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Bordeneuve-Plante P, Boussion S, Rama M, Brunelle P, Thuillier C, Vanlerberghe C, Caumes R, Colson C, Ait-Yahya E, Ghoumid J, Smol T. Expanded phenotypic spectrum of UDP-glucose-6-dehydrogenase recessive neurodevelopmental disorder: Two novel descriptions with or without epileptic encephalopathy. Am J Med Genet A 2024:e63820. [PMID: 38997820 DOI: 10.1002/ajmg.a.63820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/27/2024] [Accepted: 07/07/2024] [Indexed: 07/14/2024]
Abstract
Recent advances in the understanding of infantile developmental epileptic encephalopathies (IDEE) have revealed the association of biallelic pathogenic variants in UGDH. In this study, we report two novel combinations identified by exome sequencing: p.(Arg135Trp) with p.(Arg65*) and p.(Arg102Trp) with p.(Arg65*). Both combinations share a common pathogenic nonsense variant, with the missense variants strategically located in the NAD-binding domain of the UGDH protein, predicted in structural models to create new interactions with the central domain. The first patient exhibited the typical UGDH-related disease phenotype and progressive microcephaly, a rarely reported feature. In contrast, the second patient presented an atypical phenotype, including absence of seizure, severe intellectual disability, ataxic gait, and abnormal eye movements. This comprehensive analysis extends the phenotypic spectrum of UGDH syndrome beyond early infantile intractable encephalopathy to include intellectual disability without epilepsy.
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Affiliation(s)
| | - Simon Boussion
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
- CHU Lille, Clinique de Génétique, CRMR Déficiences Intellectuelles de Causes Rares, Lille, France
| | - Mélanie Rama
- CHU Lille, Institut de Génétique Médicale, Lille, France
| | - Perrine Brunelle
- CHU Lille, Institut de Génétique Médicale, Lille, France
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
| | | | - Clémence Vanlerberghe
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
- CHU Lille, Clinique de Génétique, CRMR Déficiences Intellectuelles de Causes Rares, Lille, France
| | - Roseline Caumes
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
- CHU Lille, Clinique de Génétique, CRMR Déficiences Intellectuelles de Causes Rares, Lille, France
| | - Cindy Colson
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
- CHU Lille, Clinique de Génétique, CRMR Déficiences Intellectuelles de Causes Rares, Lille, France
| | - Emilie Ait-Yahya
- CHU Lille, Unité de Bio-informatique, Plateau de Biologie-Moléculaire, Lille, France
| | - Jamal Ghoumid
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
- CHU Lille, Clinique de Génétique, CRMR Déficiences Intellectuelles de Causes Rares, Lille, France
| | - Thomas Smol
- CHU Lille, Institut de Génétique Médicale, Lille, France
- Univ. Lille, ULR7364 - RADEME - Maladies RAres du Developpement embryonnaire et du Métabolisme, Lille, France
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Alaamery M, Massadeh S, Aldarwish M, Albesher N, Aljawini N, Alahmed O, Kashgari A, Walsh CA, Eyaid W. Case report: A founder UGDH variant associated with developmental epileptic encephalopathy in Saudi Arabia. Front Genet 2024; 14:1294214. [PMID: 38292436 PMCID: PMC10824937 DOI: 10.3389/fgene.2023.1294214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Congenital disorders of glycosylation (CDG) are a group of more than 100 rare genetic disorders characterized by impaired glycosylation of proteins and lipids. The clinical presentation of CDG varies tremendously, from single-organ to multi-organ involvement and from prenatal death to a normal adult phenotype. In this case study, we report a large consanguineous family with multiple children suffering from cerebral palsy, seizure, developmental and epileptic encephalopathy, and global developmental delay. Whole-exome sequencing (WES) analysis revealed a homozygous variant in the UDP-glucose dehydrogenase (UGDH) gene (c.950G>A; p.R317Q) which segregates with the familial phenotype with a plausible autosomal recessive mode of inheritance, indicating a potential disease-causing association. The UGDH gene encodes the UDP-glucose dehydrogenase, a key enzyme in the synthesis of specific extracellular matrix constituents (proteoglycans and glycolipids) involved in neural migration and connectivity during early brain development. Many pathogenic mutations of UGDH have been reported in recent literature works. However, the variant identified in this study has been observed only in the Saudi population (13 families) and not in any other ethnic background, suggesting that it may be an ancient founder mutation.
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Affiliation(s)
- Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Manar Aldarwish
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nour Albesher
- Saudi Genome Program, National Centre for Genomic Technologies, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nora Aljawini
- KACST-BWH Centre of Excellence for Biomedicine, Joint Centres of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Othman Alahmed
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Amna Kashgari
- King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Radiology, King Abdullah Specialized Children’s Hospital, King Abdul Aziz Medical City, Riyadh, Saudi Arabia
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Department of Pediatrics, Boston Children’s Hospital, and Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Wafaa Eyaid
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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3
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Jiang L, Bi S, Lin L, He F, Deng F. Phenotypic and genetic characteristics of 24 cases of early infantile epileptic encephalopathy in East China, including a rare case of biallelic UGDH mutations. Mol Genet Genomic Med 2023; 11:e2269. [PMID: 37593999 PMCID: PMC10724516 DOI: 10.1002/mgg3.2269] [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: 01/30/2023] [Revised: 04/13/2023] [Accepted: 07/27/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Early infantile epileptic encephalopathy (EIEE) is a group of highly heterogeneous diseases, both phenotypically and genetically. Usually, it starts early on and manifests as intractable epilepsy, abnormal electroencephalogram, and growth retardation/intellectual impairment. With the advent of next-generation sequencing (NGS), its genetic etiology has attracted increasing clinical attention. This study aimed to investigate the genetic characteristics and clinical phenotypes of patients with EIEE from a central hospital in Eastern China. METHODS This study retrospectively included the gene variants from 24 EIEE-positive patients admitted between January 2021 and January 2022 to a hospital in Anhui Province, China. The genetic diagnosis was performed in all cases by trio-based whole-exome sequencing (WES). Additionally, Video electroencephalogram (VEEG) and neuroimaging examinations were performed. RESULTS A total of 24 children were included. The average age at the first seizure was approximately 5 months. About 42% of children had developmental retardation of varying degrees, 43% had brain structural abnormalities, and 64% had VEEG abnormalities. In addition, other phenotypes, including endocrine metabolism and cardiac structural abnormalities, have been independently reported. In total, fifteen pathogenic gene variants were identified in 24 patients. The main pathogenic genes identified were SCN1A (25%, 6/24), KCNQ2 (8.3%, 2/24), and TBC1D24 (8.3%, 2/24). We also found an extremely rare case of EIEE84 type caused by biallelic UGDH gene variants, predicting that this variant might affect the stability of the protein structure. CONCLUSIONS SCN1A pathogenic variants are the main factor leading to EIEE, similar to previously published cohort reports. NGS is useful for accurate clinical diagnoses and precise treatment choices. We also reported a rare case of EIEE84 caused by variants in the UGDH gene in a Chinese patient. This study further enriches the known spectrum of pathogenic EIEE genes.
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Affiliation(s)
- Liangliang Jiang
- Department of NeurologyChildren's Hospital of Anhui Medical University (Anhui Provincial Children's Hospital)HefeiChina
| | - Shaohua Bi
- Department of NeonatologyChildren's Hospital of Anhui Medical University (Anhui Provincial Children's Hospital)HefeiChina
| | - Li Lin
- Department of NeurologyChildren's Hospital of Anhui Medical University (Anhui Provincial Children's Hospital)HefeiChina
| | - Fan He
- Department of NeurologyChildren's Hospital of Anhui Medical University (Anhui Provincial Children's Hospital)HefeiChina
| | - Fang Deng
- Department of NephrologyChildren's Hospital of Anhui Medical University (Anhui Provincial Children's Hospital)HefeiChina
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Liu Y, Li Y, Li G, Chu H. The molecular mechanism of Y473 phosphorylation of UGDH relieves the inhibition effect of UDP-glucose on HuR. Phys Chem Chem Phys 2023; 25:8714-8724. [PMID: 36896759 DOI: 10.1039/d3cp00227f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Uridine diphosphate glucose (UDP-Glc) is able to accelerate the decay of snail family transcriptional repressor 1 (SNAI1) mRNA by inhibiting Hu antigen R (HuR, an RNA-binding protein), thereby preventing cancer invasiveness and drug resistance. Nevertheless, the phosphorylation of tyrosine 473 (Y473) of UDP-glucose dehydrogenase (UGDH is capable of converting UDP-Glc to uridine diphosphate glucuronic acid (UDP-GlcUA)) weakens the inhibition of UDP-Glc to HuR, thus initiating the epithelial-mesenchymal transformation of tumor cells and promoting tumor cell migration and metastasis. To address the mechanism, we performed molecular dynamics simulations combined with molecular mechanics generalized Born surface area (MM/GBSA) analysis on wild-type and Y473 phosphorylated UGDH and HuR, UDP-Glc, UDP-GlcUA complexes. We demonstrated that Y473 phosphorylation was able to enhance the binding between UGDH and the HuR/UDP-Glc complex. Compared with HuR, UGDH has a stronger binding ability with UDP-Glc; therefore, UDP-Glc was inclined to bind to UGDH and then was catalyzed to UDP-GlcUA by UGDH, which relieved the inhibition of UDP-Glc to HuR. In addition, the binding ability of HuR for UDP-GlcUA was lower than its affinity for UDP-Glc, significantly reducing the inhibition of HuR. Hence, HuR bound to SNAI1 mRNA more easily to increase the stability of mRNA. Our results revealed the micromolecular mechanism of Y473 phosphorylation of UGDH regulating the interaction between UGDH and HuR as well as relieving the inhibition of UDP-Glc on HuR, which contributed to understanding the role of UGDH and HuR in tumor metastasis and developing small molecule drugs targeting the interaction between UGDH and HuR.
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Affiliation(s)
- Ye Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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5
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Alyafee Y, Al Tuwaijri A, Umair M, Alharbi M, Haddad S, Ballow M, Alayyar L, Alam Q, Althenayyan S, Al Ghilan N, Al Khaldi A, Faden MS, Al Sufyan H, Alfadhel M. Non-invasive prenatal testing for autosomal recessive disorders: A new promising approach. Front Genet 2022; 13:1047474. [PMID: 36406136 PMCID: PMC9669374 DOI: 10.3389/fgene.2022.1047474] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Background: In pregnant women at risk of autosomal recessive (AR) disorders, prenatal diagnosis of AR disorders primarily involves invasive procedures, such as chorionic villus sampling and amniocentesis. Methods: We collected blood samples from four pregnant women in their first trimester who presented a risk of having a child with an AR disorder. Cell-free DNA (cfDNA) was extracted, amplified, and double-purified to reduce maternal DNA interference. Additionally, whole-genome amplification was performed for traces of residual purified cfDNA for utilization in subsequent applications. Results: Based on our findings, we detected the fetal status with the family corresponding different genes, i.e., LZTR1, DVL2, HBB, RNASEH2B, and MYO7A, as homozygous affected, wild-type, and heterozygous carriers, respectively. Results were subsequently confirmed by prenatal amniocentesis. The results of AmpFLSTR™ Identifiler™ presented a distinct profile from the corresponding mother profile, thereby corroborating the result reflecting the genetic material of the fetus. Conclusion: Herein, we detected AR disease mutations in the first trimester of pregnancy while surmounting limitations associated with maternal genetic material interference. Importantly, such detection strategies would allow the screening of pregnant women for common AR diseases, especially in highly consanguineous marriage populations. This technique would open avenues for the early detection and prevention of recessive diseases among the population.
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Affiliation(s)
- Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mashael Alharbi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Shahad Haddad
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Maryam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Latifah Alayyar
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Saleh Althenayyan
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nadia Al Ghilan
- Maternal Fetal Medicine Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Aziza Al Khaldi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Majid S. Faden
- Department of Obstetrics and Gynaecology, Maternal Fetal Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hamad Al Sufyan
- Assisted Reproductive Technology Laboratories, Thuriah Medical Center, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNG-HA, Riyadh, Saudi Arabia
- *Correspondence: Majid Alfadhel,
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Al Hawsawi K, Al Jabri M, Dajam MS, Almahdi B, Alhawsawi WK, Abbas S, Al Tuwaijri A, Umair M, Alfadhel M, Al-Khenaizan S. Case Report: Bi-allelic missense variant in the desmocollin 3 gene causes hypotrichosis and recurrent skin vesicles. Front Genet 2022; 13:994509. [PMID: 36061207 PMCID: PMC9428628 DOI: 10.3389/fgene.2022.994509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Hypotrichosis with Recurrent Skin Vesicles (HYPTSV) is an extremely rare condition, having autosomal recessive inheritance. Here in we report a 4-years- old Saudi boy who presented with a history of recurrent skin blisters that are localized to the extremities and hypotrichosis since birth.Methods: The present study describes a consanguineous Saudi family segregating HYPTSV in an autosomal recessive fashion. A single proband (II-1) exhibited features such as diffused non-scarring alopecia on the scalp, intraepidermal blister, post-inflammatory hyperpigmented macules, and follicular hyperkeratosis. DNA of the index was subjected to whole-genome sequencing (WGS). Furthermore, 3D protein modeling was performed for the mutated and normal protein.Results: WGS revealed a novel bi-allelic missense variant (c.154G>C; p. Val52Leu) in the DSC3 gene, which segregated perfectly using Sanger sequencing. In addition, 3D protein modeling revealed a substantial change in the mutated DSC3 protein as compared to the normal DSC3 protein.Conclusion: This is the 3rd novel variant reported in the DSC3 gene associated with the HYPTSV phenotype. This report further strengthens the evidence that bi-allelic variants in the DSC3 cause severe HYPTSV in humans.
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Affiliation(s)
- Khalid Al Hawsawi
- Dermatology Department, King Abdulaziz Hospital, Makkah, Saudi Arabia
| | - Mazin Al Jabri
- Dermatology Department, Hera General Hospital, Makkah, Saudi Arabia
| | - Mazen S Dajam
- Dermatology Department, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | - Bashaer Almahdi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Waseem K Alhawsawi
- Dermatology Department, King Fahad Hospital of The University, Al Khobar, Saudi Arabia
| | - Safdar Abbas
- Department of Biological Science, Dartmouth College, Hanover, NH, United States
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGH), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
- Genetics and Precision Medicine Department, King Abdullah Specialized Children Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Sultan Al-Khenaizan
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- Department of Dermatology, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
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7
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Mackowetzky K, Dicipulo R, Fox SC, Philibert DA, Todesco H, Doshi JD, Kawakami K, Tierney K, Waskiewicz AJ. Retinoic acid signaling regulates late stages of semicircular canal morphogenesis and otolith maintenance in the zebrafish inner ear. Dev Dyn 2022; 251:1798-1815. [PMID: 35710880 DOI: 10.1002/dvdy.510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The vitamin A derivative all-trans retinoic acid (RA) regulates early stages of inner ear development. As the early disruption of the RA pathway results in profound mispatterning of the developing inner ear, this confounds analyses of specific roles in later stages. Therefore, we used the temporal-specific exposure of all-trans RA or diethylaminobenzaldehyde to evaluate RA functions in late otic development. RESULTS Perturbing late RA signaling causes behavioral defects analogous to those expected in larvae suffering from vestibular dysfunction. These larvae also demonstrate malformations of the semi-circular canals, as visualized through (a) use of the transgenic strain nkhspdmc12a, a fluorescent reporter expressed in otic epithelium; and (b) injection of the fluorescent lipophilic dye DiI. We also noted the altered expression of genes encoding ECM proteins or modifying enzymes. Other malformations of the inner ear observed in our work include the loss or reduced size of the utricular and saccular otoliths, suggesting a role for RA in otolith maintenance. CONCLUSION Our work has identified a previously undescribed late phase of RA activity in otic development, demonstrating that vestibular defects observed in human patients in relation to perturbed RA signaling are not solely due to its early disruption in otic development.
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Affiliation(s)
- Kacey Mackowetzky
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Renée Dicipulo
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Sabrina C Fox
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Women & Children's Health Research Institute, Edmonton, Alberta, Canada
| | - Danielle A Philibert
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Hayley Todesco
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jainil D Doshi
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Shizuoka, Japan
| | - Keith Tierney
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew J Waskiewicz
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Women & Children's Health Research Institute, Edmonton, Alberta, Canada
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8
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Zimmer BM, Barycki JJ, Simpson MA. Mechanisms of coordinating hyaluronan and glycosaminoglycan production by nucleotide sugars. Am J Physiol Cell Physiol 2022; 322:C1201-C1213. [PMID: 35442826 DOI: 10.1152/ajpcell.00130.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hyaluronan is a versatile macromolecule capable of an exceptional range of functions from cushioning and hydration to dynamic signaling in development and disease. Because of its critical roles, hyaluronan production is regulated at multiple levels including epigenetic, transcriptional, and post-translational control of the three hyaluronan synthase (HAS) enzymes. Precursor availability can dictate the rate and amount of hyaluronan synthesized and shed by the cells producing it. However, the nucleotide-activated sugar substrates for hyaluronan synthesis by HAS also participate in exquisitely fine tuned cross talking pathways that intersect with central carbohydrate metabolism. Multiple UDP-sugars have alternative metabolic fates and exhibit coordinated and reciprocal allosteric control of enzymes within their biosynthetic pathways to preserve appropriate precursor ratios for accurate partitioning among downstream products, while also sensing and maintaining energy homeostasis. Since the dysregulation of nucleotide sugar and hyaluronan synthesis is associated with multiple pathologies, these pathways offer opportunities for therapeutic intervention. Recent structures of several key rate-limiting enzymes in the UDP-sugar synthesis pathways have offered new insights to the overall regulation of hyaluronan production by precursor fate decisions. The details of UDP-sugar control and the structural basis for underlying mechanisms are discussed in this review.
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Affiliation(s)
- Brenna M Zimmer
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Joseph J Barycki
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Melanie A Simpson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
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9
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Vymětal J, Jakubec D, Galgonek J, Vondrášek J. Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures. Nucleic Acids Res 2021; 49:W15-W20. [PMID: 34019656 PMCID: PMC8262704 DOI: 10.1093/nar/gkab377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/10/2021] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
Interactions among amino acid residues are the principal contributor to the stability of the three-dimensional structure of a protein. The Amino Acid Interactions (INTAA) web server (https://bioinfo.uochb.cas.cz/INTAA/) has established itself as a unique computational resource, which enables users to calculate the contribution of individual residues in a biomolecular structure to its total energy using a molecular mechanical scoring function. In this update, we describe major additions to the web server which help solidify its position as a robust, comprehensive resource for biomolecular structure analysis. Importantly, a new continuum solvation model was introduced, allowing more accurate representation of electrostatic interactions in aqueous media. In addition, a low-overhead pipeline for the estimation of evolutionary conservation in protein chains has been added. New visualization options were introduced as well, allowing users to easily switch between and interrelate the energetic and evolutionary views of the investigated structures.
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Affiliation(s)
- Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic
| | - David Jakubec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic.,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Praha 1, 118 00, Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha 6, 160 00, Czech Republic
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10
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Anderson LM, Fox DB, Chesney KL, Coates JR, Torres BT, Lyons LA. Skeletal Manifestations of Heritable Disproportionate Dwarfism in Cats as Determined by Radiography and Magnetic Resonance Imaging. Vet Comp Orthop Traumatol 2021; 34:327-337. [PMID: 34082456 DOI: 10.1055/s-0041-1730355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVE The aim of this study was to characterize the radiographic alignment of thoracic and pelvic limbs and evaluate for intervertebral disc disease in cats with feline disproportionate dwarfism (FDD). STUDY DESIGN Observational cross-sectional study. Radiographic joint orientation angles were measured in 10 thoracic and pelvic limbs from 5 FDD cats and compared with those angles measured in 24 thoracic limbs and 100 pelvic limbs from skeletally normal cats. Magnetic resonance imaging of the spine was performed in 2 FDD cats for the evaluation of pathology of the intervertebral discs or vertebrae. RESULTS All limbs from FDD cats possessed deformities. FDD humeri demonstrated procurvatum proximally, and recurvatum distally in the sagittal plane, but showed no difference in the frontal plane. FDD radii possessed excessive recurvatum proximally, and procurvatum distally in the sagittal plane, and varus proximally and valgus distally in the frontal plane. Whereas no torsion was discernible in the humeri, all radii had external torsion. In the frontal plane, FDD femurs exhibited varus both proximally and distally whereas the tibia possessed proximal valgus and distal varus. No torsion in the pelvic limbs was observed. No spinal pathology was detected in the FDD cats included in the original study. CONCLUSION Feline disproportionate dwarfism results in significant appendicular deformity in all limbs. The incidence of intervertebral disc degeneration in FDD cats is inconclusive.
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Affiliation(s)
- Lisa M Anderson
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
| | - Derek B Fox
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
| | - Kari L Chesney
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
| | - Joan R Coates
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
| | - Bryan T Torres
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States
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11
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Alfadhel M, Umair M, Almuzzaini B, Asiri A, Al Tuwaijri A, Alhamoudi K, Alyafee Y, Al-Owain M. Identification of the TTC26 Splice Variant in a Novel Complex Ciliopathy Syndrome with Biliary, Renal, Neurological, and Skeletal Manifestations. Mol Syndromol 2021; 12:133-140. [PMID: 34177428 DOI: 10.1159/000513829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/16/2020] [Indexed: 12/27/2022] Open
Abstract
Ciliopathies constitute heterogeneous disorders that result from mutations in ciliary proteins. These proteins play an important role in the development of organs, physiology, and signaling pathways, and sequence variations in the genes encoding these proteins are associated with multisystem disorders. In this study, we describe a severe ciliopathy disorder that segregates in an autosomal recessive manner in a nonconsanguineous Saudi family. The proband exhibited features such as cholestasis, cystic dilatation of intrahepatic biliary ducts, diabetes insipidus, dysmorphic facial features, optic atrophy, pituitary hypoplasia, hydrocephalus, aqueductal stenosis, hyperextensible knee joints, bilateral knee dislocation, polydactyly, and syndactyly. Whole-genome sequencing and Sanger sequencing revealed a homozygous splice site variant (c.4-1G>C; NM_024926.3) in the tetratricopeptide repeat domain 26 (TTC26) gene located in chromosome 7q34, which cosegregated perfectly with the disease phenotype. qRT-PCR revealed a substantial decrease in the expression of the TTC26 gene as compared to the normal control, suggesting the pathogenicity of the identified variant. This report further strengthens the evidence that homozygous variants in the TTC26 gene cause severe ciliopathies with diverse phenotypes. We named this newly characterized condition as BRENS syndrome, which stands for biliary, renal, neurological, and skeletal features.
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Affiliation(s)
- Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,King Saud Bin Abdulaziz University for Health Sciences, MNGH, Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children's Hospital, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,King Saud Bin Abdulaziz University for Health Sciences, MNGH, Riyadh, Saudi Arabia
| | - Bader Almuzzaini
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,King Saud Bin Abdulaziz University for Health Sciences, MNGH, Riyadh, Saudi Arabia
| | - Abdulaziz Asiri
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Faculty of Applied Medical Sciences, University of Bisha, Bisha, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,King Saud Bin Abdulaziz University for Health Sciences, MNGH, Riyadh, Saudi Arabia
| | - Khaloud Alhamoudi
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,King Saud Bin Abdulaziz University for Health Sciences, MNGH, Riyadh, Saudi Arabia
| | - Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,King Saud Bin Abdulaziz University for Health Sciences, MNGH, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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12
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Buckley RM, Davis BW, Brashear WA, Farias FHG, Kuroki K, Graves T, Hillier LW, Kremitzki M, Li G, Middleton RP, Minx P, Tomlinson C, Lyons LA, Murphy WJ, Warren WC. A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism. PLoS Genet 2020; 16:e1008926. [PMID: 33090996 PMCID: PMC7581003 DOI: 10.1371/journal.pgen.1008926] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/10/2020] [Indexed: 12/30/2022] Open
Abstract
The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBio long sequence reads that significantly improve sequence representation and assembly contiguity. The whole genome sequences of 54 domestic cats were aligned to the reference to identify single nucleotide variants (SNVs) and structural variants (SVs). Across all cats, 16 SNVs predicted to have deleterious impacts and in a singleton state were identified as high priority candidates for causative mutations. One candidate was a stop gain in the tumor suppressor FBXW7. The SNV is found in cats segregating for feline mediastinal lymphoma and is a candidate for inherited cancer susceptibility. SV analysis revealed a complex deletion coupled with a nearby potential duplication event that was shared privately across three unrelated cats with dwarfism and is found within a known dwarfism associated region on cat chromosome B1. This SV interrupted UDP-glucose 6-dehydrogenase (UGDH), a gene involved in the biosynthesis of glycosaminoglycans. Importantly, UGDH has not yet been associated with human dwarfism and should be screened in undiagnosed patients. The new high-quality cat genome reference and the compilation of sequence variation demonstrate the importance of these resources when searching for disease causative alleles in the domestic cat and for identification of feline biomedical models. The practice of genomic medicine is predicated on the availability of a high quality reference genome and an understanding of the impact of genome variation. Such resources have lead to countless discoveries in humans, however by working exclusively within the framework of human genetics, our potential for understanding diseases biology is limited, as similar analyses in other species have often lead to novel insights. The generation of Felis_catus_9.0, a new high quality reference genome for the domestic cat, helps facilitate the expansion of genomic medicine into the Felis lineage. Using Felis_catus_9.0 we analyze the landscape of genomic variation from a collection of 54 cats within the context of human gene constraint. The distribution of variant impacts in cats is correlated with patterns of gene constraint in humans, indicating the utility of this reference for identifying novel mutations that cause phenotypes relevant to human and cat health. Moreover, structural variant analysis revealed a novel variant for feline dwarfism in UGDH, a gene that has not been associated with dwarfism in any other species, suggesting a role for UGDH in cases of undiagnosed dwarfism in humans.
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Affiliation(s)
- Reuben M. Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Wesley A. Brashear
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Fabiana H. G. Farias
- Department of Psychiatry, Washington University, St. Louis, Missouri, United States of America
- NeuroGenomics and Informatics, Washington University, St. Louis, Missouri, United States of America
| | - Kei Kuroki
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - Tina Graves
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - LaDeana W. Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Gang Li
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | | | - Patrick Minx
- Donald Danforth Plant Science, St Louis, Missouri, United States of America
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, United States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Wesley C. Warren
- Division of Animal Sciences, School of Medicine, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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13
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Zimmer BM, Barycki JJ, Simpson MA. Integration of Sugar Metabolism and Proteoglycan Synthesis by UDP-glucose Dehydrogenase. J Histochem Cytochem 2020; 69:13-23. [PMID: 32749901 DOI: 10.1369/0022155420947500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Regulation of proteoglycan and glycosaminoglycan synthesis is critical throughout development, and to maintain normal adult functions in wound healing and the immune system, among others. It has become increasingly clear that these processes are also under tight metabolic control and that availability of carbohydrate and amino acid metabolite precursors has a role in the control of proteoglycan and glycosaminoglycan turnover. The enzyme uridine diphosphate (UDP)-glucose dehydrogenase (UGDH) produces UDP-glucuronate, an essential precursor for new glycosaminoglycan synthesis that is tightly controlled at multiple levels. Here, we review the cellular mechanisms that regulate UGDH expression, discuss the structural features of the enzyme, and use the structures to provide a context for recent studies that link post-translational modifications and allosteric modulators of UGDH to its function in downstream pathways.
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Affiliation(s)
- Brenna M Zimmer
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Joseph J Barycki
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
| | - Melanie A Simpson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina
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