalanine level. The phenylalanine breath test is useful for the diagnosis of BH4-responsive PAH deficiency and determination of the optimal dosage of BH4 without increasing blood phenylalanine level.
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Affiliation(s)
- Yoshiyuki Okano
- Department of Pediatrics, Osaka City University Graduate School of Medicine, 1-4-3 Asahimachi, Abeno-ku, Osaka 545-8585, Japan.
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Desviat LR, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P, Clavero S, Ugarte M. Propionic acidemia: mutation update and functional and structural effects of the variant alleles. Mol Genet Metab 2004; 83:28-37. [PMID: 15464417 DOI: 10.1016/j.ymgme.2004.08.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 07/27/2004] [Accepted: 08/02/2004] [Indexed: 12/22/2022]
Abstract
Mutations in the PCCA or PCCB genes, encoding both subunits of propionyl-CoA carboxylase, result in propionic acidemia, a life-threatening inborn error of metabolism with autosomal recessive inheritance. To date, 41 mutations in the PCCA gene and 54 in the PCCB gene have been reported, most of them single base substitutions causing amino acid replacements, and a variety of small insertions and deletions and splicing defects. A greater heterogeneity is observed in the PCCA gene, specially in Caucasians, with no prevalent mutations, while in the Japanese population three mutations account for more than half of the alleles studied. For the PCCB gene a limited number of mutations is responsible for the majority of the alleles characterized in both Caucasian and Oriental populations. These two populations show a different mutational spectrum, only sharing some involving CpG dinucleotides probably as recurrent mutational events. Functional characterization of the mutant missense alleles has been accomplished using different prokaryotic and eukaryotic systems, and the structural consequences have been analyzed in the available crystal models. For the PCCA gene, the main molecular effect of the expressed mutations is related to protein instability, except two mutations in the active site predictably affecting ATP binding. In the PCCB gene the majority of the analyzed mutations are predicted to alter the active site conformation resulting in diminished activity. A few carboxy-terminal PCCB mutations affect the interaction between subunits and the assembly with PCCA to form a functional PCC oligomer. The amount of normal transcripts resulting from some PCCA and PCCB splicing mutations has also been analyzed. Overall, the data generated from the expression analysis reveal potential genotype-phenotype correlations for this clinically heterogeneous disorder.
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Affiliation(s)
- L R Desviat
- Centro de Biología Molecular "Severo Ochoa" CSIC-UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Potter MA, Zeesman S, Brennan B, Kobayashi K, Gao HZ, Tabata A, Saheki T, Whelan DT. Pregnancy in a healthy woman with untreated citrullinemia. ACTA ACUST UNITED AC 2004; 129A:77-82. [PMID: 15266621 DOI: 10.1002/ajmg.a.20559] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report the clinical and biochemical data on a second successful pregnancy in a woman with citrullinemia due to argininosuccinate synthetase deficiency (CTLN1). Despite very elevated plasma and urine citrulline and little or no measurable argininosuccinate synthetase enzyme activity on cultured skin fibroblasts, this 29-year-old woman, who was identified through newborn screening, has remained asymptomatic throughout her life. Mutation analysis has recently revealed that she is a compound heterozygote for a known and a novel mutation (IVS15-1G > C and K310Q, respectively). Many newborn screening programs have recently been expanded to include citrullinemia and numerous asymptomatic hypercitrullinemic infants and children have been identified. It is now important to define prognostic indicators that will help with treatment decisions and genetic counseling for these patients. This patient, as the only citrullinemic adult who has been followed prospectively, contributes important information in this regard. In addition, her child was unaffected by the high citrulline levels demonstrated in amniotic fluid and breast milk suggesting that citrulline is not teratogenic. Although pregnancy is an important risk factor for women with CTLN1, it appears that females with citrullinemia can have normal pregnancy outcomes, as long as metabolic crisis is avoided.
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Affiliation(s)
- Murray A Potter
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.
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Takarada Y, Kagawa S, Okano Y, Tanizawa T. Rapid single-base mismatch detection in genotyping for phenylketonuria. Mol Biotechnol 2003; 24:233-42. [PMID: 12777691 DOI: 10.1385/mb:24:3:233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Phenylketonuria (PKU) is a metabolic disorder that results from a deficiency of hepatic phenylalanine hydroxylase (PAH). Identification of the PKU genotype is useful for predicting clinical PKU phenotype. More than 400 mutations resulting in PAH deficiency have been reported worldwide. We used a genedetecting instrument to identify the nine prevalent Japanese mutations in the PAH gene among 31 PKU patients as a preliminary study. This instrument can automatically detect mutations through the use of allelespecific oligonucleotide (ASO) capture probes, and gave results comparable to those of sequencing studies. Each country has uniquely prevalent and specific mutations causing PKU, and less than 50 types of such mutations are generally present in each country. Early genotyping of PKU makes it possible to identify the phenotype and select the optimal therapy for the disease. For early genotyping, the instrumental method described here shortens the time required for genotyping based on mRNA and/or genomic DNA of PKU parents.
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Affiliation(s)
- Yutaka Takarada
- OYOBO Co., Ltd., 10-24, TOYO-CHO, Tsuruga-shi, Fukui-ken, 914-0047, Japan.
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Kemsley JN, Wasinger EC, Datta S, Mitić N, Acharya T, Hedman B, Caradonna JP, Hodgson KO, Solomon EI. Spectroscopic and kinetic studies of PKU-inducing mutants of phenylalanine hydroxylase: Arg158Gln and Glu280Lys. J Am Chem Soc 2003; 125:5677-86. [PMID: 12733906 DOI: 10.1021/ja029106f] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin-dependent, nonheme iron enzyme that catalyzes the hydroxylation of L-Phe to L-Tyr in the rate-limiting step of phenylalanine catabolism. This reaction is tightly coupled in the wild-type enzyme to oxidation of the tetrahydropterin cofactor. Dysfunction of PAH activity in humans leads to the disease phenylketonuria (PKU). We have investigated two PKU-inducing mutants, Arg158Gln and Glu280Lys, using kinetic methods, magnetic circular dichrosim (MCD) spectroscopy, and X-ray absorption spectroscopy (XAS). Analysis of the products produced by the mutant enzymes shows that although both oxidize pterin at more than twice the rate of wild-type enzyme, these reactions are only approximately 20% coupled to production of L-Tyr. Previous MCD and XAS studies had demonstrated that the resting Fe(II) site is six-coordinate in the wild-type enzyme and converts to a five-coordinate site when both L-Phe and reduced pterin are present in the active site. Although the Arg158Gln mutant forms the five-coordinate site when both cosubstrates are bound, the Fe(II) site of the Glu280Lys mutant remains six-coordinate. These results provide insight into the PAH reaction and disease mechanism at a molecular level, indicating that the first step of the mechanism is formation of a peroxy-pterin species, which subsequently reacts with the Fe(II) site if the pterin is properly oriented for formation of an Fe-OO-pterin bridge and an open coordination position is available on the Fe(II).
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Affiliation(s)
- Jyllian N Kemsley
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Santana da Silva LC, Carvalho TS, da Silva FB, Morari L, Fachel AA, Pires R, Refosco LF, Desnick RJ, Giugliani R, Saraiva Pereira ML. Molecular characterization of phenylketonuria in South Brazil. Mol Genet Metab 2003; 79:17-24. [PMID: 12765842 DOI: 10.1016/s1096-7192(03)00032-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Phenylketonuria (PKU) is an autosomal recessive disorder due to phenylalanine hydroxylase (PAH) deficiency. The PAH gene, located at 12q22-q24.1, includes about 90kb and contains 13 exons. To date, more than 420 different alterations have been identified in the PAH gene. To determine the nature and frequency of PAH mutations in PKU patients from South Brazil, mutation analysis was performed on genomic DNA from 23 unrelated PKU patients. The 13 exons and flanking regions of the PAH gene were amplified by PCR and the amplicons were analyzed by single strand conformation polymorphism (SSCP). Amplicons that showed abnormal migration patterns were analyzed by restriction endonuclease digestion and/or sequencing. Twenty-two previously reported mutations were identified including R261X, R408W, IVS2nt5g-->c, R261Q, and V388M. Polymorphisms were observed in 48.8% of the PKU patients, the most frequent being IVS2nt19t-->c, V245V, and IVS12nt-35c-->t. In addition, two novel sequence variants were identified: 1378g-->t in the 3(')-untranslated region in exon 13 which may be disease-causing and an intron 12 polymorphism, IVS12nt-15t-->c. The mutation spectrum in the patients from Southern Brazil differed from that observed in patients from other Latin American countries and further defined the molecular heterogeneity of this disease.
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