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Liu A, Zhao J, Shah M, Migliorati JM, Tawfik SM, Bahal R, Rasmussen TP, Manautou JE, Zhong XB. Nedosiran, a Candidate siRNA Drug for the Treatment of Primary Hyperoxaluria: Design, Development, and Clinical Studies. ACS Pharmacol Transl Sci 2022; 5:1007-1016. [PMID: 36407951 PMCID: PMC9667536 DOI: 10.1021/acsptsci.2c00110] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Indexed: 11/28/2022]
Abstract
Due to the lack of treatment options for the genetic disease primary hyperoxaluria (PH), including three subtypes PH1, PH2, and PH3, caused by accumulation of oxalate forming kidney stones, there is an urgent need for the development of a drug therapy aside from siRNA drug lumasiran for patients with PH1. After the recent success of drug therapies based on small interfering RNA (siRNA), nedosiran is currently being developed for the treatment of three types of PH as a siRNA-based modality. Through specific inhibition of lactate dehydrogenase enzyme, the key enzyme in biosynthesis of oxalate in liver, phase 1, 2, and 3 clinical trials of nedosiran have achieved the desired primary end point of reduction of urinary oxalate levels in patients with PH1. More PH2 and PH3 patients need to be tested for efficacy. It has also produced a favorable secondary end point on safety and toxicity in PH patients. In addition to common injection site reactions that resolved spontaneously, no severe nedosiran treatment-associated adverse events were reported. Based on the positive results in the clinical studies, nedosiran is a candidate siRNA drug to treat PH patients.
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Affiliation(s)
- Anna Liu
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Jenny Zhao
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Milan Shah
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Julia M. Migliorati
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Sherouk M. Tawfik
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Raman Bahal
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Theodore P. Rasmussen
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Jose E. Manautou
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
| | - Xiao-bo Zhong
- Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Connecticut, Storrs, Connecticut06269, United States
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2
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Lopes‐Marques M, Pacheco AR, Peixoto MJ, Cardoso AR, Serrano C, Amorim A, Prata MJ, Cooper DN, Azevedo L. Common polymorphic OTC variants can act as genetic modifiers of enzymatic activity. Hum Mutat 2021; 42:978-989. [PMID: 34015158 PMCID: PMC8362079 DOI: 10.1002/humu.24221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022]
Abstract
Understanding the role of common polymorphisms in modulating the clinical phenotype when they co‐occur with a disease‐causing lesion is of critical importance in medical genetics. We explored the impact of apparently neutral common polymorphisms, using the gene encoding the urea cycle enzyme, ornithine transcarbamylase (OTC), as a model system. Distinct combinations of genetic backgrounds embracing two missense polymorphisms were created in cis with the pathogenic p.Arg40His replacement. In vitro enzymatic assays revealed that the polymorphic variants were able to modulate OTC activity both in the presence or absence of the pathogenic lesion. First, we found that the combination of the minor alleles of polymorphisms p.Lys46Arg and p.Gln270Arg significantly enhanced enzymatic activity in the wild‐type protein. Second, enzymatic assays revealed that the minor allele of the p.Gln270Arg polymorphism was capable of ameliorating OTC activity when combined in cis with the pathogenic p.Arg40His replacement. Structural analysis predicted that the minor allele of the p.Gln270Arg polymorphism would serve to stabilize the OTC wild‐type protein, thereby corroborating the results of the experimental assays. Our findings demonstrate the potential importance of cis‐interactions between common polymorphic variants and pathogenic missense mutations and illustrate how standing genetic variation can modulate protein function.
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Affiliation(s)
- Mónica Lopes‐Marques
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Ana Rita Pacheco
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
| | - Maria João Peixoto
- ICVS‐ Life and Health Sciences Research Institute, School of MedicineUniversity of MinhoBragaPortugal
- ICVS/3B's‐PT Government Associate LaboratoryBragaGuimarãesPortugal
| | - Ana Rita Cardoso
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Catarina Serrano
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - António Amorim
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Maria João Prata
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - David N. Cooper
- Institute of Medical Genetics; School of MedicineCardiff UniversityCardiffUK
| | - Luísa Azevedo
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
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3
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Murad H, Alhalabi MB, Dabboul A, Alfakseh N, Nweder MS, Zghib Y, Wannous H. Molecular analysis of the AGXT gene in Syrian patients suspected with primary hyperoxaluria type 1. BMC Med Genomics 2021; 14:146. [PMID: 34082749 PMCID: PMC8176596 DOI: 10.1186/s12920-021-00996-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterization of the molecular basis of primary hyperoxaluria type 1 (PH-1) in Syria has been accomplished through the analysis of 90 unrelated chromosomes from 45 Syrians patients with PH-1 from different regions. METHODS Alanine glyoxylate aminotransferase (AGXT) gene mutations have been analyzed by using molecular detection methods based on the direct DNA sequencing for all exons of the AGXT gene. RESULTS Seventeen pathogenic mutations were detected in our patients. Six mutations were novels. The three most frequent mutations were c.33_34insC (p.Lys12fs) in Exon 1, c.584 T < G; p.Met195Arg in exon 5 and c.1007 T > A (p.Val336Asp) in exon 10, with a frequency of 33.3%, 12.2%, and 11.1%, respectively. CONCLUSION DNA sequencing used in this study can offer a useful method to investigate the mutations in Syrian PH-1 patients, and could offer an accurate tool for prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Hossam Murad
- Human Genetics Division, Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria.
| | - Mohamad Baseel Alhalabi
- Human Genetics Division, Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | - Amir Dabboul
- Human Genetics Division, Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | - Nour Alfakseh
- Human Genetics Division, Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | - Mohamad Sayah Nweder
- Human Genetics Division, Molecular Biology and Biotechnology Department, Human Genetics Division, Atomic Energy Commission of Syria, P.O. Box 6091, Damascus, Syria
| | | | - Hala Wannous
- Chlidien's Hospital of Damascus, Damascus, Syria
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4
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Dindo M, Mandrile G, Conter C, Montone R, Giachino D, Pelle A, Costantini C, Cellini B. The ILE56 mutation on different genetic backgrounds of alanine:glyoxylate aminotransferase: Clinical features and biochemical characterization. Mol Genet Metab 2020; 131:171-180. [PMID: 32792227 DOI: 10.1016/j.ymgme.2020.07.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 01/20/2023]
Abstract
Primary Hyperoxaluria type I (PH1) is a rare disease caused by mutations in the AGXT gene encoding alanine:glyoxylate aminotransferase (AGT), a liver enzyme involved in the detoxification of glyoxylate, the failure of which results in accumulation of oxalate and kidney stones formation. The role of protein misfolding in the AGT deficit caused by most PH1-causing mutations is increasingly being recognized. In addition, the genetic background in which a mutation occurs is emerging as a critical risk factor for disease onset and/or severity. Based on these premises, in this study we have analyzed the clinical, biochemical and cellular effects of the p.Ile56Asn mutation, recently described in a PH1 patient, as a function of the residue at position 11, a hot-spot for both polymorphic (p.Pro11Leu) and pathogenic (p.Pro11Arg) mutations. We have found that the p.Ile56Asn mutation induces a structural defect mostly related to the apo-form of AGT. The effects are more pronounced when the substitution of Ile56 is combined with the p.Pro11Leu and, at higher degree, the p.Pro11Arg mutation. As compared with the non-pathogenic forms, AGT variants display reduced expression and activity in mammalian cells. Vitamin B6, a currently approved treatment for PH1, can overcome the effects of the p.Ile56Asn mutation only when it is associated with Pro at position 11. Our results provide a first proof that the genetic background influences the effects of PH1-causing mutations and the responsiveness to treatment and suggest that molecular and cellular studies can integrate clinical data to identify the best therapeutic strategy for PH1 patients.
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Affiliation(s)
- Mirco Dindo
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy; Genetica e Thalassemia Unit, San Luigi University Hospital, Orbassano (TO), Italy
| | - Carolina Conter
- Department of Neurological, Biomedical, and Movement Sciences, University of Verona, Verona, Italy
| | - Rosa Montone
- Department of Neurological, Biomedical, and Movement Sciences, University of Verona, Verona, Italy
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy
| | - Alessandra Pelle
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano (TO), Italy
| | - Claudio Costantini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Perugia, Italy.
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5
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Cardoso AR, Lopes-Marques M, Silva RM, Serrano C, Amorim A, Prata MJ, Azevedo L. Essential genetic findings in neurodevelopmental disorders. Hum Genomics 2019; 13:31. [PMID: 31288856 PMCID: PMC6617629 DOI: 10.1186/s40246-019-0216-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) represent a growing medical challenge in modern societies. Ever-increasing sophisticated diagnostic tools have been continuously revealing a remarkably complex architecture that embraces genetic mutations of distinct types (chromosomal rearrangements, copy number variants, small indels, and nucleotide substitutions) with distinct frequencies in the population (common, rare, de novo). Such a network of interacting players creates difficulties in establishing rigorous genotype-phenotype correlations. Furthermore, individual lifestyles may also contribute to the severity of the symptoms fueling a large spectrum of gene-environment interactions that have a key role on the relationships between genotypes and phenotypes.Herein, a review of the genetic discoveries related to NDDs is presented with the aim to provide useful general information for the medical community.
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Affiliation(s)
- Ana R Cardoso
- i3S - Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Mónica Lopes-Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Raquel M Silva
- Department of Medical Sciences and iBiMED, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.,Present Address: Center for Interdisciplinary Research in Health (CIIS), Institute of Health Sciences (ICS), Universidade Católica Portuguesa, 3504-505, Viseu, Portugal
| | - Catarina Serrano
- i3S - Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Maria J Prata
- i3S - Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Luísa Azevedo
- i3S - Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution Group, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007, Porto, Portugal.
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6
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Yang H, Male M, Li Y, Wang N, Zhao C, Jin S, Hu J, Chen Z, Ye Z, Xu H. Efficacy of Hydroxy-L-proline (HYP) analogs in the treatment of primary hyperoxaluria in Drosophila Melanogaster. BMC Nephrol 2018; 19:167. [PMID: 29980178 PMCID: PMC6035412 DOI: 10.1186/s12882-018-0980-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
Background Substrate reduction therapy with analogs reduces the accumulation of substrates by inhibiting the metabolic pathways involved in their biosynthesis, providing new treatment options for patients with primary hyperoxalurias (PHs) that often progress to end-stage renal disease (ESRD). This research aims to evaluate the inhibition efficacy of Hydroxy-L-proline (HYP) analogs against calcium oxalate (CaOx) crystal formation in the Drosophila Melanogaster (D. Melanogaster) by comparing them with Pyridoxine (Vitamin B6). Methods Three stocks of Drosophila Melanogaster (W118, CG3926 RNAi, and Act5C-GAL4/CyO) were utilized. Two stocks (CG3926 RNAi and Act5C-GAL4 /CyO) were crossed to generate the Act5C > dAGXT RNAi recombinant line (F1 generation) of D. Melanogaster which was used to compare the efficacy of Hydroxy-L-proline (HYP) analogs inhibiting CaOx crystal formation with Vitamin B6 as the traditional therapy for primary hyperoxaluria. Results Nephrolithiasis model was successfully constructed by downregulating the function of the dAGXT gene in D. Melanogaster (P-Value = 0.0045). Furthermore, the efficacy of Hydroxy-L-proline (HYP) analogs against CaOx crystal formation was demonstrated in vivo using D. Melanogaster model; the results showed that these L-Proline analogs were better in inhibiting stone formation at very low concentrations than Vitamin B6 (IC50 = 0.6 and 1.8% for standard and dietary salt growth medium respectively) compared to N-acetyl-L-Hydroxyproline (IC50 = 0.1% for both standard and dietary salt growth medium) and Baclofen (IC50 = 0.06 and 0.1% for standard and dietary salt growth medium respectively). Analysis of variance (ANOVA) also showed that Hydroxy-L-proline (HYP) analogs were better alternatives for CaOx inhibition at very low concentration especially when both genetics and environmental factors are intertwined (p < 0.0008) for the dietary salt growth medium and (P < 0.063) for standard growth medium. Conclusion Addition of Hydroxy-L-Proline analogs to growth medium resulted in the reduction of CaOx crystals formation. These analogs show promise as potential inhibitors for oxalate reduction in Primary Hyperoxaluria.
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Affiliation(s)
- Huan Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Musa Male
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- College of Life Sciences, Hubei University, Wuhan, China
| | - Ning Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenming Zhao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Jin
- College of Life Sciences, Hubei University, Wuhan, China
| | - Juncheng Hu
- College of Life Sciences, Hubei University, Wuhan, China
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China.,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jie Fang Avenue, Wuhan, 430030, China. .,Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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7
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Daga A, Majmundar AJ, Braun DA, Gee HY, Lawson JA, Shril S, Jobst-Schwan T, Vivante A, Schapiro D, Tan W, Warejko JK, Widmeier E, Nelson CP, Fathy HM, Gucev Z, Soliman NA, Hashmi S, Halbritter J, Halty M, Kari JA, El-Desoky S, Ferguson MA, Somers MJG, Traum AZ, Stein DR, Daouk GH, Rodig NM, Katz A, Hanna C, Schwaderer AL, Sayer JA, Wassner AJ, Mane S, Lifton RP, Milosevic D, Tasic V, Baum MA, Hildebrandt F. Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis. Kidney Int 2017; 93:204-213. [PMID: 28893421 DOI: 10.1016/j.kint.2017.06.025] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/05/2017] [Accepted: 06/30/2017] [Indexed: 01/07/2023]
Abstract
The incidence of nephrolithiasis continues to rise. Previously, we showed that a monogenic cause could be detected in 11.4% of individuals with adult-onset nephrolithiasis or nephrocalcinosis and in 16.7-20.8% of individuals with onset before 18 years of age, using gene panel sequencing of 30 genes known to cause nephrolithiasis/nephrocalcinosis. To overcome the limitations of panel sequencing, we utilized whole exome sequencing in 51 families, who presented before age 25 years with at least one renal stone or with a renal ultrasound finding of nephrocalcinosis to identify the underlying molecular genetic cause of disease. In 15 of 51 families, we detected a monogenic causative mutation by whole exome sequencing. A mutation in seven recessive genes (AGXT, ATP6V1B1, CLDN16, CLDN19, GRHPR, SLC3A1, SLC12A1), in one dominant gene (SLC9A3R1), and in one gene (SLC34A1) with both recessive and dominant inheritance was detected. Seven of the 19 different mutations were not previously described as disease-causing. In one family, a causative mutation in one of 117 genes that may represent phenocopies of nephrolithiasis-causing genes was detected. In nine of 15 families, the genetic diagnosis may have specific implications for stone management and prevention. Several factors that correlated with the higher detection rate in our cohort were younger age at onset of nephrolithiasis/nephrocalcinosis, presence of multiple affected members in a family, and presence of consanguinity. Thus, we established whole exome sequencing as an efficient approach toward a molecular genetic diagnosis in individuals with nephrolithiasis/nephrocalcinosis who manifest before age 25 years.
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Affiliation(s)
- Ankana Daga
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Amar J Majmundar
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Department of Pharmacology, Brain Korea 21 Program for Leading Universities and Students Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shirlee Shril
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Tilman Jobst-Schwan
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Asaf Vivante
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Schapiro
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Weizhen Tan
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jillian K Warejko
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugen Widmeier
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Caleb P Nelson
- Department of Urology and General Pediatrics, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanan M Fathy
- Pediatric Nephrology Unit, Alexandria University, Alexandria, Egypt
| | - Zoran Gucev
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt; Egyptian Group for Orphan Renal Diseases, Cairo, Egypt
| | - Seema Hashmi
- Department of Pediatric Nephrology, Sindh Institute of Urology and Transplantation, Karachi, Pakistan
| | - Jan Halbritter
- Division of Endocrinology and Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
| | - Margarita Halty
- School of Medicine, Department of Pediatrics, Centro Hospitalario Pereira Rossell, Montevideo, Uruguay
| | - Jameela A Kari
- Pediatric Nephrology Center of Excellence and Pediatrics Department, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Sherif El-Desoky
- Pediatric Nephrology Center of Excellence and Pediatrics Department, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Michael A Ferguson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J G Somers
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avram Z Traum
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Deborah R Stein
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nancy M Rodig
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Avi Katz
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christian Hanna
- Division of Pediatric Nephrology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew L Schwaderer
- Division of Nephrology, Department of Pediatrics, Nationwide Children's Hospital/The Ohio State University, Columbus, Ohio, USA
| | - John A Sayer
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Ari J Wassner
- Division of Endocrinology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Danko Milosevic
- Department of Pediatric Nephrology, Dialysis and Transplantation, Clinical Hospital Center Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, Macedonia
| | - Michelle A Baum
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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Krishnamurthy S, Kartha GB, Venkateswaran VS, Prasannakumar M, Mahadevan S, Gowda M, Pelle A, Giachino D. Primary Hyperoxaluria Type 1 with Homozygosity for a Double-mutated AGXT Allele in a 2-year-old Child. Indian J Nephrol 2017; 27:402-405. [PMID: 28904440 PMCID: PMC5590421 DOI: 10.4103/ijn.ijn_261_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Primary hyperoxaluria (PH) Type 1 is a rare, genetic disorder caused by deficiency of the liver enzyme alanine-glyoxylate aminotransferase, which is encoded by AGXT gene. We report a 2-year-old South Indian Tamil child with nephrocalcinosis due to PH Type 1, in whom a homozygous genotype for two missense mutations in the AGXT gene was found: first, a C to G transversion (c. 32C>G) in exon 1 resulting in the amino acid substitution p.Pro11Arg; second, a T to A transversion (c. 167T>A) in exon 2 resulting in p.Ile56Asn. A therapy based on potassium citrate and pyridoxine was started. This is the first report of molecular testing-proven childhood onset-PH Type 1 from South India and is notable for the co-occurrence of two missense mutations in one AGXT allele, which might lead to different and more severe phenotype than each mutation alone. To the best of our knowledge, AGXT allele carrying two already known mutations has not been previously reported.
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Affiliation(s)
- S Krishnamurthy
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - G B Kartha
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - V S Venkateswaran
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - M Prasannakumar
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - S Mahadevan
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - M Gowda
- Department of Obstetrics and Gynecology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - A Pelle
- Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Orbassano, Torino, Italy
| | - D Giachino
- Department of Clinical and Biological Sciences, University of Torino, San Luigi University Hospital, Orbassano, Torino, Italy
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M'dimegh S, Omezzine A, M'barek I, Moussa A, Mabrouk S, Kaarout H, Souche G, Chemli J, Aloui S, Aquaviva-Bourdain C, Achour A, Abroug S, Bouslama A. Mutational Analysis of Agxt in Tunisian Population with Primary Hyperoxaluria Type 1. Ann Hum Genet 2016; 81:1-10. [PMID: 27935012 DOI: 10.1111/ahg.12178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/10/2016] [Indexed: 01/25/2023]
Abstract
BACKGROUND Primary hyperoxaluria type 1 (PH1) is an autosomal recessive metabolic disorder caused by inherited mutations in the AGXT gene encoding liver peroxisomal alanine:glyoxylate aminotransferase (AGT). PH1 is a clinically and genetically heterogeneous disorder. The aim of our study was to analyze and characterize the mutational spectrum of PH1 in Tunisian patients. MATERIALS AND METHODS Molecular studies of 146 Tunisian patients suspected with PH were performed by PCR/Restriction fragment length polymorphism (RFLP) to detect seven mutations described as the most common. Direct sequencing for the 11 exons was performed in patients in whom any mutation was not identified. RESULTS The genetic diagnosis of PH1 was confirmed in 62.3% of patients. The first molecular approach based on PCR/restriction enzyme test was positive in 37.6% of patients, whereas the second molecular approach based on whole gene sequencing was successful in 24% of cases. Twelve pathogenic mutations were detected in our cohort. Two mutations were novel, and five were detected for the first time in Tunisians. The three most frequent mutations were p.Ile244Thr, p.Gly190Arg, and c.33dupC, with a frequency of 43.4%, 21.4%, and 13.1%, respectively. CONCLUSION The two novel mutations detected in our study extend the spectrum of known AGXT gene mutations. The screen for the mutations identified in this study can provide a useful, cost-effective, and first-line investigation in Tunisian PH1 patients.
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Affiliation(s)
- Saoussen M'dimegh
- Biochemistry Department, Sahloul University Hospital, Sousse, Tunisia
| | - Asma Omezzine
- Biochemistry Department, Sahloul University Hospital, Sousse, Tunisia
| | - Ibtihel M'barek
- Biochemistry Department, Sahloul University Hospital, Sousse, Tunisia
| | - Amira Moussa
- Biochemistry Department, Sahloul University Hospital, Sousse, Tunisia
| | - Sameh Mabrouk
- Biochemistry Department, Sahloul University Hospital, Sousse, Tunisia
| | - Hayet Kaarout
- Internal Medicine A Department, Charles Nicolle University Hospital, Tunis, Tunisia
| | - Geneviéve Souche
- Laboratory of Inborn Metabolic Diseases, Centre de Biologie Est, Hospices Civils de Lyon, Lyon, France
| | - Jalel Chemli
- Pediatric Department, Sahloul University Hospital, Sousse, Tunisia
| | - Sabra Aloui
- Nephrology Department, Fatouma Bourguiba University Hospital, Monastir, Tunisia
| | - Cécile Aquaviva-Bourdain
- Laboratory of Inborn Metabolic Diseases, Centre de Biologie Est, Hospices Civils de Lyon, Lyon, France
| | | | - Saoussen Abroug
- Pediatric Department, Sahloul University Hospital, Sousse, Tunisia
| | - Ali Bouslama
- Biochemistry Department, Sahloul University Hospital, Sousse, Tunisia
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10
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Genetic defects underlying renal stone disease. Int J Surg 2016; 36:590-595. [PMID: 27838384 DOI: 10.1016/j.ijsu.2016.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
Abstract
Renal stones are common and are usually secondary to risk factors affecting the solubility of substances in the urinary tract. Primary, that is genetic, causes are rare but nevertheless are important to recognise so that appropriate treatments can be instigated and the risks to other family members acknowledged. A brief overview of the investigation of renal stones from a biochemical point of view is presented with emphasis on the problems that can arise. The genetic basis of renal stone disease caused by (i) derangement of a metabolic pathway, (ii) diversion to an insoluble product, (iii) failure of transport and (iv) renal tubular acidosis is described by reference to the disorders of adenine phosphoribosyl transferase (APRT) deficiency, primary hyperoxaluria, cystinuria and autosomal dominant distal renal tubular acidosis.
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11
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High throughput cell-based assay for identification of glycolate oxidase inhibitors as a potential treatment for Primary Hyperoxaluria Type 1. Sci Rep 2016; 6:34060. [PMID: 27670739 PMCID: PMC5037430 DOI: 10.1038/srep34060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 09/05/2016] [Indexed: 12/11/2022] Open
Abstract
Glycolate oxidase (GO) and alanine:glyoxylate aminotransferase (AGT) are both involved in the peroxisomal glyoxylate pathway. Deficiency in AGT function causes the accumulation of intracellular oxalate and the primary hyperoxaluria type 1 (PH1). AGT enhancers or GO inhibitors may restore the abnormal peroxisomal glyoxylate pathway in PH1 patients. With stably transformed cells which mimic the glyoxylate metabolic pathway, we developed an indirect glycolate cytotoxicity assay in a 1,536-well plate format for high throughput screening. This assay can be used to identify compounds that reduce indirect glycolate-induced cytotoxicity by either enhancing AGT activity or inhibiting GO. A pilot screen of 4,096 known compounds identified two membrane permeable GO inhibitors: dichromate salt and colistimethate. We also developed a GO enzyme assay using the hydrogen peroxide-Amplex red reporter system. The IC50 values of potassium dichromate, sodium dichromate, and colistimethate sodium were 0.096, 0.108, and 2.3 μM in the GO enzyme assay, respectively. Further enzyme kinetic study revealed that both types of compounds inhibit GO activity by the mixed linear inhibition. Our results demonstrate that the cell-based assay and GO enzyme assay developed in this study are useful for further screening of large compound libraries for drug development to treat PH1.
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12
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Two novel AGXT mutations identified in primary hyperoxaluria type-1 and distinct morphological and structural difference in kidney stones. Sci Rep 2016; 6:33652. [PMID: 27644547 PMCID: PMC5028881 DOI: 10.1038/srep33652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/30/2016] [Indexed: 12/02/2022] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare genetic disease characterized by excessive oxalate accumulation in plasma and urine, resulting in various phenotypes because of allelic and clinical heterogeneity. This study aimed to detect disease-associated genetic mutations in three PH1 patients in a Chinese family. All AGXT exons and 3 common polymorphisms which might synergistically interact with mutations, including P11L, I340 M and IVSI+74 bp were analyzed by direct sequencing in all family members. It demonstrated that in each of three patients, a previously reported nonsense mutation p.R333* was in cis with a novel missense mutation p.M49L in the minor allele characterized by the polymorphism of 74-bp duplication in intron 1, while the other novel missense mutation p.N72I was in trans with both p.R333* and P.M49L in the major allele. Kidney stones from two sibling patients were also observed though stereomicroscopic examination and scanning electron microscopy. Distinct morphological and inner-structure differences in calculi were noticed, suggesting clinical heterozygosity of PH1 to a certain extent. In brief, two novel missense mutations were identified probably in association with PH1, a finding which should provide an accurate tool for prenatal diagnosis, genetic counseling and screening for potential presymptomatic individuals.
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Montioli R, Oppici E, Dindo M, Roncador A, Gotte G, Cellini B, Borri Voltattorni C. Misfolding caused by the pathogenic mutation G47R on the minor allele of alanine:glyoxylate aminotransferase and chaperoning activity of pyridoxine. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1280-9. [DOI: 10.1016/j.bbapap.2015.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/03/2015] [Indexed: 12/22/2022]
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15
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Liver peroxisomal alanine:glyoxylate aminotransferase and the effects of mutations associated with Primary Hyperoxaluria Type I: An overview. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1212-9. [PMID: 25620715 DOI: 10.1016/j.bbapap.2014.12.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 12/19/2014] [Accepted: 12/20/2014] [Indexed: 11/21/2022]
Abstract
Liver peroxisomal alanine:glyoxylate aminotransferase (AGT) (EC 2.6.1.44) catalyses the conversion of l-alanine and glyoxylate to pyruvate and glycine, a reaction that allows glyoxylate detoxification. Inherited mutations on the AGXT gene encoding AGT lead to Primary Hyperoxaluria Type I (PH1), a rare disorder characterized by the deposition of calcium oxalate crystals primarily in the urinary tract. Here we describe the results obtained on the biochemical features of AGT as well as on the molecular and cellular effects of polymorphic and pathogenic mutations. A complex scenario on the molecular pathogenesis of PH1 emerges in which the co-inheritance of polymorphic changes and the condition of homozygosis or compound heterozygosis are two important factors that determine the enzymatic phenotype of PH1 patients. All the reported data represent relevant steps toward the understanding of genotype/phenotype correlations, the prediction of the response of the patients to the available therapies, and the development of new therapeutic approaches. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.
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Pharmacologic rescue of an enzyme-trafficking defect in primary hyperoxaluria 1. Proc Natl Acad Sci U S A 2014; 111:14406-11. [PMID: 25237136 DOI: 10.1073/pnas.1408401111] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Primary hyperoxaluria 1 (PH1; Online Mendelian Inheritance in Man no. 259900), a typically lethal biochemical disorder, may be caused by the AGT(P11LG170R) allele in which the alanine:glyoxylate aminotransferase (AGT) enzyme is mistargeted from peroxisomes to mitochondria. AGT contains a C-terminal peroxisomal targeting sequence, but mutations generate an N-terminal mitochondrial targeting sequence that directs AGT from peroxisomes to mitochondria. Although AGT(P11LG170R) is functional, the enzyme must be in the peroxisome to detoxify glyoxylate by conversion to alanine; in disease, amassed glyoxylate in the peroxisome is transported to the cytosol and converted to oxalate by lactate dehydrogenase, leading to kidney failure. From a chemical genetic screen, we have identified small molecules that inhibit mitochondrial protein import. We tested whether one promising candidate, Food and Drug Administration (FDA)-approved dequalinium chloride (DECA), could restore proper peroxisomal trafficking of AGT(P11LG170R). Indeed, treatment with DECA inhibited AGT(P11LG170R) translocation into mitochondria and subsequently restored trafficking to peroxisomes. Previous studies have suggested that a mitochondrial uncoupler might work in a similar manner. Although the uncoupler carbonyl cyanide m-chlorophenyl hydrazone inhibited AGT(P11LG170R) import into mitochondria, AGT(P11LG170R) aggregated in the cytosol, and cells subsequently died. In a cellular model system that recapitulated oxalate accumulation, exposure to DECA reduced oxalate accumulation, similar to pyridoxine treatment that works in a small subset of PH1 patients. Moreover, treatment with both DECA and pyridoxine was additive in reducing oxalate levels. Thus, repurposing the FDA-approved DECA may be a pharmacologic strategy to treat PH1 patients with mutations in AGT because an additional 75 missense mutations in AGT may also result in mistrafficking.
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