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Erdal İ, Yıldız Y, Kuseyri Hübschmann O, Haas D, Günbey C, Ertuğrul İ, Yalnızoğlu D. Dihydropyrimidinase deficiency with atrioventricular septal defect: a case report. J Pediatr Endocrinol Metab 2024; 0:jpem-2023-0518. [PMID: 38958169 DOI: 10.1515/jpem-2023-0518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024]
Abstract
OBJECTIVES Dihydropyrimidinase deficiency is a rare autosomal recessive disorder of the pyrimidine degradation pathway, with fewer than 40 patients published. Clinical findings are variable and some patients may remain asymptomatic. Global developmental delay and increased susceptibility to 5-fluorouracil are commonly reported. Here we present atrioventricular septal defect as a novel feature in dihydropyrimidinase deficiency. CASE PRESENTATION A four-year-old male with global developmental delay, dysmorphic facies, autistic features and a history of seizures was diagnosed with dihydropyrimidinase deficiency based on strikingly elevated urinary dihydrouracil and dihydrothymine and a homozygous pathogenic nonsense variant in DPYS gene. He had a history of complete atrioventricular septal defect corrected surgically in infancy. CONCLUSIONS This is the second report of congenital heart disease in dihydropyrimidinase deficiency, following a single patient with a ventricular septal defect. The rarity of the disease and the variability of the reported findings make it difficult to describe a disease-specific clinical phenotype. The mechanism of neurological and other systemic findings is unclear. Dihydropyrimidinase deficiency should be considered in patients with microcephaly, developmental delay, epilepsy and autistic traits. We suggest that congenital heart disease may also be a rare phenotypic feature.
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Affiliation(s)
- İzzet Erdal
- Division of Pediatric Metabolism, Department of Pediatrics, Hacettepe University İhsan Doğramacı Children's Hospital, Ankara, Türkiye
- Clinic of Pediatric Metabolic Diseases, Etlik City Hospital, Ankara, Türkiye
| | - Yılmaz Yıldız
- Division of Pediatric Metabolism, Department of Pediatrics, Hacettepe University İhsan Doğramacı Children's Hospital, Ankara, Türkiye
| | - Oya Kuseyri Hübschmann
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Dorothea Haas
- Division of Child Neurology and Metabolic Medicine, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Ceren Günbey
- Division of Pediatric Neurology, Department of Pediatrics, Hacettepe University İhsan Doğramacı Children's Hospital, Ankara, Türkiye
| | - İlker Ertuğrul
- Division of Pediatric Cardiology, Department of Pediatrics, Hacettepe University İhsan Doğramacı Children's Hospital, Ankara, Türkiye
| | - Dilek Yalnızoğlu
- Division of Pediatric Neurology, Department of Pediatrics, Hacettepe University İhsan Doğramacı Children's Hospital, Ankara, Türkiye
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Albokhari D, Alharbi O, Blesson A, Jain M. The diagnostic odyssey of a patient with dihydropyrimidinase deficiency: a case report and review of the literature. Cold Spring Harb Mol Case Stud 2023; 9:a006319. [PMID: 38199782 PMCID: PMC10815279 DOI: 10.1101/mcs.a006319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
Dihydropyrimidinase (DHP) deficiency is an autosomal recessive metabolic disorder caused by biallelic pathogenic variants of DPYS Patients with DHP deficiency exhibit a broad spectrum of phenotypes, ranging from severe neurological and gastrointestinal involvement to cases with no apparent symptoms. The biochemical diagnosis of DHP deficiency is based on the detection of a significant amount of dihydropyrimidines in urine, plasma, and cerebrospinal fluid samples. Molecular genetic testing, specifically the identification of biallelic pathogenic variants in DPYS, has proven instrumental in confirming the diagnosis and facilitating family studies. This case study documents the diagnostic journey of an 18-yr-old patient with DHP deficiency, highlighting features at the severe end of the clinical spectrum. Notably, our patient exhibited previously unreported skeletal features that positively responded to bisphosphonate treatment, contributing valuable insights to the clinical characterization of DHP deficiency. Additionally, a novel DPYS variant was identified and confirmed pathogenicity through metabolic testing, further expanding the variant spectrum of the gene. Our case emphasizes the importance of a comprehensive diagnostic approach using genetic sequencing and metabolic testing for accurate diagnosis.
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Affiliation(s)
- Daniah Albokhari
- Department of Pediatrics, Taibah University College of Medicine, Medina 42353, Saudi Arabia
- King Faisal Specialist Hospital and Research Center, Medina 42523, Saudi Arabia
| | - Ohood Alharbi
- Taibah University College of Medicine, Medina 42353, Saudi Arabia
| | - Alyssa Blesson
- Department of Bone/Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Mahim Jain
- Department of Bone/Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA;
- Department of Genetic Medicine, Johns Hopkins Medical Institute, Baltimore, Maryland 21205, USA
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3
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Hishinuma E, Narita Y, Rico EMG, Ueda A, Obuchi K, Tanaka Y, Saito S, Tadaka S, Kinoshita K, Maekawa M, Mano N, Nakayoshi T, Oda A, Hirasawa N, Hiratsuka M. Functional Characterization of 12 Dihydropyrimidinase Allelic Variants in Japanese Individuals for the Prediction of 5-Fluorouracil Treatment-Related Toxicity. Drug Metab Dispos 2023; 51:165-173. [PMID: 36414408 DOI: 10.1124/dmd.122.001045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/11/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
The drug 5-fluorouracil (5-FU) is the first-choice chemotherapeutic agent against advanced-stage cancers. However, 10% to 30% of treated patients experience grade 3 to 4 toxicity. The deficiency of dihydropyrimidinase (DHPase), which catalyzes the second step of the 5-FU degradation pathway, is correlated with the risk of developing toxicity. Thus, genetic polymorphisms within DPYS, the DHPase-encoding gene, could potentially serve as predictors of severe 5-FU-related toxicity. We identified 12 novel DPYS variants in 3554 Japanese individuals, but the effects of these mutations on function remain unknown. In the current study, we performed in vitro enzymatic analyses of the 12 newly identified DHPase variants. Dihydrouracil or dihydro-5-FU hydrolytic ring-opening kinetic parameters, Km and Vmax , and intrinsic clearance (CLint = Vmax /Km ) of the wild-type DHPase and eight variants were measured. Five of these variants (R118Q, H295R, T418I, Y448H, and T513A) showed significantly reduced CLint compared with that in the wild-type. The parameters for the remaining four variants (V59F, D81H, T136M, and R490H) could not be determined as dihydrouracil and dihydro-5-FU hydrolytic ring-opening activity was undetectable. We also determined DHPase variant protein stability using cycloheximide and bortezomib. The mechanism underlying the observed changes in the kinetic parameters was clarified using blue-native polyacrylamide gel electrophoresis and three-dimensional structural modeling. The results suggested that the decrease or loss of DHPase enzymatic activity was due to reduced stability and oligomerization of DHPase variant proteins. Our findings support the use of DPYS polymorphisms as novel pharmacogenomic markers for predicting severe 5-FU-related toxicity in the Japanese population. SIGNIFICANCE STATEMENT: DHPase contributes to the degradation of 5-fluorouracil, and genetic polymorphisms that cause decreased activity of DHPase can cause severe toxicity. In this study, we performed functional analysis of 12 DHPase variants in the Japanese population and identified 9 genetic polymorphisms that cause reduced DHPase function. In addition, we found that the ability to oligomerize and the conformation of the active site are important for the enzymatic activity of DHPase.
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Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Yoko Narita
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Evelyn Marie Gutiérrez Rico
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Akiko Ueda
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Kai Obuchi
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Yoshikazu Tanaka
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Sakae Saito
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Shu Tadaka
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Masamitsu Maekawa
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Nariyasu Mano
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Tomoki Nakayoshi
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Akifumi Oda
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Noriyasu Hirasawa
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Masahiro Hiratsuka
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
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Lin ES, Huang YH, Yang PC, Peng WF, Huang CY. Complexed Crystal Structure of the Dihydroorotase Domain of Human CAD Protein with the Anticancer Drug 5-Fluorouracil. Biomolecules 2023; 13:149. [PMID: 36671534 PMCID: PMC9856072 DOI: 10.3390/biom13010149] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Dihydroorotase (DHOase) is the third enzyme in the pathway used for the biosynthesis of pyrimidine nucleotides. In mammals, DHOase is active in a trifunctional enzyme, CAD, which also carries out the activities of carbamoyl phosphate synthetase and aspartate transcarbamoylase. Prior to this study, it was unknown whether the FDA-approved clinical drug 5-fluorouracil (5-FU), which is used as an anticancer therapy, could bind to the DHOase domain of human CAD (huDHOase). Here, we identified huDHOase as a new 5-FU binding protein, thereby extending the 5-FU interactome to this human enzyme. In order to investigate where 5-FU binds to huDHOase, we solved the complexed crystal structure at 1.97 Å (PDB ID 8GVZ). The structure of huDHOase complexed with malate was also determined for the sake of comparison (PDB ID 8GW0). These two nonsubstrate ligands were bound at the active site of huDHOase. It was previously established that the substrate N-carbamoyl-L-aspartate is either bound to or moves away from the active site, but it is the loop that is extended towards (loop-in mode) or moved away (loop-out mode) from the active site. DHOase also binds to nonsubstrate ligands via the loop-out mode. In contrast to the Escherichia coli DHOase model, our complexed structures revealed that huDHOase binds to either 5-FU or malate via the loop-in mode. We further characterized the binding of 5-FU to huDHOase using site-directed mutagenesis and the fluorescence quenching method. Considering the loop-in mode, the dynamic loop in huDHOase should be a suitable drug-targeting site for further designing inhibitors and clinical chemotherapies to suppress pyrimidine biosynthesis in cancer cell lines.
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Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
| | - Yen-Hua Huang
- Department of Beauty Science, National Taichung University of Science and Technology, Taichung City 403, Taiwan
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Po-Chun Yang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
| | - Wei-Feng Peng
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medicine, College of Medicine, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Pediatrics, National Taiwan University Children’s Hospital, Taipei 100, Taiwan
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 402, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung City 402, Taiwan
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5
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Molecular Insights into How the Dimetal Center in Dihydropyrimidinase Can Bind the Thymine Antagonist 5-Aminouracil: A Different Binding Mode from the Anticancer Drug 5-Fluorouracil. Bioinorg Chem Appl 2022; 2022:1817745. [PMID: 35198016 PMCID: PMC8860565 DOI: 10.1155/2022/1817745] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/27/2022] [Indexed: 12/20/2022] Open
Abstract
Dihydropyrimidinase (DHPase) is a key enzyme for pyrimidine degradation. DHPase contains a binuclear metal center in which two Zn ions are bridged by a posttranslationally carbamylated lysine. DHPase catalyzes the hydrolysis of dihydrouracil to N-carbamoyl-β-alanine. Whether 5-aminouracil (5-AU), a thymine antagonist and an anticancer drug that can block DNA synthesis and induce replication stress, can interact with DHPase remains to be investigated. In this study, we determined the crystal structure of Pseudomonas aeruginosa DHPase (PaDHPase) complexed with 5-AU at 2.1 Å resolution (PDB entry 7E3U). This complexed structure revealed that 5-AU interacts with Znα (3.2 Å), Znβ (3.0 Å), the main chains of residues Ser289 (2.8 Å) and Asn337 (3.3 Å), and the side chain of residue Tyr155 (2.8 Å). These residues are also known as the substrate-binding sites of DHPase. Dynamic loop I (amino acid residues Pro65-Val70) in PaDHPase is not involved in the binding of 5-AU. The fluorescence quenching analysis and site-directed mutagenesis were used to confirm the binding mode revealed by the complexed crystal structure. The 5-AU binding mode of PaDHPase is, however, different from that of 5-fluorouracil, the best-known fluoropyrimidine used for anticancer therapy. These results provide molecular insights that may facilitate the development of new inhibitors targeting DHPase and constitute the 5-AU interactome.
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An Evaluation of the Diagnostic Accuracy of a Panel of Variants in DPYD and a Single Variant in ENOSF1 for Predicting Common Capecitabine Related Toxicities. Cancers (Basel) 2021; 13:cancers13071497. [PMID: 33805100 PMCID: PMC8037940 DOI: 10.3390/cancers13071497] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary 5-Fluorouracil (5-FU) is a chemotherapy drug that can cause severe toxicity in some patients. A protein, an action molecule in our cells, called dihydropyrimidine dehydrogenase, or DPD for short, is important in clearing 5-FU from the body. Some people have versions of DPD that do not clear 5-FU very well. This causes active drug to stay in the body too long, causing toxicities such as diarrhoea or low levels of blood cells important for fighting infections. Current guidelines identify four sequence changes in the gene that encodes DPD with high level evidence of an impact on protein activity. Our study aims to calculate the frequency of a set of variants identified in patients with DPD deficiency in patients that were part of a clinical trial called QUASAR 2. We go on to test how well the DPD deficiency variants and a set of common variants previously shown to be associated with 5-FU toxicity can predict a person’s risk of 5-Fluorouracil induced toxicity. Our research is important for working out the best way to identify patients at risk of toxicity so high risk patients can be given lower doses of 5-Fluorouracil or be treated with a different drug all together. Abstract Efficacy of 5-Fluorouracil (5-FU)-based chemotherapy is limited by significant toxicity. Tests based upon variants in the Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines with high level evidence of a link to dihydropyrimidine dehydrogenase (DPD) phenotype and 5-FU toxicity are available to identify patients at high risk of severe adverse events (AEs). We previously reported associations between rs1213215, rs2612091, and NM_000110.3:c.1906-14763G>A (rs12022243) and capecitabine induced toxicity in clinical trial QUASAR 2. We also identified patients with DPD deficiency alleles NM_000110.3: c.1905+1G>A, NM_000110.3: c.2846C>T, NM_000110.3:c.1679T>G and NM_000110.3:c.1651G>A. We have now assessed the frequency of thirteen additional DPYD deficiency variants in 888 patients from the QUASAR 2 clinical trial. We also compared the area under the curve (AUC)—a measure of diagnostic accuracy—of the high-level evidence variants from the CPIC guidelines plus and minus additional DPYD deficiency variants and or common variants associated with 5-FU toxicity. Including additional DPYD deficiency variants retained good diagnostic accuracy for serious adverse events (AEs) and improved sensitivity for predicting grade 4 haematological toxicities (sensitivity 0.75, specificity 0.94) but the improvement in AUC for this toxicity was not significant. Larger datasets will be required to determine the benefit of including additional DPYD deficiency variants not observed here. Genotyping two common alleles statistically significantly improves AUC for prediction of risk of HFS and may be clinically useful (AUC difference 0.177, sensitivity 0.84, specificity 0.31).
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In Vitro Assessment of Fluoropyrimidine-Metabolizing Enzymes: Dihydropyrimidine Dehydrogenase, Dihydropyrimidinase, and β-Ureidopropionase. J Clin Med 2020; 9:jcm9082342. [PMID: 32707991 PMCID: PMC7464968 DOI: 10.3390/jcm9082342] [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: 06/12/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 01/22/2023] Open
Abstract
Fluoropyrimidine drugs (FPs), including 5-fluorouracil, tegafur, capecitabine, and doxifluridine, are among the most widely used anticancer agents in the treatment of solid tumors. However, severe toxicity occurs in approximately 30% of patients following FP administration, emphasizing the importance of predicting the risk of acute toxicity before treatment. Three metabolic enzymes, dihydropyrimidine dehydrogenase (DPD), dihydropyrimidinase (DHP), and β-ureidopropionase (β-UP), degrade FPs; hence, deficiencies in these enzymes, arising from genetic polymorphisms, are involved in severe FP-related toxicity, although the effect of these polymorphisms on in vivo enzymatic activity has not been clarified. Furthermore, the clinical usefulness of current methods for predicting in vivo activity, such as pyrimidine concentrations in blood or urine, is unknown. In vitro tests have been established as advantageous for predicting the in vivo activity of enzyme variants. This is due to several studies that evaluated FP activities after enzyme metabolism using transient expression systems in Escherichia coli or mammalian cells; however, there are no comparative reports of these results. Thus, in this review, we summarized the results of in vitro analyses involving DPD, DHP, and β-UP in an attempt to encourage further comparative studies using these drug types and to aid in the elucidation of their underlying mechanisms.
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A novel stop-gain mutation in DPYS gene causing Dihidropyrimidinase deficiency, a case report. BMC MEDICAL GENETICS 2020; 21:138. [PMID: 32600357 PMCID: PMC7325154 DOI: 10.1186/s12881-020-01070-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 06/16/2020] [Indexed: 11/17/2022]
Abstract
Background Dihidropyrimidinase (DHP) deficiency is an inherited inborn error of pyrimidine metabolism with a variable clinical presentation and even asymptomatic subjects. Dihydropyrimidinase is encoded by the DPYS gene, thus pathogenic mutations in this gene can cause DHP deficiency. To date, several variations in the DPYS gene have been reported but only 23 of them have been confirmed to be pathogenic. Therefore, the biochemical, clinical and genetic aspects of this disease are still unclear. Case presentation Here, we report a 22-year-old woman with DHP deficiency. To identify the genetic cause of DHP deficiency in this patient, Whole Exome Sequencing (WES) was performed, which revealed a novel homozygote stop gain mutation (NM_001385: Exon 9, c.1501 A > T, p.K501X) in the DPYS gene. Sanger sequencing was carried out on proband and other family members in order to confirm the identified mutation. According to the homozygote genotype of the patient and heterozygote genotype of her parents, the autosomal recessive pattern of inheritance was confirmed. In addition, bioinformatics analysis of the identified variant using Mutation Taster and T-Coffee Multiple Sequence Alignment showed the pathogenicity of mutation. Moreover, mRNA expression level of DPYS gene in the proband’s liver biopsy showed about 6-fold reduction compared to control, which strongly suggested the pathogenicity of the identified mutation. Conclusions This study identified a novel pathogenic stop gain mutation in DPYS gene in a DHP deficient patient. Our findings can improve the knowledge about the genetic basis of the disease and also provide information for accurate genetic counseling for the families at risk of these types of disorders.
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Huang CY. Structure, catalytic mechanism, posttranslational lysine carbamylation, and inhibition of dihydropyrimidinases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:63-96. [PMID: 32951816 DOI: 10.1016/bs.apcsb.2020.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dihydropyrimidinase catalyzes the reversible hydrolytic ring opening of dihydrouracil and dihydrothymine to N-carbamoyl-β-alanine and N-carbamyl-β-aminoisobutyrate, respectively. Dihydropyrimidinase from microorganisms is normally known as hydantoinase because of its role as a biocatalyst in the synthesis of d- and l-amino acids for the industrial production of antibiotic precursors and its broad substrate specificity. Dihydropyrimidinase belongs to the cyclic amidohydrolase family, which also includes imidase, allantoinase, and dihydroorotase. Although these metal-dependent enzymes share low levels of amino acid sequence homology, they possess similar active site architectures and may use a similar mechanism for catalysis. By contrast, the five human dihydropyrimidinase-related proteins possess high amino acid sequence identity and are structurally homologous to dihydropyrimidinase, but they are neuronal proteins with no dihydropyrimidinase activity. In this chapter, we summarize and discuss current knowledge and the recent advances on the structure, catalytic mechanism, and inhibition of dihydropyrimidinase.
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Affiliation(s)
- Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung City, Taiwan
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Huang YH, Ning ZJ, Huang CY. Crystal structure of dihydropyrimidinase in complex with anticancer drug 5-fluorouracil. Biochem Biophys Res Commun 2019; 519:160-165. [PMID: 31481233 DOI: 10.1016/j.bbrc.2019.08.153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 12/29/2022]
Abstract
Dihydropyrimidinase (DHPase) catalyzes the reversible cyclization of dihydrouracil to N-carbamoyl-β-alanine in the second step of the pyrimidine degradation pathway. Whether 5-fluorouracil (5-FU), the best-known fluoropyrimidine that is used to target the enzyme thymidylate synthase for anticancer therapy, can bind to DHPase remains unknown. In this study, we found that 5-FU can form a stable complex with Pseudomonas aeruginosa DHPase (PaDHPase). The crystal structure of PaDHPase complexed with 5-FU was determined at 1.76 Å resolution (PDB entry 6KLK). Various interactions between 5-FU and PaDHPase were examined. Six residues, namely, His61, Tyr155, Asp316, Cys318, Ser289 and Asn337, of PaDHPase were involved in 5-FU binding. Except for Cys318, these residues are also known as the substrate-binding sites of DHPase. 5-FU interacts with the main chains of residues Ser289 (3.0 Å) and Asn337 (3.2 Å) and the side chains of residues Tyr155 (2.8 Å) and Cys318 (2.9 Å). Mutation at either Tyr155 or Cys318 of PaDHPase caused a low 5-FU binding activity of PaDHPase. This structure and the binding mode provided molecular insights into how the dimetal center in DHPase undergoes a conformational change during 5-FU binding. Further research can directly focus on revisiting the role of DHPase in anticancer therapy.
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Affiliation(s)
- Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Zhi-Jun Ning
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan.
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Tsuchiya H, Akiyama T, Kuhara T, Nakajima Y, Ohse M, Kurahashi H, Kato T, Maeda Y, Yoshinaga H, Kobayashi K. A case of dihydropyrimidinase deficiency incidentally detected by urine metabolome analysis. Brain Dev 2019; 41:280-284. [PMID: 30384990 DOI: 10.1016/j.braindev.2018.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/29/2018] [Accepted: 10/16/2018] [Indexed: 10/28/2022]
Abstract
Dihydropyrimidinase deficiency is a rare autosomal recessive disease affecting the second step of pyrimidine degradation. It is caused by mutations in the DPYS gene. Only approximately 30 cases have been reported to date, with a phenotypical variability ranging from asymptomatic to severe neurological illness. We report a case of dihydropyrimidinase deficiency incidentally detected by urine metabolome analysis. Gas chromatography-mass spectrometry-based urine metabolomics demonstrated significant elevations of dihydrouracil and dihydrothymine, which were subsequently confirmed by a quantitative analysis using liquid chromatography-tandem mass spectrometry. Genetic testing of the DPYS gene revealed two mutations: a novel mutation (c.175G > T) and a previously reported mutation (c.1469G > A). Dihydropyrimidinase deficiency is probably underdiagnosed, considering its wide phenotypical variability, nonspecific neurological presentations, and an estimated prevalence of 2/20,000. As severe 5-fluorouracil-associated toxicity has been reported in patients and carriers of congenital pyrimidine metabolic disorders, urinary pyrimidine analysis should be considered for those who will undergo 5-fluorouracil treatment.
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Affiliation(s)
- Hiroki Tsuchiya
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan; Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan; Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Tomiko Kuhara
- Japan Clinical Metabolomics Institute, Kahoku, Ishikawa, Japan
| | - Yoko Nakajima
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Morimasa Ohse
- Japan Clinical Metabolomics Institute, Kahoku, Ishikawa, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Yasuhiro Maeda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Harumi Yoshinaga
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan; Department of Child Neurology, NHO Minami-Okayama Medical Center, Okayama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan; Department of Child Neurology, Okayama University Hospital, Okayama, Japan
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Nakajima Y, Meijer J, Dobritzsch D, Ito T, Zhang C, Wang X, Watanabe Y, Tashiro K, Meinsma R, Roelofsen J, Zoetekouw L, van Kuilenburg ABP. Dihydropyrimidinase deficiency in four East Asian patients due to novel and rare DPYS mutations affecting protein structural integrity and catalytic activity. Mol Genet Metab 2017; 122:216-222. [PMID: 29054612 DOI: 10.1016/j.ymgme.2017.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 01/07/2023]
Abstract
Dihydropyrimidinase (DHP) is the second enzyme of the pyrimidine degradation pathway and catalyzes the ring opening of 5,6-dihydrouracil and 5,6-dihydrothymine. To date, only 31 genetically confirmed patients with a DHP deficiency have been reported and the clinical, biochemical and genetic spectrum of DHP deficient patients is, therefore, still largely unknown. Here, we show that 4 newly identified DHP deficient patients presented with strongly elevated levels of 5,6-dihydrouracil and 5,6-dihydrothymine in urine and a highly variable clinical presentation, ranging from asymptomatic to infantile spasm and reduced white matter and brain atrophy. Analysis of the DHP gene (DPYS) showed the presence of 8 variants including 4 novel/rare missense variants and one novel deletion. Functional analysis of recombinantly expressed DHP mutants carrying the p.M250I, p.H295R, p.Q334R, p.T418I and the p.R490H variant showed residual DHP activities of 2.0%, 9.8%, 9.7%, 64% and 0.3%, respectively. The crystal structure of human DHP indicated that all point mutations were likely to cause rearrangements of loops shaping the active site, primarily affecting substrate binding and stability of the enzyme. The observation that the identified mutations were more prevalent in East Asians and the Japanese population indicates that DHP deficiency may be more common than anticipated in these ethnic groups.
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Affiliation(s)
- Yoko Nakajima
- Fujita Health University School of Medicine, Department of Pediatrics, Toyoake 470-1192, Japan; Academic Medical Center, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105, AZ, Amsterdam, The Netherlands
| | - Judith Meijer
- Academic Medical Center, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105, AZ, Amsterdam, The Netherlands
| | - Doreen Dobritzsch
- Uppsala University, Department of Chemistry, Biomedical Center, S-751 24 Uppsala, Sweden
| | - Tetsuya Ito
- Fujita Health University School of Medicine, Department of Pediatrics, Toyoake 470-1192, Japan
| | - Chunhua Zhang
- MILS International, Department of Research and Development, Kanazawa 921-8105, Japan
| | - Xu Wang
- Beijing Children's Hospital, Capital University of Medical Sciences, Department of Neurology, Beijing 100045, China
| | - Yoriko Watanabe
- Kurume University, School of Medicine, Department of Pediatrics, Kurume 830-0011, Japan
| | - Kyoko Tashiro
- Kurume University, School of Medicine, Research Institute of Medical Mass Spectrometry, Kurume 830-0011, Japan
| | - Rutger Meinsma
- Academic Medical Center, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105, AZ, Amsterdam, The Netherlands
| | - Jeroen Roelofsen
- Academic Medical Center, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105, AZ, Amsterdam, The Netherlands
| | - Lida Zoetekouw
- Academic Medical Center, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105, AZ, Amsterdam, The Netherlands
| | - André B P van Kuilenburg
- Academic Medical Center, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105, AZ, Amsterdam, The Netherlands.
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Abstract
Cancer treatment is becoming more and more individually based as a result of the large inter-individual differences that exist in treatment outcome and toxicity when patients are treated using population-based drug doses. Polymorphisms in genes encoding drug-metabolizing enzymes and transporters can significantly influence uptake, metabolism, and elimination of anticancer drugs. As a result, the altered pharmacokinetics can greatly influence drug efficacy and toxicity. Pharmacogenetic screening and/or drug-specific phenotyping of cancer patients eligible for treatment with chemotherapeutic drugs, prior to the start of anticancer treatment, can identify patients with tumors that are likely to be responsive or resistant to the proposed drugs. Similarly, the identification of patients with an increased risk of developing toxicity would allow either dose adaptation or the application of other targeted therapies. This review focuses on the role of genetic polymorphisms significantly altering the pharmacokinetics of anticancer drugs. Polymorphisms in DPYD, TPMT, and UGT1A1 have been described that have a major impact on the pharmacokinetics of 5-fluorouracil, mercaptopurine, and irinotecan, respectively. For other drugs, however, the association of polymorphisms with pharmacokinetics is less clear. To date, the influence of genetic variations on the pharmacokinetics of the increasingly used monoclonal antibodies has hardly been investigated. Some studies indicate that genes encoding the Fcγ-receptor family are of interest, but more research is needed to establish if screening before the start of therapy is beneficial. Considering the profound impact of polymorphisms in drug transporters and drug-metabolizing enzymes on the pharmacokinetics of chemotherapeutic drugs and hence, their toxicity and efficacy, pharmacogenetic and pharmacokinetic profiling should become the standard of care.
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Affiliation(s)
| | | | - André B P van Kuilenburg
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Emma Children's Hospital, F0-220, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
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14
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Kuilenburg ABPV, Meijer J, Tanck MWT, Dobritzsch D, Zoetekouw L, Dekkers LL, Roelofsen J, Meinsma R, Wymenga M, Kulik W, Büchel B, Hennekam RCM, Largiadèr CR. Phenotypic and clinical implications of variants in the dihydropyrimidine dehydrogenase gene. Biochim Biophys Acta Mol Basis Dis 2016; 1862:754-762. [PMID: 26804652 DOI: 10.1016/j.bbadis.2016.01.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/21/2015] [Accepted: 01/08/2016] [Indexed: 12/22/2022]
Abstract
Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in the catabolism of the pyrimidine bases uracil, thymine and the antineoplastic agent 5-fluorouracil. Genetic variations in the gene encoding DPD (DPYD) have emerged as predictive risk alleles for 5FU-associated toxicity. Here we report an in-depth analysis of genetic variants in DPYD and their consequences for DPD activity and pyrimidine metabolites in 100 Dutch healthy volunteers. 34 SNPs were detected in DPYD and 15 SNPs were associated with altered plasma concentrations of pyrimidine metabolites. DPD activity was significantly associated with the plasma concentrations of uracil, the presence of a specific DPYD mutation (c.1905+1G>A) and the combined presence of three risk variants in DPYD (c.1905+1G>A, c.1129-5923C>G, c.2846A>T), but not with an altered uracil/dihydrouracil (U/UH2) ratio. Various haplotypes were associated with different DPD activities (haplotype D3, a decreased DPD activity; haplotype F2, an increased DPD activity). Functional analysis of eight recombinant mutant DPD enzymes showed a reduced DPD activity, ranging from 35% to 84% of the wild-type enzyme. Analysis of a DPD homology model indicated that the structural effect of the novel p.G401R mutation is most likely minor. The clinical relevance of the p.D949V mutation was demonstrated in a cancer patient heterozygous for the c.2846A>T mutation and a novel nonsense mutation c.1681C>T (p.R561X), experiencing severe grade IV toxicity. Our studies showed that the endogenous levels of uracil and the U/UH2 ratio are poor predictors of an impaired DPD activity. Loading studies with uracil to identify patients with a DPD deficiency warrants further investigation.
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Affiliation(s)
- André B P van Kuilenburg
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands.
| | - Judith Meijer
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael W T Tanck
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Doreen Dobritzsch
- Department of Chemistry, Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden
| | - Lida Zoetekouw
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Jeroen Roelofsen
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Rutger Meinsma
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Machteld Wymenga
- Department of Oncology, Medisch Spectrum Twente, Enschede, The Netherlands
| | - Wim Kulik
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Barbara Büchel
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Raoul C M Hennekam
- Departments of Clinical Chemistry, Pediatrics, Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Emma Children's Hospital, University of Amsterdam, Amsterdam, The Netherlands
| | - Carlo R Largiadèr
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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Altered Pre-mRNA Splicing Caused by a Novel Intronic Mutation c.1443+5G>A in the Dihydropyrimidinase (DPYS) Gene. Int J Mol Sci 2016; 17:ijms17010086. [PMID: 26771602 PMCID: PMC4730329 DOI: 10.3390/ijms17010086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/28/2015] [Accepted: 01/04/2016] [Indexed: 11/17/2022] Open
Abstract
Dihydropyrimidinase (DHP) deficiency is an autosomal recessive disease caused by mutations in the DPYS gene. Patients present with highly elevated levels of dihydrouracil and dihydrothymine in their urine, blood and cerebrospinal fluid. The analysis of the effect of mutations in DPYS on pre-mRNA splicing is hampered by the fact that DHP is primarily expressed in liver and kidney cells. The minigene approach can detect mRNA splicing aberrations using cells that do not express the endogenous mRNA. We have used a minigene-based approach to analyze the effects of a presumptive pre-mRNA splicing mutation in two newly identified Chinese pediatric patients with DHP deficiency. Mutation analysis of DPYS showed that both patients were compound heterozygous for a novel intronic mutation c.1443+5G>A in intron 8 and a previously described missense mutation c.1001A>G (p.Q334R) in exon 6. Wild-type and the mutated minigene constructs, containing exons 7, 8 and 9 of DPYS, yielded different splicing products after expression in HEK293 cells. The c.1443+5G>A mutation resulted in altered pre-mRNA splicing of the DPYS minigene construct with full skipping of exon 8. Analysis of the DHP crystal structure showed that the deletion of exon 8 severely affects folding, stability and homooligomerization of the enzyme as well as disruption of the catalytic site. Thus, the analysis suggests that the c.1443+5G>A mutation results in aberrant splicing of the pre-mRNA encoding DHP, underlying the DHP deficiency in two unrelated Chinese patients.
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Kummer D, Froehlich TK, Joerger M, Aebi S, Sistonen J, Amstutz U, Largiadèr CR. Dihydropyrimidinase and β-ureidopropionase gene variation and severe fluoropyrimidine-related toxicity. Pharmacogenomics 2015; 16:1367-77. [DOI: 10.2217/pgs.15.81] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aims: To assess the association of DPYS and UPB1 genetic variation, encoding the catabolic enzymes downstream of dihydropyrimidine dehydrogenase, with early-onset toxicity from fluoropyrimidine-based chemotherapy. Patients & methods: The coding and exon-flanking regions of both genes were sequenced in a discovery subset (164 patients). Candidate variants were genotyped in the full cohort of 514 patients. Results & conclusions: Novel rare deleterious variants in DPYS (c.253C > T and c.1217G > A) were detected once each in toxicity cases and may explain the occurrence of severe toxicity in individual patients, and associations of common variants in DPYS (c.1–1T > C: padjusted = 0.003; OR = 2.53; 95% CI: 1.39–4.62, and c.265–58T > C: padjusted = 0.039; OR = 0.61; 95% CI: 0.38–0.97) with 5-fluorouracil toxicity were replicated.
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Affiliation(s)
- Dominic Kummer
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, & University of Bern, INO-F, CH-3010 Bern, Switzerland
- Graduate School for Cellular & Biomedical Sciences, University of Bern, Freiestrasse 1, CH-3012 Bern, Switzerland
| | - Tanja K Froehlich
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, & University of Bern, INO-F, CH-3010 Bern, Switzerland
| | - Markus Joerger
- Department of Medical Oncology & Hematology, Cantonal Hospital St. Gallen, Rorschacherstrasse 95, CH-9007 St. Gallen, Switzerland
| | - Stefan Aebi
- Division of Medical Oncology, Cantonal Hospital Lucerne, Spitalstrasse, CH-6000 Lucerne 16, Switzerland
| | - Johanna Sistonen
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, & University of Bern, INO-F, CH-3010 Bern, Switzerland
| | - Ursula Amstutz
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, & University of Bern, INO-F, CH-3010 Bern, Switzerland
| | - Carlo R Largiadèr
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, & University of Bern, INO-F, CH-3010 Bern, Switzerland
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Genetic polymorphisms of dihydropyrimidinase in a Japanese patient with capecitabine-induced toxicity. PLoS One 2015; 10:e0124818. [PMID: 25915935 PMCID: PMC4411063 DOI: 10.1371/journal.pone.0124818] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 03/20/2015] [Indexed: 01/12/2023] Open
Abstract
Dihydropyrimidinase (DHP) is the second enzyme in the catabolic pathway of uracil, thymine, and chemotherapeutic fluoropyrimidine agents such as 5-fluorouracil (5-FU). Thus, DHP deficiency might be associated with 5-FU toxicity during fluoropyrimidine chemotherapy. We performed genetic analyses of the family of a patient with advanced colon cancer who underwent radical colectomy followed by treatment with 5-FU prodrug capecitabine and developed severe toxicity attributable to a lack of DHP. We measured urinary uracil and dihydrouracil, and genotyped DPYS in the patient and her family. We also measured the allele frequency of DPYS polymorphisms in 391 unrelated Japanese subjects. The patient had compound heterozygous missense and nonsense polymorphisms comprising c.1001A>G (p.Gln334Arg) in exon 6 and c.1393C>T (p.Arg465Ter) in exon 8, which are known to result in a DHP enzyme with little or no activity. The urinary dihydrouracil/uracil ratio in the patient was 17.08, while the mean ± SD urinary dihydrouracil/uracil ratio in family members who were heterozygous or homozygous for wild-type DPYS was 0.25 ± 0.06. In unrelated subjects, 8 of 391 individuals were heterozygous for the c.1001A>G mutation, while the c.1393C>T mutation was not identified. This is the first report of a DHP-deficient patient with DPYS compound heterozygous polymorphisms who was treated with a fluoropyrimidine, and our findings suggest that polymorphisms in the DPYS gene are pharmacogenomic markers associated with severe 5-FU toxicity in Japanese patients.
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Ni M, Duley J, George R, Charles B, Shannon C, McGeary R, Norris R. Simultaneous determination of thymine and its sequential catabolites dihydrothymine and β-ureidoisobutyrate in human plasma and urine using liquid chromatography–tandem mass spectrometry with pharmacokinetic application. J Pharm Biomed Anal 2013; 78-79:129-35. [DOI: 10.1016/j.jpba.2013.01.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 01/18/2013] [Accepted: 01/19/2013] [Indexed: 11/16/2022]
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van Kuilenburg ABP, Dobritzsch D, Meijer J, Krumpel M, Selim LA, Rashed MS, Assmann B, Meinsma R, Lohkamp B, Ito T, Abeling NGGM, Saito K, Eto K, Smitka M, Engvall M, Zhang C, Xu W, Zoetekouw L, Hennekam RCM. ß-ureidopropionase deficiency: phenotype, genotype and protein structural consequences in 16 patients. Biochim Biophys Acta Mol Basis Dis 2012; 1822:1096-108. [PMID: 22525402 DOI: 10.1016/j.bbadis.2012.04.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 03/29/2012] [Accepted: 04/09/2012] [Indexed: 12/26/2022]
Abstract
ß-ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyzes the conversion of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid to ß-alanine and ß-aminoisobutyric acid, ammonia and CO(2). To date, only five genetically confirmed patients with a complete ß-ureidopropionase deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 11 newly identified ß-ureidopropionase deficient patients as well as the analysis of the mutations in a three-dimensional framework. Patients presented mainly with neurological abnormalities (intellectual disabilities, seizures, abnormal tonus regulation, microcephaly, and malformations on neuro-imaging) and markedly elevated levels of N-carbamyl-ß-alanine and N-carbamyl-ß-aminoisobutyric acid in urine and plasma. Analysis of UPB1, encoding ß-ureidopropionase, showed 6 novel missense mutations and one novel splice-site mutation. Heterologous expression of the 6 mutant enzymes in Escherichia coli showed that all mutations yielded mutant ß-ureidopropionase proteins with significantly decreased activity. Analysis of a homology model of human ß-ureidopropionase generated using the crystal structure of the enzyme from Drosophila melanogaster indicated that the point mutations p.G235R, p.R236W and p.S264R lead to amino acid exchanges in the active site and therefore affect substrate binding and catalysis. The mutations L13S, R326Q and T359M resulted most likely in folding defects and oligomer assembly impairment. Two mutations were identified in several unrelated ß-ureidopropionase patients, indicating that ß-ureidopropionase deficiency may be more common than anticipated.
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Affiliation(s)
- André B P van Kuilenburg
- Academic Medical Center, Emma Children's Hospital, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, 1105 AZ Amsterdam, The Netherlands.
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Dihydropyrimidinase deficiency: the first feline case of dihydropyrimidinuria with clinical and molecular findings. JIMD Rep 2012; 6:21-6. [PMID: 23430934 DOI: 10.1007/8904_2012_139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/28/2012] [Accepted: 03/01/2012] [Indexed: 05/13/2023] Open
Abstract
Dihydropyrimidinase (DHP, EC 3.5.2.2) is the second enzyme of the pyrimidine degradation pathway and a deficiency of this enzyme is responsible for a rare inborn metabolic syndrome characterized by dihydropyrimidinuria. Here we report a cat with DHP deficiency, manifesting malnutrition, depression, vomiting, and hyperammonemia. A gas chromatographic-mass spectrometric analysis of urinary metabolic substances showed the presence of large amounts of dihydrouracil and dihydrothymine and moderate amounts of uracil and thymine, suggesting DHP deficiency. Analysis of the feline DPYS gene encoding DHP demonstrated that the cat was homozygous for the missense mutation c.1303G>A (p.G435R) in exon 8, which corresponds to a known mutation in a human patient with DHP deficiency. Population screening in 1,000 cats did not reveal any animal possessing this mutation, suggesting the prevalence of the mutant allele to be very low. This is the first report of naturally occurring DHP deficiency in animals and the cat represents a model of the human disease.
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Otsubo Y, Asahina Y, Noguchi A, Sato Y, Ando Y, Uyama Y. Similarities and differences between US and Japan as to pharmacogenomic biomarker information in drug labels. Drug Metab Pharmacokinet 2011; 27:142-9. [PMID: 22201121 DOI: 10.2133/dmpk.dmpk-11-rv-082] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pharmacogenomics (PGx) has been utilized as a tool to improve a drug's benefit/risk ratio and the efficiency of drug developments. In order to examine what factors are involved to determine the level of contexts (contents and descriptions) of drug-PGx biomarker information, we graded sections of Japanese package inserts and US drug labels into six levels according to the importance of cautions in regards to clinical practice and compared similarities and differences of the contexts between the two countries. Out of 54 contexts identified, 33 (61%) were graded differently between Japan and the US. The different contexts were mainly related to metabolizing enzymes used in terms of safety, therapeutic areas other than oncology, outcome before 1993, Japan-based companies having marketing authorization and no PGx data on the Japanese population. We describe the potential reasons that could lead to the differences between the two countries such as genetic differences and quantitative evidence in the Japanese population, and also discuss future perspectives to improve PGx utilization in clinical practices in Japan.
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Affiliation(s)
- Yasuto Otsubo
- Office of New Drug II, Pharmaceuticals and Medical Devices Agency (PMDA), Tokyo, Japan
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Horinouchi H, Sekine I. [The cutting-edge of medicine; Ethnic and gender differences in lung cancer]. NIHON NAIKA GAKKAI ZASSHI. THE JOURNAL OF THE JAPANESE SOCIETY OF INTERNAL MEDICINE 2011; 100:3064-3071. [PMID: 22175154 DOI: 10.2169/naika.100.3064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Hidehito Horinouchi
- Division of Internal Medicine and Thoracic Oncology, National Cancer Center Hospital, Japan
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Muhale FA, Wetmore BA, Thomas RS, McLeod HL. Systems pharmacology assessment of the 5-fluorouracil pathway. Pharmacogenomics 2011; 12:341-50. [PMID: 21449674 DOI: 10.2217/pgs.10.188] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AIM To assess the impact of the 5-fluorouracil (5-FU) drug-pathway genes on cytotoxicity, and determine whether loss-of-function analyses coupled with functional assays can help prioritize pharmacogenomic candidate genes. MATERIALS & METHODS Dose-response experiments were used to quantify the phenotype of sensitivity to 5-FU following the specific knockdown of genes selected from the 5-FU PharmGKB drug pathway in three human colorectal cell lines. Changes in sensitivity were considered significant if the IC(50) for shRNA-exposed cells were three standard deviations outside the mean IC(50) for control-treated cells. RESULTS Of the 24 genes analyzed, 13 produced significant changes on the phenotype of sensitivity to 5-FU (DHFR, DPYS, DTYMK, DUT, FPGS, GGH, NME1, NT5C, RRM1, TYMS, UCK2, UNG and UMPS). CONCLUSION The RNAi screening strategy enabled prioritization of the genes from the 5-FU drug pathway. Further validation of the genes credentialed in this study should include gene activity or expression and mutation analyses of clinical samples.
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Affiliation(s)
- Filipe A Muhale
- UNC Institute for Pharmacogenomics & Individualized Therapy, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599-7361, USA
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Dihydropyrimidinase deficiency: Phenotype, genotype and structural consequences in 17 patients. Biochim Biophys Acta Mol Basis Dis 2010; 1802:639-48. [PMID: 20362666 DOI: 10.1016/j.bbadis.2010.03.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 03/09/2010] [Accepted: 03/26/2010] [Indexed: 01/15/2023]
Abstract
Dihydropyrimidinase (DHP) is the second enzyme of the pyrimidine degradation pathway and catalyses the ring opening of 5,6-dihydrouracil and 5,6-dihydrothymine. To date, only 11 individuals have been reported suffering from a complete DHP deficiency. Here, we report on the clinical, biochemical and molecular findings of 17 newly identified DHP deficient patients as well as the analysis of the mutations in a three-dimensional framework. Patients presented mainly with neurological and gastrointestinal abnormalities and markedly elevated levels of 5,6-dihydrouracil and 5,6-dihydrothymine in plasma, cerebrospinal fluid and urine. Analysis of DPYS, encoding DHP, showed nine missense mutations, two nonsense mutations, two deletions and one splice-site mutation. Seventy-one percent of the mutations were located at exons 5-8, representing 41% of the coding sequence. Heterologous expression of 11 mutant enzymes in Escherichia coli showed that all but two missense mutations yielded mutant DHP proteins without significant activity. Only DHP enzymes containing the mutations p.R302Q and p.T343A possessed a residual activity of 3.9% and 49%, respectively. The crystal structure of human DHP indicated that the point mutations p.R490C, p.R302Q and p.V364M affect the oligomerization of the enzyme. In contrast, p.M70T, p.D81G, p.L337P and p.T343A affect regions near the di-zinc centre and the substrate binding site. The p.S379R and p.L7V mutations were likely to cause structural destabilization and protein misfolding. Four mutations were identified in multiple unrelated DHP patients, indicating that DHP deficiency may be more common than anticipated.
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Martínez-Rodríguez S, Martínez-Gómez AI, Clemente-Jiménez JM, Rodríguez-Vico F, García-Ruíz JM, Las Heras-Vázquez FJ, Gavira JA. Structure of dihydropyrimidinase from Sinorhizobium meliloti CECT4114: New features in an amidohydrolase family member. J Struct Biol 2010; 169:200-8. [DOI: 10.1016/j.jsb.2009.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 10/01/2009] [Accepted: 10/24/2009] [Indexed: 11/29/2022]
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Contribution of dihydropyrimidinase gene alterations to the development of serious toxicity in fluoropyrimidine-treated cancer patients. Cancer Chemother Pharmacol 2009; 65:661-9. [DOI: 10.1007/s00280-009-1071-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/07/2009] [Indexed: 01/22/2023]
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Kuhara T, Ohse M, Inoue Y, Shinka T. Five cases of beta-ureidopropionase deficiency detected by GC/MS analysis of urine metabolome. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:214-221. [PMID: 18853477 DOI: 10.1002/jms.1500] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The clinical presentation of inborn errors of pyrimidine degradation varies considerably from asymptomatic to severe neurological illness. We have reported a method to screen for and make a chemical diagnosis of beta-ureidopropionase deficiency, leading to the discovery of the first asymptomatic case of this disease. In this method, the recovery of beta-ureidopropionate and beta-ureidoisobutyrate, the key biomarkers, was very high,and the adoption of GC/MS and targeted analysis enabled us to simultaneously obtain information related and unrelated to pyrimidine metabolism. The present study reports the results of a large-scale screening of 24,000 newborns using dried urine on filter paper. Identification of a total of four asymptomatic patients among newborns suggests the high incidence (1/6000) of this disease in Japan. While these newborns were asymptomatic, two additional cases detected at the age of 5 years as well as 3 months with this method for high-risk screening had autism and West syndrome, respectively.The key biomarkers and alpha-ureidobutyrate used as an internal standard were found to give not only their di-trimethylsilyl derivatives but also tri-trimethylsilyl derivatives, upon derivatization. The mass spectra and retention times of their tri-trimethylsilyl derivatives and data handling for quantification of the markers are presented.Identification of individuals with defects in pyrimidine metabolism would realize personalized medication in cancer chemotherapy with pyrimidine analogs such as 5-fluorouracil.
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Affiliation(s)
- T Kuhara
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku-gun, Ishikawa 920-0293, Japan.
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van Kuilenburg ABP, Stroomer AEM, Bosch AM, Duran M. Beta-alanine and beta-aminoisobutyric acid levels in two siblings with dihydropyrimidinase deficiency. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 27:825-9. [PMID: 18600547 DOI: 10.1080/15257770802146445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Dihydropyrimidinase (DHP) deficiency is an inborn error of the pyrimidine degradation pathway, affecting the hydrolytic ring opening of the dihydropyrimidines. In two siblings with a complete DHP deficiency and a variable clinical presentation, a normal concentration of beta-alanine and strongly decreased levels of beta-aminoisobutyric acid were observed in plasma, urine and CSF. No major differences were observed for the concentrations of the beta-amino acids in plasma and urine between the symptomatic and asymptomatic sibling. Thus, the relevance of the shortage of beta-aminoisobutyric acid for the onset of a clinical phenotype in patients with DHP deficiency remains to be established.
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Affiliation(s)
- A B P van Kuilenburg
- Academic Medical Center, Department of Clinical Chemistry, University of Amsterdam, Amsterdam, The Netherlands.
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Genetic regulation of beta-ureidopropionase and its possible implication in altered uracil catabolism. Pharmacogenet Genomics 2008; 18:25-35. [PMID: 18216719 DOI: 10.1097/fpc.0b013e3282f2f134] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVE Approximately 30-40% of grade III-IV toxicity to 5-FU has been associated with partial or profound deficiency in dihydropyrimidine dehydrogenase (DPD), the first of three enzymes in the catabolic pathway of fluoropyrimidines. There remains, however, a subset of patients presenting with 5-FU-associated toxicity despite normal DPD activity, suggesting possible deficiencies in enzymes downstream of DPD: dihydropyrimidinase (DHP), encoded by the DPYS gene, and/or beta-ureidopropionase (BUP-1), encoded by the UPB1 gene. Previously, we reported the identification of inactivating mutations in the DPYS gene that could potentially alter the uracil catabolic pathway in healthy individuals with normal DPD enzyme activity. This study investigates the possible role of UPB1 genetic variations in the regulation of the uracil catabolic pathway in individuals presenting with a deficient uracil breath test (13C-UraBT) despite normal DPD enzyme activity. METHODS This study included 219 healthy asymptomatic volunteers with known DPD enzyme activity and [2-(13)C]-uracil breath test (UraBT). All samples were genotyped for sequence variations in the UPB1 gene using denaturing high performance liquid chromatography (DHPLC) and Surveyor enzyme digestion with confirmation of detected sequence variants by direct sequencing. RESULTS Seven novel and six previously reported sequence variations were identified, including one nonconservative mutation, which demonstrated 97.3% reduction in BUP-1 activity when expressed in the RKO cell line. CONCLUSION Data presented in this study demonstrate that alterations of uracil catabolism are not limited to DPD and/or DHP deficiency and that inactivating mutations in the UPB1 gene might impair uracil catabolism.
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Schnackerz KD, Dobritzsch D. Amidohydrolases of the reductive pyrimidine catabolic pathway purification, characterization, structure, reaction mechanisms and enzyme deficiency. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:431-44. [PMID: 18261476 DOI: 10.1016/j.bbapap.2008.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 01/07/2008] [Accepted: 01/09/2008] [Indexed: 12/26/2022]
Abstract
In the reductive pyrimidine catabolic pathway uracil and thymine are converted to beta-alanine and beta-aminoisobutyrate. The amidohydrolases of this pathway are responsible for both the ring opening of dihydrouracil and dihydrothymine (dihydropyrimidine amidohydrolase) and the hydrolysis of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyrate (beta-alanine synthase). The review summarizes what is known about the properties, kinetic parameters, three-dimensional structures and reaction mechanisms of these proteins. The two amidohydrolases of the reductive pyrimidine catabolic pathway have unrelated folds, with dihydropyrimidine amidohydrolase belonging to the amidohydrolase superfamily while the beta-alanine synthase from higher eukaryotes belongs to the nitrilase superfamily. beta-Alanine synthase from Saccharomyces kluyveri is an exception to the rule and belongs to the Acyl/M20 family.
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Genetic regulation of dihydropyrimidinase and its possible implication in altered uracil catabolism. Pharmacogenet Genomics 2007; 17:973-87. [DOI: 10.1097/fpc.0b013e3282f01788] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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van Kuilenburg ABP, Meijer J, Dobritzsch D, Meinsma R, Duran M, Lohkamp B, Zoetekouw L, Abeling NGGM, van Tinteren HLG, Bosch AM. Clinical, biochemical and genetic findings in two siblings with a dihydropyrimidinase deficiency. Mol Genet Metab 2007; 91:157-64. [PMID: 17383919 DOI: 10.1016/j.ymgme.2007.02.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/09/2007] [Accepted: 02/09/2007] [Indexed: 10/23/2022]
Abstract
Dihydropyrimidinase (DHP) is the second enzyme of the pyrimidine degradation pathway and it catalyses the ring opening of 5,6-dihydrouracil and 5,6-dihydrothymine to N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid, respectively. To date, only nine individuals have been reported suffering from a complete DHP deficiency. We report two siblings presenting with strongly elevated levels of 5,6-dihydrouracil and 5,6-dihydrothymine in plasma, cerebrospinal fluid and urine. One of the siblings had a severe delay in speech development and white matter abnormalities, whereas the other one was free of symptoms. Analysis of the DHP gene (DPYS) showed that both patients were compound heterozygous for the missense mutation 1078T>C (W360R) in exon 6 and a novel missense mutation 1235G>T (R412M) in exon 7. Heterologous expression of the mutant enzymes in Escherichia coli showed that both missense mutations resulted in a mutant DHP enzyme without residual activity. Analysis of the crystal structure of eukaryotic DHP from the yeast Saccharomyces kluyveri and the slime mold Dictyostelium discoideum suggests that the W360R and R412M mutations lead to structural instability of the enzyme which could potentially impair the assembly of the tetramer.
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Affiliation(s)
- André B P van Kuilenburg
- Academic Medical Center, University of Amsterdam, Emma Children's Hospital, P.O. Box 22700, 1100 DE Amsterdam, The Netherlands.
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Sparidans RW, Bosch TM, Jörger M, Schellens JHM, Beijnen JH. Liquid chromatography–tandem mass spectrometric assay for the analysis of uracil, 5,6-dihydrouracil and β-ureidopropionic acid in urine for the measurement of the activities of the pyrimidine catabolic enzymes. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 839:45-53. [PMID: 16513432 DOI: 10.1016/j.jchromb.2006.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2005] [Revised: 02/07/2006] [Accepted: 02/11/2006] [Indexed: 11/15/2022]
Abstract
A liquid chromatography-tandem mass spectrometric assay for the determination of uracil, 5,6-dihydrouracil and beta-ureidopropionic acid in urine was developed to measure the activities of enzymes involved in pyrimidine breakdown. The assay was required to investigate the relation between the uracil-dihydrouracil ratio and toxicities observed after treatment with fluoropyrimidines drugs. After addition of stable isotopically labelled internal standards, the analytes were isolated from a 100-microl urine sample using liquid-liquid extraction with ethyl acetate-2-propanol. Compounds were separated on an Atlantis dC18 column, using ammonium acetate-formic acid in water as the eluent. The eluate was totally led into an electrospray interface with positive ionisation and the analytes were quantified using triple quadrupole mass spectrometry. The assay was validated in the range 1.6-1600 microM, using both, artificial urine and pooled urine as matrices. Intra-day precisions were < or = 8% and inter-day precisions were < or = 10%. Accuracies between 91 and 108% were found. The analytes were chemically stable under all relevant conditions and the assay was successfully applied in two clinical studies of cancer patients treated with 5-fluorouracil or capecitabine.
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Affiliation(s)
- Rolf W Sparidans
- Utrecht University, Faculty of Science, Department of Pharmaceutical Sciences, Section of Biomedical Analysis, Division of Drug Toxicology, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
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Ito S, Kawamura T, Inada M, Inoue Y, Hirao Y, Koga T, Kunizaki JI, Shimizu T, Sato H. Physiologically based pharmacokinetic modelling of the three-step metabolism of pyrimidine using C-uracil as an in vivo probe. Br J Clin Pharmacol 2006; 60:584-93. [PMID: 16305582 PMCID: PMC1884889 DOI: 10.1111/j.1365-2125.2005.02472.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
AIMS Approximately 80% of uracil is excreted as beta-alanine, ammonia and CO2 via three sequential reactions. The activity of the first enzyme in this scheme, dihydropyrimidine dehydrogenase (DPD), is reported to be the key determinant of the cytotoxicity and side-effects of 5-fluorouracil. The aim of the present study was to re-evaluate the pharmacokinetics of uracil and its metabolites using a sensitive assay and based on a newly developed, physiologically based pharmacokinetic (PBPK) model. METHODS [2-(13)C]Uracil was orally administrated to 12 healthy males at escalating doses of 50, 100 and 200 mg, and the concentrations of [2-(13)C]uracil, [2-(13)C]5,6-dihydrouracil and beta-ureidopropionic acid (ureido-(13)C) in plasma and urine and (13)CO2 in breath were measured by liquid chromatography-tandem mass spectrometry and gas chromatograph-isotope ratio mass spectrometry, respectively. RESULTS The pharmacokinetics of [2-(13)C]uracil were nonlinear. The elimination half-life of [2-(13)C]5,6-dihydrouracil was 0.9-1.4 h, whereas that of [2-(13)C]uracil was 0.2-0.3 h. The AUC of [2-(13)C]5,6-dihydrouracil was 1.9-3.1 times greater than that of [2-(13)C]uracil, whereas that of ureido-(13)C was 0.13-0.23 times smaller. The pharmacokinetics of (13)CO2 in expired air were linear and the recovery of (13)CO2 was approximately 80% of the dose. The renal clearance of [2-(13)C]uracil was negligible. CONCLUSION A PBPK model to describe (13)CO2 exhalation after orally administered [2-(13)C]uracil was successfully developed. Using [2-(13)C]uracil as a probe, this model could be useful in identifying DPD-deficient patients at risk of 5-fluorouracil toxicity.
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Affiliation(s)
- Suminobu Ito
- Department of Clinical Pharmacology, Juntendo University School of MedicineTokyo
| | | | | | - Yoshiharu Inoue
- Formulation Research Institute, Otsuka Pharmaceutical Co., LtdTokushima
| | - Yukihiro Hirao
- Department of Drug Metabolism, Drug Safety Research Centre, Tokushima Research Institute, Otsuka Pharmaceutical Co., LtdTokushima
| | - Toshihisa Koga
- Department of Drug Metabolism, Drug Safety Research Centre, Tokushima Research Institute, Otsuka Pharmaceutical Co., LtdTokushima
| | | | | | - Hitoshi Sato
- Department of Clinical and Molecular Pharmacokinetics/Pharmacodynamics, School of Pharmaceutical Sciences, Showa UniversityTokyo, Japan
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Lohkamp B, Andersen B, Piškur J, Dobritzsch D. The crystal structures of dihydropyrimidinases reaffirm the close relationship between cyclic amidohydrolases and explain their substrate specificity. J Biol Chem 2006; 281:13762-13776. [PMID: 16517602 DOI: 10.1074/jbc.m513266200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, dihydropyrimidinase catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Here we describe the three-dimensional structures of dihydropyrimidinase from two eukaryotes, the yeast Saccharomyces kluyveri and the slime mold Dictyostelium discoideum, determined and refined to 2.4 and 2.05 angstroms, respectively. Both enzymes have a (beta/alpha)8-barrel structural core embedding the catalytic di-zinc center, which is accompanied by a smaller beta-sandwich domain. Despite loop-forming insertions in the sequence of the yeast enzyme, the overall structures and architectures of the active sites of the dihydropyrimidinases are strikingly similar to each other, as well as to those of hydantoinases, dihydroorotases, and other members of the amidohydrolase superfamily of enzymes. However, formation of the physiologically relevant tetramer shows subtle but nonetheless significant differences. The extension of one of the sheets of the beta-sandwich domain across a subunit-subunit interface in yeast dihydropyrimidinase underlines its closer evolutionary relationship to hydantoinases, whereas the slime mold enzyme shows higher similarity to the noncatalytic collapsin-response mediator proteins involved in neuron development. Catalysis is expected to follow a dihydroorotase-like mechanism but in the opposite direction and with a different substrate. Complexes with dihydrouracil and N-carbamyl-beta-alanine obtained for the yeast dihydropyrimidinase reveal the mode of substrate and product binding and allow conclusions about what determines substrate specificity, stereoselectivity, and the reaction direction among cyclic amidohydrolases.
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Affiliation(s)
- Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Birgit Andersen
- Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden
| | - Jure Piškur
- Department of Cell and Organism Biology, Lund University, SE-22362 Lund, Sweden
| | - Doreen Dobritzsch
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, Sweden.
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van Kuilenburg ABP, Meinsma R, van Gennip AH. Pyrimidine Degradation Defects and Severe 5‐Fluorouracil Toxicity. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2004; 23:1371-5. [PMID: 15571261 DOI: 10.1081/ncn-200027624] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
5-Fluorouracil (5FU) remains one of the most frequently prescribed chemotherapeutic drugs for the treatment of cancer. Recently, the pivotal role of the catabolic pathway of 5FU in the determination of toxicity towards 5FU has been highlighted. Patients with a (partial) dihydropyrimidine dehydrogenase deficiency proved to be at risk of developing severe toxicity after the administration of 5FU. A partial dihydropyrimidinase deficiency proved to be a novel pharmacogenetic disorder associated with severe 5FU toxicity.
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Affiliation(s)
- A B P van Kuilenburg
- Academic Medical Center, University of Amsterdam, Emma Children's Hospital and Department of Clinical Chemistry, Amsterdam, The Netherlands
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Mattison LK, Ezzeldin H, Carpenter M, Modak A, Johnson MR, Diasio RB. Rapid identification of dihydropyrimidine dehydrogenase deficiency by using a novel 2-13C-uracil breath test. Clin Cancer Res 2004; 10:2652-8. [PMID: 15102667 DOI: 10.1158/1078-0432.ccr-03-0374] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Dihydropyrimidine dehydrogenase (DPD)-deficient cancer patients have been shown to develop severe toxicity after administration of 5-fluorouracil. Routine determination of DPD activity is limited by time-consuming and labor-intensive methods. The purpose of this study was to develop a simple and rapid 2-(13)C-uracil breath test, which could be applied in most clinical settings to detect DPD-deficient cancer patients. EXPERIMENTAL DESIGN Fifty-eight individuals (50 "normal," 7 partially, and 1 profoundly DPD-deficient) ingested an aqueous solution of 2-(13)C-uracil (6 mg/kg). (13)CO(2) levels were determined in exhaled breath at various time intervals up to 180 min using IR spectroscopy (UBiT-IR(300)). DPD enzyme activity and DPYD genotype were determined by radioassay and denaturing high-performance liquid chromatography, respectively. RESULTS The mean (+/-SE) C(max), T(max), delta over baseline values at 50 min (DOB(50)) and cumulative percentage of (13)C dose recovered (PDR) for normal, partially, and profoundly DPD-deficient individuals were 186.4 +/- 3.9, 117.1 +/- 9.8, and 3.6 DOB; 52 +/- 2, 100 +/- 18.4, and 120 min; 174.1 +/- 4.6, 89.6 +/- 11.6, and 0.9 DOB(50); and 53.8 +/- 1.0, 36.9 +/- 2.4, and <1 PDR, respectively. The differences between the normal and DPD-deficient individuals were highly significant (all Ps <0.001). CONCLUSIONS We demonstrated statistically significant differences in the 2-(13)C-uracil breath test indices (C(max), T(max), DOB(50), and PDR) among healthy and DPD-deficient individuals. These data suggest that a single time-point determination (50 min) could rapidly identify DPD-deficient individuals with a less costly and time-consuming method that is applicable for most hospitals or physicians' offices.
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Affiliation(s)
- Lori K Mattison
- University of Alabama at Birmingham, Division of Clinical Pharmacology and Toxicology, 35294, USA
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Abstract
Germline variants can be used to study breast cancer susceptibility as well as the variable response to both drug and radiation therapy used in the treatment of breast cancer. In addition to germline high-penetrance mutations important in familial and hereditary breast cancer, a substantial component of breast cancer risk can be attributed to the combined effect of many low-risk germline polymorphisms involved in relevant pathways like those of DNA repair, adhesion, carcinogen and estrogen metabolism. Additionally, the identification of sequence variants in genes involved in response to chemotherapy and radiation treatment, has created the opportunity to apply genomics to individualized treatment. The continued insight into the molecular pathways involved in drug and radiation response has enabled progress in tailoring therapies in such a way as to both maximize efficacy and minimize toxicity. Polymorphisms in genes encoding drug-metabolizing enzymes, drug transporters and drug targets can be used to predict toxicity and response to pharmacologic agents used in breast cancer treatment. Similarly, germline variants in genes involved in DNA repair, radiation-induced fibrosis and reactive oxygen species may be used to predict response to radiation therapy. As a result, pharmacogenomics is rapidly evolving to affect the entire spectrum of breast cancer management, influencing both prevention and treatment choices.
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Affiliation(s)
- Stella C Lymberis
- Department of Radiation Oncology and NYU Cancer Institute, New York University School of Medicine, New York, NY, USA
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40
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van Kuilenburg ABP, van Lenthe H, van Cruchten A, Kulik W. Quantification of 5,6-dihydrouracil by HPLC-electrospray tandem mass spectrometry. Clin Chem 2004; 50:236-8. [PMID: 14709662 DOI: 10.1373/clinchem.2003.026229] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- André B P van Kuilenburg
- Academic Medical Center, University of Amsterdam, Emma Children's Hospital and Department of Clinical Chemistry, PO Box 22700, 1100 DE Amsterdam, The Netherlands.
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41
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Kuhara T. Diagnosis and monitoring of inborn errors of metabolism using urease-pretreatment of urine, isotope dilution, and gas chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 781:497-517. [PMID: 12450676 DOI: 10.1016/s1570-0232(02)00670-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
To diagnose inborn errors of metabolism, it would be desirable to simultaneously analyze and quantify organic acids, purines, pyrimidines, amino acids, sugars, polyols, and other compounds using a single-step fractionation; unfortunately, no such method currently exists. The present article will be concerned primarily with a practical yet comprehensive diagnostic procedure of inborn errors of metabolism (IEM). This procedure involves the use of urine or eluates from urine on filter paper, stable isotope dilution, and gas chromatography-mass spectrometry (GC-MS). This procedure not only offers reliable and quantitative evidence for diagnosing, understanding and monitoring the diseases, but also provides evidence for the diagnosis of new kinds of IEM. In this review, the differential diagnosis for hyperammonemia are described; deficiencies of ornithine carbamoyl transferase, argininosuccinate synthase (citrullinemia), argininosuccinate lyase and arginase, lysinuric protein intolerance, hyperammonemia-hyperornithinemia-homocitrullinemia syndrome, and citrullinemia type II. The diagnosis of IEM of purine and pyrimidine such as deficiencies of hypoxanthine-guanine phosphoribosyl transferase, adenine phosphoribosyl transferase, dihydropyrimidine dehydrogenase, dihydropyrimidinase and beta-ureidopropionase are described. During the pilot study for newborn screening, we found neonates with diseases at a rate of 1 per 1,400 including propionic acidemia, methylmalonic acidemia, orotic aciduria, beta-ureidopropionase deficiency, lactic aciduria and neuroblastoma. A rapid and reliable prenatal diagnosis for propionic acidemia is also described.
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Affiliation(s)
- Tomiko Kuhara
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa 920-0293, Japan.
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Ohse M, Matsuo M, Ishida A, Kuhara T. Screening and diagnosis of beta-ureidopropionase deficiency by gas chromatographic/mass spectrometric analysis of urine. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:954-962. [PMID: 12271438 DOI: 10.1002/jms.354] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Dihydropyrimidine dehydrogenase (DHPDase), dihydropyrimidinase (DHPase) and beta-ureidopropionase (betaUPase) are the enzymes that catalyze the first, second, and third steps of the degradation of pyrimidines, respectively. beta-Ureidopropionate (betaUP) and beta-ureidoisobutyrate (betaUIB) are increased in the urine of patients with betaUPase deficiency. The original case in which betaUPase deficiency was discovered by NMR spectroscopy was an 11-month-old patient who presented with hypotonia and dystonic movement. We detected a second but asymptomatic case during a pilot study of neonatal screening with filter-paper urine, urease pretreatment and gas chromatography/mass spectrometry (GC/MS). The urease pretreatment of urine without fractionation resulted in a high recovery of these polar ureide compounds and allowed the highly sensitive GC/MS detection and diagnosis of betaUPase deficiency. betaUP and betaUIB were identified using GC/MS techniques. In the urine of the neonate with betaUPase deficiency, betaUP and betaUIB were persistently increased. Thymine, 5,6-dihydrothymine and 5,6-dihydrouracil were increased only moderately but significantly. It is known that thymine and uracil increase markedly in DHPDase deficiency, and 5,6-dihydrothymine and 5,6-dihydrouracil increase in DHPase deficiency. Therefore, betaUPase deficiency can be differentially diagnosed from the first and second enzyme deficiencies. Application of this specific and sensitive diagnostic procedure will lead to an understanding of the clinical heterogeneity of betaUPase deficiency. Furthermore, the identification of patients with defects in pyrimidine metabolism will enable doctors to avoid cancer chemotherapy with pyrimidine analogues such as 5-fluorouracil, which could be dangerous for these patients.
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Affiliation(s)
- Morimasa Ohse
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, 1-1 Daigaku, Uchinada-machi, Kahoku-gun, Ishikawa 920-0293, Japan
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Van Gennip AH, Van Lenthe H, Ito T, Bootsma AH, Van Cruchten AC, Wada Y, Van Kuilenburg AB. HPLC/ESI tandem-MS of liquid urine or urine soaked filter-paper strips for the detection of thymine-uraciluria and dihydropyrimidinuria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2002; 486:377-82. [PMID: 11783519 DOI: 10.1007/0-306-46843-3_72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- A H Van Gennip
- Academic Medical Center, University of Amsterdam, Emma Children's Hospital, The Netherlands
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Kuhara T. Diagnosis of inborn errors of metabolism using filter paper urine, urease treatment, isotope dilution and gas chromatography-mass spectrometry. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 758:3-25. [PMID: 11482733 DOI: 10.1016/s0378-4347(01)00138-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review will be concerned primarily with a practical yet comprehensive diagnostic procedure for the diagnosis or even mass screening of a variety of metabolic disorders. This rapid, highly sensitive procedure offers possibilities for clinical chemistry laboratories to extend their diagnostic capacity to new areas of metabolic disorders. The diagnostic procedure consists of the use of urine or filter paper urine, preincubation of urine with urease, stable isotope dilution, and gas chromatography-mass spectrometry. Sample preparation from urine or filter paper urine, creatinine determination, stable isotope-labeled compounds used, and GC-MS measurement conditions are described. Not only organic acids or polar ones but also amino acids, sugars, polyols, purines, pyrimidines and other compounds are simultaneously analyzed and quantified. In this review, a pilot study for screening of 22 target diseases in newborns we are conducting in Japan is described. A neonate with presymptomatic propionic acidemia was detected among 10,000 neonates in the pilot study. The metabolic profiles of patients with ornithine carbamoyl transferase deficiency, fructose-1,6-bisphosphatase deficiency or succinic semialdehyde dehydrogenase deficiency obtained by this method are presented as examples. They were compared to those obtained by the conventional solvent extraction methods or by the tandem mass spectrometric method currently done with dried filter blood spots. The highly sensitive, specific and comprehensive features of our procedure are also demonstrated by its use in establishing the chemical diagnosis of pyrimidine degradation defects in order to prevent side effects of pyrimidine analogs such as 5-flurouracil, and the differential diagnosis of three types of homocystinuria, orotic aciduria, uraciluria and other urea cycle disorders. Evaluation of the effects of liver transplantation or nutritional conditions such as folate deficiency in patients with inborn errors of metabolism is also described.
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Affiliation(s)
- T Kuhara
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan.
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45
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Kuhara T, Ohdoi C, Ohse M. Simple gas chromatographic-mass spectrometric procedure for diagnosing pyrimidine degradation defects for prevention of severe anticancer side effects. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2001; 758:61-74. [PMID: 11482736 DOI: 10.1016/s0378-4347(01)00143-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Inborn errors of pyrimidine degradation, dihydropyrimidine dehydrogenase deficiency and dihydropyrimidinase deficiency, are less rare than has generally been assumed. Many asymptomatic cases have been reported, and in patients with symptoms, the clinical abnormalities are variable and nonspecific. Withdrawal of pyrimidine analogues such as 5-fluorouracil (5FU), a commonly used anticancer drug, from the cancer chemotherapy regimens of patients with pyrimidine degradation deficiencies, however, is critical because 5FU is degraded in vivo by pyrimidine-degradative enzymes. Patients with these deficiencies suffer from severe neurotoxicity, sometimes leading to death, following administration of 5FU, and even otherwise asymptomatic homozygotes or heterozygotes may develop severe clinical symptoms upon administration of such medication. Therefore, a rapid and specific method for identifying cancer patients with these enzyme deficiencies prior to treatment with 5FU is critical. To address this problem, we established methods for highly sensitive yet specific determinations of thymine, uracil, dihydrothymine, dihydrouracil, orotate and creatinine simultaneously in 0.1-ml liquid urine or filter-paper urine. This method involves stable isotope dilution, a simplified urease treatment previously described and gas chromatography-mass spectrometry without prior fractionation. The high recovery and low C.V. values were obtained and healthy control values were also determined for these metabolites. Using artificially prepared urine specimens simulating these disorders. the chemical diagnosis can be made clearly, and no further analysis appears to be required for differential chemical diagnosis.
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Affiliation(s)
- T Kuhara
- Division of Human Genetics, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan.
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46
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Defects in Pyrimidine Degradation Identified by HPLC-Electrospray Tandem Mass Spectrometry of Urine Specimens or Urine-soaked Filter Paper Strips. Clin Chem 2000. [DOI: 10.1093/clinchem/46.12.1916] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Background: Urinary concentrations of thymine, uracil, and their degradation products are useful indicators of deficiencies of enzymes of the pyrimidine degradation pathway. We describe a rapid, specific method to measure these concentrations to detect inborn errors of pyrimidine metabolism.
Methods: We used urine or urine-soaked filter-paper strips as samples and measured thymine, uracil, and their degradation products dihydrothymine, dihydrouracil, N-carbamyl-β-aminoisobutyric acid, and N-carbamyl-β-alanine. Reversed-phase HPLC was combined with electrospray ionization tandem mass spectrometry, and detection was performed by multiple-reaction monitoring. Stable-isotope-labeled reference compounds were used as internal standards.
Results: All pyrimidine degradation products could be measured in one analytical run of 15 min. Detection limits were 0.4–4 μmol/L. The intraassay imprecision (CV) of urine samples with added compounds was 1.3–12% for liquid urines and 1.0–10% for filter-paper extracts of the urines. The interassay imprecision (CV) was 3–11% (100–200 μmol/L). Recoveries were 89–99% at 100–200 μmol/L and 95–106% at 1 mmol/L in liquid urines, and 93–103% at 100–200 μmol/L and 100–106% at 1 mmol/L in filter-paper samples. Correct identifications of deficiencies of the pyrimidine-degrading enzymes were readily made with urine samples from patients with known defects.
Conclusions: HPLC with electrospray ionization tandem mass spectrometry allows rapid testing for disorders of the pyrimidine degradation pathway, and filter-paper samples allow easy collection, transport, and storage of urine samples.
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Imaeda M, Sumi S, Ohba S, Kidouchi K, Kodama K, Fujimoto S, Togari H, Wada Y. Screening for pyrimidine metabolism disorders using dried filter-paper urine samples: method development and a pilot study in Nagoya City, Japan. TOHOKU J EXP MED 2000; 190:23-32. [PMID: 10750737 DOI: 10.1620/tjem.190.23] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A screening system for pyrimidine metabolism disorders by measurement with high-performance liquid chromatography using dried filter-paper urine samples is presented. This system permits the simultaneous determination of dihydrouracil, uracil, orotic acid and pseudouridine. The coefficient of variations for the four compounds on the filter-paper urine samples were 0.010 approximately 0.069 and the recoveries were 98.5 approximately 107.1%. The detection limits of the four compounds were 2 approximately 20 micromol/liter. The correlation between the filter-paper urine samples and liquid urine samples was excellent (0.938-0.988). We supeculated that this method could be used to detect pyrimidine metabolism disorders, such as dihydropyrimidinuria, dihydropyrimidine dehydrogenase deficiency and hereditary orotic aciduria. As a pilot study, we have analyzed dried filter-paper urine samples from 34, 200 healthy Japanese, and found three cases of dihydropyrimidinuria without clinical symptoms.
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Affiliation(s)
- M Imaeda
- Department of Pediatrics, Nagoya City University Medical School, Nagoya, Japan
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Maeda T, Sumi S, Hayashi K, Kidouchi K, Owaki T, Togari H, Fujimoto S, Wada Y. Automated determination of 5-fluorouracil and its metabolite in urine by high-performance liquid chromatography with column switching. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 731:267-73. [PMID: 10510780 DOI: 10.1016/s0378-4347(99)00233-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report a quantitative assay of 5-fluorouracil (FU) and its metabolite, 5-fluorodihydrouracil (FDHU) in human urine by used a column-switching high-performance liquid chromatographic method. The analyses were carried out using a molecular exclusion column for sample purification, and a cation-exchange column for separation. Each sample required only 40 min to analyze, and required no preparation other than filtration. Linearity was verified up to 1000 nmol/ml (r > 0.993). The recovery of FU was 96-101%; recovery of FDHU was 96-105%. The imprecision (RSD) for FU (10-100 nmol/ml) was < 1.5%, same-day (n = 5), and < 1.8%, day-to-day (n = 5). The imprecision (RSD) for FDHU (10-100 nmol/ml) was < 3.2%, same-day (n = 5), and < 4.0%, day-to-day (n = 5). The detection limits were, respectively, 0.1 nmol/ml. We measured FU and FDHU in urine of seven cancer patients after oral administration of FU. The cumulative quantity ratio of the FDHU and FU (FDHU/FU) excreted in their urine within 120 min after FU administration was a constant value in all seven patients. Based on these results, we believe that our method provides a useful tool for evaluating FU metabolism.
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Affiliation(s)
- T Maeda
- Department of Hospital Pharmacy, Nagoya City University Hospital, Japan.
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Van Kuilenburg AB, Van Lenthe H, Van Gennip AH. Radiochemical assay for determination of dihydropyrimidinase activity using reversed-phase high-performance liquid chromatography. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1999; 729:307-14. [PMID: 10410956 DOI: 10.1016/s0378-4347(99)00173-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A radiochemical assay was developed to measure the activity of dihydropyrimidinase (DHP) in human liver homogenates. The method is based on the separation of radiolabeled dihydrouracil from N-carbamyl-beta-alanine by HPLC with on-line detection of radioactivity combined with detection of 14CO2 by liquid scintillation counting. The assay was linear with time and protein concentration. The minimum amount of radiolabeled products which could be determined proved to be 12 pmol using a purified stock solution of [2-(14)C]-5,6-dihydrouracil. This highly sensitive assay is especially suitable to identify patients with a dihydropyrimidinase deficiency.
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Affiliation(s)
- A B Van Kuilenburg
- Academic Medical Center, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
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