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Zhang L, Liu J, Wang H, Xu Z, Wang Y, Chen Y, Peng H. Low UPB1 Level Correlates With Poor Prognosis in Lung Adenocarcinoma. Appl Immunohistochem Mol Morphol 2024; 32:44-52. [PMID: 37859333 DOI: 10.1097/pai.0000000000001159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/11/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVES Lung adenocarcinoma (LUAD) is a critical cancer with high mortality, worse prognosis, and crucial lymphatic metastasis. Consequently, prognostic biomarkers for LUAD are truly required. β-Ureidopropionase (UPB1) is abnormally expressed in various cancers. However, the function of UPB1 in LUAD is still ambiguous. This study aimed to explore the expression profile and prognostic significance of UPB1 in LUAD. MATERIALS AND METHODS The differential UPB1 levels in pan cancers and their prognostic significance were comprehensively investigated through Gene Expression Profiling Interactive Analysis, UALCAN, Tumor Immune Estimation Resource, and Kaplan-Meier plotter platform. The correlation between UPB1 and tumor infiltration immune cells was explored using Tumor Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, and Tumor-Immune System Interactions and Drug Bank database databases. RESULTS The UPB1 level was abnormally expressed in pan-tumor tissue than in adjacent tissue from The Cancer Genome Atlas tool. Low UPB1 level was correlated with poor overall survival in patients with LUAD. Furthermore, a comparison of the various pathologic characteristics of LUAD between high and low UPB1 level subgroups revealed that low UPB1 expression was correlated with lymph node metastasis. Kaplan-Meier survival analysis indicated that a low UPB1 level was associated with worse progression‑free survival and overall survival in patients with LUAD. Univariate and multivariate analyses suggested that UPB1 could be a useful prognostic indicator for LUAD. Abnormal UPB1 may be correlated with aberrant LUAD immune infiltration, prompting a worse survival outcome. CONCLUSIONS Results showed that low UPB1 is correlated with a worse prognosis of LUAD and may be a valuable prognostic indicator for LUAD.
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Affiliation(s)
- Libin Zhang
- Department of Thoracic Surgery, Yan'an Hospital affiliated to Kunming Medical University, Yunnan Province, China
| | - Jun Liu
- Department of Thoracic Surgery, The First People'sHospital of Yunnan Province, Yunnan Province, China
| | - Han Wang
- Department of Thoracic Surgery, The First People'sHospital of Yunnan Province, Yunnan Province, China
| | - Zheyuan Xu
- Department of Thoracic Surgery, The First People'sHospital of Yunnan Province, Yunnan Province, China
| | - Yang Wang
- Department of Thoracic Surgery, The First People'sHospital of Yunnan Province, Yunnan Province, China
| | - Yun Chen
- Department of Thoracic Surgery, The First People'sHospital of Yunnan Province, Yunnan Province, China
| | - Hao Peng
- Department of Thoracic Surgery, The First People'sHospital of Yunnan Province, Yunnan Province, China
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Cederfelt D, Badgujar D, Au Musse A, Lohkamp B, Danielson UH, Dobritzsch D. The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces. Biomolecules 2023; 13:1763. [PMID: 38136634 PMCID: PMC10741476 DOI: 10.3390/biom13121763] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.
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Affiliation(s)
- Daniela Cederfelt
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- Department of Cell and Molecular Biology, Uppsala University, 751 23 Uppsala, Sweden
| | - Ayan Au Musse
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
- School of Science and Technology, Örebro University, 701 82 Örebro, Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77 Stockholm, Sweden;
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
| | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, 751 23 Uppsala, Sweden; (D.C.); (D.B.); (U.H.D.)
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3
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Maslarinou A, Manolopoulos VG, Ragia G. Pharmacogenomic-guided dosing of fluoropyrimidines beyond DPYD: time for a polygenic algorithm? Front Pharmacol 2023; 14:1184523. [PMID: 37256234 PMCID: PMC10226670 DOI: 10.3389/fphar.2023.1184523] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/19/2023] [Indexed: 06/01/2023] Open
Abstract
Fluoropyrimidines are chemotherapeutic agents widely used for the treatment of various solid tumors. Commonly prescribed FPs include 5-fluorouracil (5-FU) and its oral prodrugs capecitabine (CAP) and tegafur. Bioconversion of 5-FU prodrugs to 5-FU and subsequent metabolic activation of 5-FU are required for the formation of fluorodeoxyuridine triphosphate (FdUTP) and fluorouridine triphosphate, the active nucleotides through which 5-FU exerts its antimetabolite actions. A significant proportion of FP-treated patients develop severe or life-threatening, even fatal, toxicity. It is well known that FP-induced toxicity is governed by genetic factors, with dihydropyrimidine dehydrogenase (DPYD), the rate limiting enzyme in 5-FU catabolism, being currently the cornerstone of FP pharmacogenomics. DPYD-based dosing guidelines exist to guide FP chemotherapy suggesting significant dose reductions in DPYD defective patients. Accumulated evidence shows that additional variations in other genes implicated in FP pharmacokinetics and pharmacodynamics increase risk for FP toxicity, therefore taking into account more gene variations in FP dosing guidelines holds promise to improve FP pharmacotherapy. In this review we describe the current knowledge on pharmacogenomics of FP-related genes, beyond DPYD, focusing on FP toxicity risk and genetic effects on FP dose reductions. We propose that in the future, FP dosing guidelines may be expanded to include a broader ethnicity-based genetic panel as well as gene*gene and gender*gene interactions towards safer FP prescription.
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Affiliation(s)
- Anthi Maslarinou
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
| | - Vangelis G. Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
- Clinical Pharmacology Unit, Academic General Hospital of Alexandroupolis, Alexandroupolis, Greece
| | - Georgia Ragia
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
- Individualised Medicine and Pharmacological Research Solutions Center, Alexandroupolis, Greece
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4
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Dobritzsch D, Meijer J, Meinsma R, Maurer D, Monavari AA, Gummesson A, Reims A, Cayuela JA, Kuklina N, Benoist JF, Perrin L, Assmann B, Hoffmann GF, Bierau J, Kaindl AM, van Kuilenburg ABP. β-Ureidopropionase deficiency due to novel and rare UPB1 mutations affecting pre-mRNA splicing and protein structural integrity and catalytic activity. Mol Genet Metab 2022; 136:177-185. [PMID: 35151535 DOI: 10.1016/j.ymgme.2022.01.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 01/04/2023]
Abstract
β-Ureidopropionase is the third enzyme of the pyrimidine degradation pathway and catalyses the conversion of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid to β-alanine and β-aminoisobutyric acid, ammonia and CO2. To date, only a limited number of genetically confirmed patients with a complete β-ureidopropionase deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 10 newly identified β-ureidopropionase deficient individuals. Patients presented mainly with neurological abnormalities and markedly elevated levels of N-carbamyl-β-alanine and N-carbamyl-β-aminoisobutyric acid in urine. Analysis of UPB1, encoding β-ureidopropionase, showed 5 novel missense variants and two novel splice-site variants. Functional expression of the UPB1 variants in mammalian cells showed that recombinant ß-ureidopropionase carrying the p.Ala120Ser, p.Thr129Met, p.Ser300Leu and p.Asn345Ile variant yielded no or significantly decreased β-ureidopropionase activity. Analysis of the crystal structure of human ß-ureidopropionase indicated that the point mutations affect substrate binding or prevent the proper subunit association to larger oligomers and thus a fully functional β-ureidopropionase. A minigene approach showed that the intronic variants c.[364 + 6 T > G] and c.[916 + 1_916 + 2dup] led to skipping of exon 3 and 8, respectively, in the process of UPB1 pre-mRNA splicing. The c.[899C > T] (p.Ser300Leu) variant was identified in two unrelated Swedish β-ureidopropionase patients, indicating that β-ureidopropionase deficiency may be more common than anticipated.
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Affiliation(s)
- Doreen Dobritzsch
- Uppsala University, Department of Chemistry-BMC, Biomedical Center, Uppsala, Sweden
| | - Judith Meijer
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands
| | - Rutger Meinsma
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands
| | | | - Ardeshir A Monavari
- National Centre for Inherited Metabolic Disorders, Children's Health Ireland at Temple Street, Temple Street, Dublin, Ireland
| | - Anders Gummesson
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Annika Reims
- Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Jorge A Cayuela
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Natalia Kuklina
- Drammen Hospital, Pediatric Department/Habilitation Center, Vestre Viken HF, Drammen, Norway
| | - Jean-François Benoist
- Hôpital Universitaire Robert Debré, Service de Biochimie Hormonologie, Paris, France
| | - Laurence Perrin
- Hôpital Universitaire Robert Debré, Service de Biochimie Hormonologie, Paris, France
| | - Birgit Assmann
- University Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- University Children's Hospital, University of Heidelberg, Heidelberg, Germany
| | - Jörgen Bierau
- Maastricht University Medical Centre, Department of Clinical Genetics, Maastricht, the Netherlands; Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Angela M Kaindl
- Charité - Universitätsmedizin Berlin, Department of Pediatric Neurology, Center for Chronically Sick Children, Institute for Cell and Neurobiology, Berlin, Germany
| | - André B P van Kuilenburg
- Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Cancer Center Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam, the Netherlands.
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5
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Xu X, Zheng J, Zou Q, Wang C, Zhang X, Wang X, Liu Y, Shu J. Rapid screening of UPB1 gene variations by high resolution melting curve analysis. Exp Ther Med 2021; 21:403. [PMID: 33692834 PMCID: PMC7938451 DOI: 10.3892/etm.2021.9834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
The present study aimed to analyze gene mutations in patients with β-ureidopropinoase deficiency and establish a rapid detection method for β-ureidopropinoase (UPB1) pathogenic variations by high resolution melting (HRM) analysis. DNA samples with known UPB1 mutations in three patients with β-ureidopropinoase deficiency were utilized to establish a rapid detection method for UPB1 pathogenic variations by HRM analysis. Further rapid screening was performed on two patients diagnosed with β-ureidopropinoase deficiency and 50 healthy control individuals. The results showed that all known UPB1 gene mutations can be analyzed by a specially designed HRM assay. Each mutation has specific HRM profiles which could be used in rapid screening. The HRM method could correctly identify all genetic mutations in two children with β-ureidopropinoase deficiency. In addition, the HRM assay also recognized four unknown mutations. To conclude, the results support future studies of applying HRM analysis as a diagnostic approach for β-ureidopropinoase deficiency and a rapid screening method for UPB1 mutation carriers.
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Affiliation(s)
- Xiaowei Xu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Jie Zheng
- Graduate College, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Qianqian Zou
- Graduate College, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Chao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Xinjie Zhang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Xuetao Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Yang Liu
- Department of Neonatology, Tianjin Children's Hospital, Tianjin 300134, P.R. China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin 300134, P.R. China.,Tianjin Key Laboratory of Prevention and Treatment of Birth Defects, Tianjin Children's Hospital, Tianjin 300134, P.R. China
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6
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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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7
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Yokoi K, Nakajima Y, Matsuoka H, Shinkai Y, Ishihara T, Maeda Y, Kato T, Katsuno H, Masumori K, Kawada K, Yoshikawa T, Ito T, Kurahashi H. Impact of DPYD, DPYS, and UPB1 gene variations on severe drug-related toxicity in patients with cancer. Cancer Sci 2020; 111:3359-3366. [PMID: 32619063 PMCID: PMC7469832 DOI: 10.1111/cas.14553] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 01/08/2023] Open
Abstract
Cancer treatment with a fluoropyrimidine (FP) is often accompanied by severe toxicity that may be dependent on the activity of catalytic enzymes encoded by the DPYD, DPYS, and UPB1 genes. Genotype-guided dose individualization of FP therapy has been proposed in western countries, but our knowledge of the relevant genetic variants in East Asian populations is presently limited. To investigate the association between these genetic variations and FP-related high toxicity in a Japanese population, we obtained blood samples from 301 patients who received this chemotherapy and sequenced the coding exons and flanking intron regions of their DPYD, DPYS, and UPB1 genes. In total, 24 single nucleotide variants (15 in DPYD, 7 in DPYS and 2 in UPB1) were identified including 3 novel variants in DPYD and 1 novel variant in DPYS. We did not find a significant association between FP-related high toxicity and each of these individual variants, although a certain trend toward significance was observed for p.Arg181Trp and p.Gln334Arg in DPYS (P = .0813 and .087). When we focused on 7 DPYD rare variants (p.Ser199Asn, p.IIe245Phe, p.Thr305Lys, p.Glu386Ter, p.Ser556Arg, p.Ala571Asp, p.Trp621Cys) which have an allele frequency of less than 0.01% in the Japanese population and are predicted to be loss-of-function mutations by in silico analysis, the group of patients who were heterozygous carriers of at least one these rare variants showed a strong association with FP-related high toxicity (P = .003). Although the availability of screening of these rare loss-of-function variants is still unknown, our data provide useful information that may help to alleviate FP-related toxicity in Japanese patients with cancer.
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Affiliation(s)
- Katsuyuki Yokoi
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan.,Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Yoko Nakajima
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroshi Matsuoka
- Department of Gastrointestinal Surgery, Fujita Health University School of Medicine, Toyoake, Japan
| | - Yasuko Shinkai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Takuma Ishihara
- Innovative and Clinical Research Promotion Center, Gifu University Hospital Gifu University, Gifu, Japan
| | - Yasuhiro Maeda
- Center for Joint Research Facilities Support, Fujita Health University, Toyoake, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Hidetoshi Katsuno
- Department of Gastrointestinal Surgery, Fujita Health University School of Medicine, Toyoake, Japan
| | - Koji Masumori
- Department of Gastrointestinal Surgery, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kenji Kawada
- Department of Medical Oncology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsuya Ito
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
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Predicting mucositis risk associated with cytotoxic cancer treatment regimens: rationale, complexity, and challenges. Curr Opin Support Palliat Care 2019; 12:198-210. [PMID: 29547492 DOI: 10.1097/spc.0000000000000339] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW The goals of this review are to describe the complexity of factors influencing the risk of cancer regimen-related mucosal injury (CRRMI), to evaluate the contribution of the innate immune response to CRRMI risk, to compare the concordance of genome analytics in describing mechanism and risk, and to determine if common biological pathways are noted when CRRMI is compared to a disease with a similar phenotype. RECENT FINDINGS The pathogenesis of and risk for CRRMI are complex and influenced by multiple intrinsic and extrinsic factors. It is incumbent on analyses to recognize the likelihood that the interplay and cross-talk of synergistically expressed factors is critical and that the contributing weights of these factors is not uniform from patient to patient. Genomically derived analyses imply final common pathways are implicit in phenotype expression. SUMMARY The identification of specific factors (both genomic and otherwise) which contribute to CRRMI risk represents an important opportunity to apply principles of precision medicine to the management of regimen-related toxicities.
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Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism. Biochem J 2018; 475:2395-2416. [PMID: 29976570 DOI: 10.1042/bcj20180222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
β-Ureidopropionase (βUP) catalyzes the third step of the reductive pyrimidine catabolic pathway responsible for breakdown of uracil-, thymine- and pyrimidine-based antimetabolites such as 5-fluorouracil. Nitrilase-like βUPs use a tetrad of conserved residues (Cys233, Lys196, Glu119 and Glu207) for catalysis and occur in a variety of oligomeric states. Positive co-operativity toward the substrate N-carbamoyl-β-alanine and an oligomerization-dependent mechanism of substrate activation and product inhibition have been reported for the enzymes from some species but not others. Here, the activity of recombinant human βUP is shown to be similarly regulated by substrate and product, but in a pH-dependent manner. Existing as a homodimer at pH 9, the enzyme increasingly associates to form octamers and larger oligomers with decreasing pH. Only at physiological pH is the enzyme responsive to effector binding, with N-carbamoyl-β-alanine causing association to more active higher molecular mass species, and β-alanine dissociation to inactive dimers. The parallel between the pH and ligand-induced effects suggests that protonation state changes play a crucial role in the allosteric regulation mechanism. Disruption of dimer-dimer interfaces by site-directed mutagenesis generated dimeric, inactive enzyme variants. The crystal structure of the T299C variant refined to 2.08 Å resolution revealed high structural conservation between human and fruit fly βUP, and supports the hypothesis that enzyme activation by oligomer assembly involves ordering of loop regions forming the entrance to the active site at the dimer-dimer interface, effectively positioning the catalytically important Glu207 in the active site.
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10
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Identifying novel genes and biological processes relevant to the development of cancer therapy-induced mucositis: An informative gene network analysis. PLoS One 2017; 12:e0180396. [PMID: 28678827 PMCID: PMC5498049 DOI: 10.1371/journal.pone.0180396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 05/30/2017] [Indexed: 12/20/2022] Open
Abstract
Mucositis is a complex, dose-limiting toxicity of chemotherapy or radiotherapy that leads to painful mouth ulcers, difficulty eating or swallowing, gastrointestinal distress, and reduced quality of life for patients with cancer. Mucositis is most common for those undergoing high-dose chemotherapy and hematopoietic stem cell transplantation and for those being treated for malignancies of the head and neck. Treatment and management of mucositis remain challenging. It is expected that multiple genes are involved in the formation, severity, and persistence of mucositis. We used Ingenuity Pathway Analysis (IPA), a novel network-based approach that integrates complex intracellular and intercellular interactions involved in diseases, to systematically explore the molecular complexity of mucositis. As a first step, we searched the literature to identify genes that harbor or are close to the genetic variants significantly associated with mucositis. Our literature review identified 27 candidate genes, of which ERCC1, XRCC1, and MTHFR were the most frequently studied for mucositis. On the basis of this 27-gene list, we used IPA to generate gene networks for mucositis. The most biologically significant novel molecules identified through IPA analyses included TP53, CTNNB1, MYC, RB1, P38 MAPK, and EP300. Additionally, uracil degradation II (reductive) and thymine degradation pathways (p = 1.06-08) were most significant. Finally, utilizing 66 SNPs within the 8 most connected IPA-derived candidate molecules, we conducted a genetic association study for oral mucositis in the head and neck cancer patients who were treated using chemotherapy and/or radiation therapy (186 head and neck cancer patients with oral mucositis vs. 699 head and neck cancer patients without oral mucositis). The top ranked gene identified through this association analysis was RB1 (rs2227311, p-value = 0.034, odds ratio = 0.67). In conclusion, gene network analysis identified novel molecules and biological processes, including pathways related to inflammation and oxidative stress, that are relevant to mucositis development, thus providing the basis for future studies to improve the management and treatment of mucositis in patients with cancer.
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11
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Molecular profile of 5-fluorouracil pathway genes in colorectal carcinoma. BMC Cancer 2016; 16:795. [PMID: 27733154 PMCID: PMC5062913 DOI: 10.1186/s12885-016-2826-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 09/30/2016] [Indexed: 12/31/2022] Open
Abstract
Background This study addresses involvement of major 5-fluorouracil (5-FU) pathway genes in the prognosis of colorectal carcinoma patients. Methods Testing set and two validation sets comprising paired tumor and adjacent mucosa tissue samples from 151 patients were used for transcript profiling of 15 5-FU pathway genes by quantitative real-time PCR and DNA methylation profiling by high resolution melting analysis. Intratumoral molecular profiles were correlated with clinical data of patients. Protein levels of two most relevant candidate markers were assessed by immunoblotting. Results Downregulation of DPYD and upregulation of PPAT, UMPS, RRM2, and SLC29A1 transcripts were found in tumors compared to adjacent mucosa in testing and validation sets of patients. Low RRM2 transcript level significantly associated with poor response to the first-line palliative 5-FU-based chemotherapy in the testing set and with poor disease-free interval of patients in the validation set irrespective of 5-FU treatment. UPP2 was strongly methylated while its transcript absent in both tumors and adjacent mucosa. DPYS methylation level was significantly higher in tumor tissues compared to adjacent mucosa samples. Low intratumoral level of UPB1 methylation was prognostic for poor disease-free interval of the patients (P = 0.0002). The rest of the studied 5-FU genes were not methylated in tumors or adjacent mucosa. Conclusions The observed overexpression of several 5-FU activating genes and DPYD downregulation deduce that chemotherapy naïve colorectal tumors share favorable gene expression profile for 5-FU therapy. Low RRM2 transcript and UPB1 methylation levels present separate poor prognosis factors for colorectal carcinoma patients and should be further investigated. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2826-8) contains supplementary material, which is available to authorized users.
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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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13
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Lam CW, Law CY, Leung KF, Lai CK, Pak-lam Chen S, Chan B, Chan KY, Yuen YP, Mak CM, Yan-wo Chan A. NMR-based urinalysis for rapid diagnosis of β-ureidopropionase deficiency in a patient with Dravet syndrome. Clin Chim Acta 2015; 440:201-4. [PMID: 25445412 DOI: 10.1016/j.cca.2014.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 10/17/2014] [Accepted: 10/21/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Beta-ureidopropionase deficiency is a rare inborn error of metabolism (IEM) affecting pyrimidine metabolism. To-date, about 30 genetically confirmed cases had been reported. The clinical phenotypes of this condition are variable; some patients were asymptomatic while some may present with developmental delay or autistic features. In severe cases, patients may present with profound neurological deficit including hypotonia, seizures and mental retardation. Using NMR-based urinalysis, this condition can be rapidly diagnosed within 15 min. CASE An 11-month-old Chinese boy had dual molecular diagnoses, β-ureidopropionase deficiency and Dravet syndrome. He presented with intractable and recurrent convulsions, global developmental delay and microcephaly. Urine organic acid analysis using GC-MS and NMR-based urinalysis showed excessive amount of β-ureidopropionic acid and β-ureidoisobutyric acid, the two disease-specific markers for β-ureidopropionase deficiency. Genetic analysis confirmed homozygous known disease-causing mutation UPB1 NM_016327.2: c.977G>A; NP_057411.1:p.R326Q. In addition, genetic analysis for Dravet syndrome showed the presence of heterozygous disease-causing mutation SCN1A NM_001165963.1:c.4494delC; NP_001159435.1:p.F1499Lfs*2. CONCLUSIONS The differentiation between Dravet syndrome and β-ureidopropionase deficiency is clinically challenging since both conditions share overlapping clinical features. The detection of urine β-ureidoisobutyric and β-ureidopropionic acids using NMR or GC-MS is helpful in laboratory diagnosis of β-ureidopropionase deficiency. The disease-causing mutation, c.977G>A of β-ureidopropionase deficiency, is highly prevalent in Chinese population (allele frequency=1.7%); β-ureidopropionase deficiency screening test should be performed for any patients with unexplained neurological deficit, developmental delay or autism.
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Affiliation(s)
- Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Hong Kong, China.
| | - Chun-Yiu Law
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Ka-Fei Leung
- Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Chi-Kong Lai
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | | | - Bosco Chan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Kwok-Yin Chan
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, China
| | - Yuet-ping Yuen
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
| | - Chloe Miu Mak
- Department of Pathology, Princess Margaret Hospital, Hong Kong, China
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14
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Shu J, Lv X, Jiang S, Zhang Y, Zhang C, Meng Y, Situ A, Xu H, Song L. Genetic analysis of the UPB1 gene in two new Chinese families with β-ureidopropionase deficiency and the carrier frequency of the mutation c.977G>A in Northern China. Childs Nerv Syst 2014; 30:2109-14. [PMID: 25236466 DOI: 10.1007/s00381-014-2541-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 08/26/2014] [Indexed: 12/27/2022]
Abstract
PURPOSE The purpose of the study was to investigate mutations of the UPB1 gene in two Chinese families with β-ureidopropionase deficiency and the heterozygous carrier frequency in Chinese. METHODS Genomic DNA was extracted from peripheral blood leukocytes from all available family members and 500 unrelated healthy controls. Then, all exons and flanking intron regions of the UPB1 gene were amplified by PCR and analyzed by direct sequencing in two patient-families. Finally, the carrier frequency of the c.977G>A (p.R326Q) mutation was identified by PCR restriction fragment length polymorphism in 500 healthy controls. RESULTS The two patients had the same homozygous missense mutation in exon 9 (c.977G>A; p.R326Q), and the carrier frequency of this mutation was 2.8 % in the Northern Chinese population, which suggests that about 1:5,102 Chinese are expected to suffer from UPB1 deficiency. CONCLUSIONS The c.977G>A (p.R326Q) is the most common mutation of the UPB1 gene in Chinese. The predicted incidence indicates that β-ureidopropionase deficiency is significantly underdiagnosed in the Chinese population. It should be necessary to add β-ureidopropionase deficiency to high-risk screening for the symptomatic patients group.
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Affiliation(s)
- Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, Tianjin, China
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15
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Nakajima Y, Meijer J, Dobritzsch D, Ito T, Meinsma R, Abeling NGGM, Roelofsen J, Zoetekouw L, Watanabe Y, Tashiro K, Lee T, Takeshima Y, Mitsubuchi H, Yoneyama A, Ohta K, Eto K, Saito K, Kuhara T, van Kuilenburg ABP. Clinical, biochemical and molecular analysis of 13 Japanese patients with β-ureidopropionase deficiency demonstrates high prevalence of the c.977G > A (p.R326Q) mutation [corrected]. J Inherit Metab Dis 2014; 37:801-12. [PMID: 24526388 PMCID: PMC4158181 DOI: 10.1007/s10545-014-9682-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/18/2014] [Accepted: 01/21/2014] [Indexed: 11/13/2022]
Abstract
β-ureidopropionase (βUP) deficiency is an autosomal recessive disease characterized by N-carbamyl-β-amino aciduria. To date, only 16 genetically confirmed patients with βUP deficiency have been reported. Here, we report on the clinical, biochemical and molecular findings of 13 Japanese βUP deficient patients. In this group of patients, three novel missense mutations (p.G31S, p.E271K, and p.I286T) and a recently described mutation (p.R326Q) were identified. The p.R326Q mutation was detected in all 13 patients with eight patients being homozygous for this mutation. Screening for the p.R326Q mutation in 110 Japanese individuals showed an allele frequency of 0.9 %. Transient expression of mutant βUP enzymes in HEK293 cells showed that the p.E271K and p.R326Q mutations cause profound decreases in activity (≤ 1.3 %). Conversely, βUP enzymes containing the p.G31S and p.I286T mutations possess residual activities of 50 and 70 %, respectively, suggesting we cannot exclude the presence of additional mutations in the non-coding region of the UPB1 gene. Analysis of a human βUP homology model revealed that the effects of the mutations (p.G31S, p.E271K, and p.R326Q) on enzyme activity are most likely linked to improper oligomer assembly. Highly variable phenotypes ranging from neurological involvement (including convulsions and autism) to asymptomatic, were observed in diagnosed patients. High prevalence of p.R326Q in the normal Japanese population indicates that βUP deficiency is not as rare as generally considered and screening for βUP deficiency should be included in diagnosis of patients with unexplained neurological abnormalities.
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Affiliation(s)
- Yoko Nakajima
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, Netherlands,
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Magdy T, Arlanov R, Winter S, Lang T, Klein K, Toyoda Y, Ishikawa T, Schwab M, Zanger UM. ABCC11/MRP8 polymorphisms affect 5-fluorouracil-induced severe toxicity and hepatic expression. Pharmacogenomics 2014; 14:1433-48. [PMID: 24024896 DOI: 10.2217/pgs.13.139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM Because 5-fluorodeoxyuridine monophosphate (5-FdUMP), an anabolic active metabolite of 5-fluorouracil (5-FU), is a substrate of MRP8 (encoded by ABCC11), we investigated whether ABCC11 polymorphisms play a role in severe toxicity of 5-FU. PATIENTS & METHODS Genomic DNA from 672 cancer patients treated with 5-FU monotherapy and with documented toxicity according to WHO criteria was genotyped for 12 ABCC11 tag SNPs. Functional impact of polymorphisms was assessed in a Caucasian human liver cohort (n = 150) and by recombinant expression of MRP8 protein variants. RESULTS Univariate and multivariate analysis identified rs17822471 (G>A, T546M) as risk factor of severe leukopenia (p = 0.021, odds ratio [95%CI]: 3.31 [1.26-8.66]) but not of other toxicity types. MRP8 protein expression in human liver was 1.7-fold lower in carriers compared with wild-type (p = 0.02). Recombinant expression confirmed the effect of T546M on protein expression. CONCLUSION Since MRP8 is expressed in bone marrow blasts and leukocytes, lower expression may lead to intracellular accumulation of 5-FdUMP and increased risk of leukopenia.
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Affiliation(s)
- Tarek Magdy
- Dr Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Auerbachstrasse 112, D-70376 Stuttgart, Germany
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