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Bernardini G, Braconi D, Zatkova A, Sireau N, Kujawa MJ, Introne WJ, Spiga O, Geminiani M, Gallagher JA, Ranganath LR, Santucci A. Alkaptonuria. Nat Rev Dis Primers 2024; 10:16. [PMID: 38453957 DOI: 10.1038/s41572-024-00498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
Alkaptonuria is a rare inborn error of metabolism caused by the deficiency of homogentisate 1,2-dioxygenase activity. The consequent homogentisic acid (HGA) accumulation in body fluids and tissues leads to a multisystemic and highly debilitating disease whose main features are dark urine, ochronosis (HGA-derived pigment in collagen-rich connective tissues), and a painful and severe form of osteoarthropathy. Other clinical manifestations are extremely variable and include kidney and prostate stones, aortic stenosis, bone fractures, and tendon, ligament and/or muscle ruptures. As an autosomal recessive disorder, alkaptonuria affects men and women equally. Debilitating symptoms appear around the third decade of life, but a proper and timely diagnosis is often delayed due to their non-specific nature and a lack of knowledge among physicians. In later stages, patients' quality of life might be seriously compromised and further complicated by comorbidities. Thus, appropriate management of alkaptonuria requires a multidisciplinary approach, and periodic clinical evaluation is advised to monitor disease progression, complications and/or comorbidities, and to enable prompt intervention. Treatment options are patient-tailored and include a combination of medications, physical therapy and surgery. Current basic and clinical research focuses on improving patient management and developing innovative therapies and implementing precision medicine strategies.
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Affiliation(s)
- Giulia Bernardini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
| | - Daniela Braconi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Andrea Zatkova
- Institute of Clinical and Translational Research, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
- Geneton Ltd, Bratislava, Slovakia
| | | | - Mariusz J Kujawa
- 2nd Department of Radiology, Medical University of Gdansk, Gdansk, Poland
| | - Wendy J Introne
- Human Biochemical Genetics Section, Medical Genetics Branch, Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Michela Geminiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - James A Gallagher
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences University of Liverpool, Liverpool, UK
| | - Lakshminarayan R Ranganath
- Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences University of Liverpool, Liverpool, UK
- Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool University Hospital, Liverpool, UK
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
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2
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Littman J, Pietro J, Olansen J, Phornphutkul C, Aaron RK. Ochronotic Chondropathy: A Case Report. Biomedicines 2023; 11:2625. [PMID: 37892999 PMCID: PMC10604465 DOI: 10.3390/biomedicines11102625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Endogenous ochronosis, also known as alkaptonuria, is a rare disease known for its bluish-black discoloration of the skin, sclerae, and pinnae, as well as urine that turns black upon standing. Though rarely fatal, joint degradation is a common sequela, and many patients require multiple large joint arthroplasties throughout their lifetime. Though many aspects of the pathophysiological mechanisms of the disease have been described, questions remain, such as how the initiation of ochronotic pigmentation is prompted and the specific circumstances that make some tissues more resistant to pigmentation-related damage than others. In this report, we present the case of an 83-year-old female previously diagnosed with alkaptonuria including high-quality arthroscopic images displaying the fraying of articular cartilage. We also offer a summary of the latest literature on the pathophysiological mechanisms of the disease, including cellular-level changes observed in ochronotic chondrocytes, biochemical and mechanical alterations to the cartilaginous extracellular matrix, and patterns of pigmentation and joint degradation observed in humans and mice models. With these, we present an overview of the mechanisms of ochronotic chondropathy and joint degradation as the processes are currently understood. While alkaptonuria itself is rare, it has been termed a "fundamental disease," implying that its study and greater understanding have the potential to lead to insights in skeletal biology in general, as well as more common pathologies such as osteoarthritis and their potential treatment mechanisms.
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Affiliation(s)
- Jake Littman
- Department of Orthopedic Surgery, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John Pietro
- Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Jon Olansen
- Department of Orthopedic Surgery, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Chanika Phornphutkul
- Division of Human Genetics, Department of Pediatrics, Hasbro Children’s Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Roy K. Aaron
- Department of Orthopedic Surgery, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
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Abdelkhalek ZS, Mahmoud IG, Omair H, Abdulhay M, Elmonem MA. Homogentisate 1,2-dioxygenase (HGD) gene variants in young Egyptian patients with alkaptonuria. Sci Rep 2023; 13:14374. [PMID: 37658095 PMCID: PMC10474279 DOI: 10.1038/s41598-023-41200-7] [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: 02/15/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Alkaptonuria (AKU) is a rare autosomal recessive metabolic disorder caused by pathogenic variants in the homogentisate 1,2-dioxygenase (HGD) gene. This leads to a deficient HGD enzyme with the consequent accumulation of homogentisic acid (HGA) in different tissues causing complications in various organs, particularly in joints, heart valves and kidneys. The genetic basis of AKU in Egypt is completely unknown. We evaluated the clinical and genetic spectrum of six pediatric and adolescents AKU patients from four unrelated Egyptian families. All probands had a high level of HGA in urine by qualitative GC/MS before genetic confirmation by Sanger sequencing. Recruited AKU patients were four females and two males (median age 13 years). We identified four different pathogenic missense variants within HGD gene. Detected variants included a novel variant c.1079G > T;p.(Gly360Val) and three recurrent variants; c.1078G > C;p.(Gly360Arg), c.808G > A;p.(Gly270Arg) and c.473C > T;p.(Pro158Leu). All identified variants were properly segregating in the four families consistent with autosomal recessive inheritance. In this study, we reported the phenotypic and genotypic spectrum of alkaptonuria for the first time in Egypt. We further enriched the HGD-variant database with another novel pathogenic variant. The recent availability of nitisinone may promote the need for genetic confirmation at younger ages to start therapy earlier and prevent serious complications.
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Affiliation(s)
- Zeinab S Abdelkhalek
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Center of Social and Preventive Medicine, Room 409, Monira, Cairo, 11628, Egypt.
| | - Iman G Mahmoud
- Metabolic Division, Pediatrics Neurology Department, Faculty of Medicine, Cairo University Children's Hospital, Cairo, Egypt
| | - Heba Omair
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Center of Social and Preventive Medicine, Room 409, Monira, Cairo, 11628, Egypt
| | - Mohamed Abdulhay
- Pediatrics Department, Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Mohamed A Elmonem
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Center of Social and Preventive Medicine, Room 409, Monira, Cairo, 11628, Egypt
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4
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Fayette MA, Booth KTA, Lynnes TC, Luna C, Minich DJ, Wilson TE, Miller MJ. Biochemical and molecular confirmation of alkaptonuria in a Sumatran orangutan (Pongo abelii). Mol Genet Metab 2023; 139:107628. [PMID: 37354891 DOI: 10.1016/j.ymgme.2023.107628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
A 6-yr-old female orangutan presented with a history of dark urine that turned brown upon standing since birth. Repeated routine urinalysis and urine culture were unremarkable. Urine organic acid analysis showed elevation in homogentisic acid consistent with alkaptonuria. Sequence analysis identified a homozygous missense variant, c.1081G>A (p.Gly361Arg), of the homogentisate 1,2-dioxygenase (HGD) gene. Familial studies, molecular modeling, and comparison to human variant databases support this variant as the underlying cause of alkaptonuria in this orangutan. This is the first report of molecular confirmation of alkaptonuria in a nonhuman primate.
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Affiliation(s)
| | - Kevin T A Booth
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN 46202, USA
| | - Ty C Lynnes
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN 46202, USA
| | - Carolina Luna
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN 46202, USA
| | | | - Theodore E Wilson
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN 46202, USA
| | - Marcus J Miller
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN 46202, USA.
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Soltysova A, Sekelska M, Zatkova A. Breakpoints characterisation of the genomic deletions identified by MLPA in alkaptonuria patients. Eur J Hum Genet 2023; 31:485-489. [PMID: 35110678 PMCID: PMC10133314 DOI: 10.1038/s41431-022-01042-9] [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: 08/24/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 11/09/2022] Open
Abstract
Until recently, mainly DNA sequencing has been used to identify variants within the gene coding for homogentisate dioxygenase (HGD, 3q13.33) that cause alkaptonuria (AKU), an autosomal recessive inborn error of metabolism of tyrosine. In order to identify possible larger genomic deletions we have developed a novel Multiplex Ligation-dependent Probe Amplification (MLPA) assay specific for this gene (HGD-MLPA) and tested it successfully in healthy controls and in patients carrying two known previously identified HGD deletions. Subsequently, we analysed 22 AKU patients in whom only one or none classical HGD variant was found by sequencing. Using HGD-MLPA and sequencing, we identified four larger deletions encompassing from 1 to 4 exons of this gene and we defined their exact breakpoints: deletion of exons 1-4 (c.1-8460_282 + 6727del), deletion of exons 5 and 6 (c.283-9199_434 + 1688del), deletion of exon 11 (c.775-1915_879 + 1293del), and deletion of exon 13 (c.1007-1709_1188 + 1121del). We suggest including MLPA in the DNA diagnostic protocols for AKU in cases where DNA sequencing does not lead to identification of both HGD variants.
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Affiliation(s)
- Andrea Soltysova
- Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 841 04, Bratislava, Slovakia
| | - Martina Sekelska
- Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia
| | - Andrea Zatkova
- Biomedical Research Center of the Slovak Academy of Sciences, Dubravska cesta 9, 845 05, Bratislava, Slovakia.
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Grasso D, Galderisi S, Santucci A, Bernini A. Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology. Int J Mol Sci 2023; 24:ijms24065819. [PMID: 36982893 PMCID: PMC10054308 DOI: 10.3390/ijms24065819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/09/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Whenever a protein fails to fold into its native structure, a profound detrimental effect is likely to occur, and a disease is often developed. Protein conformational disorders arise when proteins adopt abnormal conformations due to a pathological gene variant that turns into gain/loss of function or improper localization/degradation. Pharmacological chaperones are small molecules restoring the correct folding of a protein suitable for treating conformational diseases. Small molecules like these bind poorly folded proteins similarly to physiological chaperones, bridging non-covalent interactions (hydrogen bonds, electrostatic interactions, and van der Waals contacts) loosened or lost due to mutations. Pharmacological chaperone development involves, among other things, structural biology investigation of the target protein and its misfolding and refolding. Such research can take advantage of computational methods at many stages. Here, we present an up-to-date review of the computational structural biology tools and approaches regarding protein stability evaluation, binding pocket discovery and druggability, drug repurposing, and virtual ligand screening. The tools are presented as organized in an ideal workflow oriented at pharmacological chaperones' rational design, also with the treatment of rare diseases in mind.
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Affiliation(s)
- Daniela Grasso
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Silvia Galderisi
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Andrea Bernini
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, 53100 Siena, Italy
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Imrich R, Zatkova A, Lukacova O, Sedlakova J, Zanova E, Vlcek M, Penesova A, Radikova Z, Havranova A, Ranganath L. Nutritional interventions for patients with alkaptonuria: A minireview. Endocr Regul 2023; 57:61-67. [PMID: 36966367 DOI: 10.2478/enr-2023-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/27/2023] Open
Abstract
Alkaptonuria (AKU, OMIM, No. 203500) is a rare, slow-progressing, irreversible, multisystemic disease resulting from a deficiency of the homogentisate 1,2-dioxygenase enzyme, which leads to the accumulation of homogentisic acid (HGA) and subsequent deposition as pigment in connective tissues called ochronosis. As a result, severe arthropathy of large joints and spondyloarthropathy with frequent fractures, ligament ruptures, and osteoporosis develops in AKU patients. Since 2020, the first-time treatment with nitisinone has become available in the European Union. Nitisinone significantly reduces HGA production and arrests ochronosis in AKU patients. However, blocking of the tyrosine metabolic pathway by the drug leads to tyrosine plasma and tissue concentrations increase. The nitisinone-induced hypertyrosinemia can lead to the development of corneal keratopathy, and once it develops, the treatment needs to be interrupted. A decrease in overall protein intake reduces the risk of the keratopathy during nitisinone-induced hypertyrosinemia in AKU patients. The low-protein diet is not only poorly tolerated by patients, but over longer periods, leads to a severe muscle loss and weight gain due to increased energy intake from carbohydrates and fats. Therefore, the development of novel nutritional approaches is required to prevent the adverse events due to nitisinone-induced hypertyrosinemia and the negative impact on skeletal muscle metabolism in AKU patients.
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Affiliation(s)
- Richard Imrich
- 1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
| | - Andrea Zatkova
- 1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Olga Lukacova
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
| | - Jana Sedlakova
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
| | | | - Miroslav Vlcek
- 1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
| | - Adela Penesova
- 1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
| | - Zofia Radikova
- 1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
| | - Andrea Havranova
- 1Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
- 2National Institute of Rheumatic Diseases, Piestany, Slovakia
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Bernini A, Spiga O, Santucci A. Structure-Function Relationship of Homogentisate 1,2-dioxygenase: Understanding the Genotype-Phenotype Correlations in the Rare Genetic Disease Alkaptonuria. Curr Protein Pept Sci 2023; 24:380-392. [PMID: 36880186 DOI: 10.2174/1389203724666230307104135] [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: 08/02/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 03/08/2023]
Abstract
Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in organs, which occurs because the homogentisate 1,2-dioxygenase (HGD) enzyme is not functional due to gene variants. Over time, HGA oxidation and accumulation cause the formation of the ochronotic pigment, a deposit that provokes tissue degeneration and organ malfunction. Here, we report a comprehensive review of the variants so far reported, the structural studies on the molecular consequences of protein stability and interaction, and molecular simulations for pharmacological chaperones as protein rescuers. Moreover, evidence accumulated so far in alkaptonuria research will be re-proposed as the bases for a precision medicine approach in a rare disease.
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Affiliation(s)
- Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
- Centro Regionale Medicina di Precisione, Siena, Italy
- ARTES 4.0, Pontedera, Italy
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Davison AS, Norman BP. Alkaptonuria – Past, present and future. Adv Clin Chem 2023. [DOI: 10.1016/bs.acc.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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Grasso D, Geminiani M, Galderisi S, Iacomelli G, Peruzzi L, Marzocchi B, Santucci A, Bernini A. Untargeted NMR Metabolomics Reveals Alternative Biomarkers and Pathways in Alkaptonuria. Int J Mol Sci 2022; 23:ijms232415805. [PMID: 36555443 PMCID: PMC9779518 DOI: 10.3390/ijms232415805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/04/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Alkaptonuria (AKU) is an ultra-rare metabolic disease caused by the accumulation of homogentisic acid (HGA), an intermediate product of phenylalanine and tyrosine degradation. AKU patients carry variants within the gene coding for homogentisate-1,2-dioxygenase (HGD), which are responsible for reducing the enzyme catalytic activity and the consequent accumulation of HGA and formation of a dark pigment called the ochronotic pigment. In individuals with alkaptonuria, ochronotic pigmentation of connective tissues occurs, leading to inflammation, degeneration, and eventually osteoarthritis. The molecular mechanisms underlying the multisystemic development of the disease severity are still not fully understood and are mostly limited to the metabolic pathway segment involving HGA. In this view, untargeted metabolomics of biofluids in metabolic diseases allows the direct investigation of molecular species involved in pathways alterations and their interplay. Here, we present the untargeted metabolomics study of AKU through the nuclear magnetic resonance of urine from a cohort of Italian patients; the study aims to unravel molecular species and mechanisms underlying the AKU metabolic disorder. Dysregulation of metabolic pathways other than the HGD route and new potential biomarkers beyond homogentisate are suggested, contributing to a more comprehensive molecular signature definition for AKU and the development of future adjuvant treatment.
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Affiliation(s)
- Daniela Grasso
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
| | - Michela Geminiani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
| | - Silvia Galderisi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
| | - Gabriella Iacomelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
| | - Luana Peruzzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
| | - Barbara Marzocchi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
- Centro Regionale Medicina di Precisione, 53100 Siena, Italy
- ARTES 4.0, 56025 Pontedera, Italy
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A, Moro 2, 53100 Siena, Italy
- Correspondence:
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Zatkova A, Olsson B, Ranganath LR, Imrich R. Analysis of the Phenotype Differences in Siblings with Alkaptonuria. Metabolites 2022; 12:990. [PMID: 36295892 PMCID: PMC9611385 DOI: 10.3390/metabo12100990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Alkaptonuria (AKU) is a rare autosomal recessive disorder caused by mutations within a gene coding for homogentisate 1,2-dioxygenase (HGD). To date, 251 different variants of this gene have been reported. The metabolic disorder in AKU leads to the accumulation of homogentisic acid (HGA), resulting in ochronosis (pigmentation of the connective tissues) and severe ochronotic spondylo-arthropathy, which usually manifests in the mid-thirties. An earlier genotype−phenotype correlation study showed no differences in serum HGA levels, absolute urinary excretion of HGA, or in the clinical symptoms between patients carrying HGD variants leading to 1% or >30% residual HGD activity. Still, as reported previously, the variance of the excretion of the HGA was smaller within affected siblings that share a common genotype. The present study is the first ever to systematically analyze the baseline clinical data of 24 AKU sibling pairs/groups collected in the SONIA 2 (Suitability Of Nitisinone In Alkaptonuria 2) study to evaluate phenotypical differences between patients carrying the same HGD genetic variants. We show that even between siblings there was considerable variability in the disease severity. This indicates that some other yet unidentified genetic, biomechanical, or environmental modifying factors may contribute to accelerated pigmentation and connective tissue damage observed in some patients.
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Affiliation(s)
- Andrea Zatkova
- Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | | | - Lakshminarayan R. Ranganath
- Department of Clinical Biochemistry and Metabolism, Royal Liverpool University Hospital, Liverpool L7 8XP, UK
| | - Richard Imrich
- Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
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Tao L, Deng C, Ma M, Zhang Y, Duan J, Li Y, Fang L, Zhou Y, He X, Wang Y, Wang M, Li L. A novel mutation in the homogentisate 1,2 dioxygenase gene identified in Chinese Hani pediatric patients with Alkaptonuria. Clin Chim Acta 2022; 532:164-171. [PMID: 35550814 DOI: 10.1016/j.cca.2022.04.998] [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: 03/08/2022] [Revised: 04/21/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Alkaptonuria (AKU) is a rare tyrosine metabolism disorder caused by homogentisate 1,2-dioxygenase (HGD) mutations and homogentisic acid (HGA) accumulation. In this study, we investigated the genotype-phenotype relationship in AKU patients with a novel HGD gene mutation from a Chinese Hani family. METHODS Routine clinical examination and laboratory evaluation were performed, urine alkalinization test and urinary gas chromatography-mass spectrometry were used to assess HGA. Gene sequencing was utilized to study the defining features of AKU. NetGene2-2.42 and BDGP software was used to predict protein structure online. Flow cytometry and RT-PCR were used to analyze HGD proteins and HGD mRNA, respectively. RESULTS Two pediatric patients fulfilled diagnostic criteria for AKU with eddish-brown or black diapers and urine HGA testing. Sequencing testing revealed that all members of this family had a novel samesense mutation c.15G>A at the edge of exon 1 of the HGD. By flow cytometry, the expression of HGD protein in the pediatric patients' peripheral blood mononuclear cells was barely expressed. NetGene2-2.42 and BDGP software showed that the mutation reduced the score of the 5' splice donor site and disrupted its normal splicing, and the RT-PCR product also demonstrated that the defect in the HGD protein was due to the lack of the first exon containing the start codon ATG after the mutation. CONCLUSIONS The novel mutation c.15G > A in HGD is associated with the AKU phenotype. It may affect the splicing of exon 1, leading to exon skipping, which impairs the structure and function of the protein.
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Affiliation(s)
- Lvyan Tao
- Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China
| | - Chengjun Deng
- Department of Gastroenterology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Mingbiao Ma
- Department of Clinical Laboratory, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China
| | - Yu Zhang
- Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China
| | - Jintao Duan
- Department of Gastroenterology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Ying Li
- Department of Gastroenterology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Li Fang
- Department of Gastroenterology, Kunming Children's Hospital, Kunming 650228, Yunnan, China
| | - Yuantao Zhou
- Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China
| | - Xiaoli He
- Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China
| | - Yan Wang
- Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China
| | - Mingying Wang
- Department of Gastroenterology, Kunming Children's Hospital, Kunming 650228, Yunnan, China.
| | - Li Li
- Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children's Hospital, Kunming 650228, Yunnan, China; Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children's Major Disease Research, Yunnan Province Clinical Research Center for Children's Health and Disease, Kunming 650228, Yunnan, China.
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Soltysova A, Kuzin A, Samarkina E, Zatkova A. Alkaptonuria in Russia. Eur J Hum Genet 2022; 30:237-242. [PMID: 34504318 PMCID: PMC8821605 DOI: 10.1038/s41431-021-00955-1] [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] [Received: 04/26/2021] [Revised: 06/28/2021] [Accepted: 08/19/2021] [Indexed: 02/03/2023] Open
Abstract
Alkaptonuria is characterized by the accumulation of homogentisic acid (HGA), part of which is excreted in the urine but the excess HGA forms a dark brown ochronotic pigment that deposits in the connective tissue (ochronosis), eventually leading to early-onset severe arthropathy. We analyzed a cohort of 48 Russian AKU families by sequencing all 14 exons (including flanking intronic sequences) of the homogentisate 1,2-dioxygenase gene (HGD) and Multiplex Ligation-dependent Probe Amplification (MLPA) analysis. Nine novel likely pathogenic HGD variants were identified, which have not been reported previously in any other country. Recently, Bychkov et al. [1] reported on the variant spectrum in another cohort of 49 Russian AKU patients. Here we summarize complete data from both cohorts that include 82 Russian AKU families. Taken together, 31 different HGD variants were found in these patients, of which 14 are novel and found only in Russia. The most common variant was c.481G>A (p.(Gly161Arg)), present in almost 54% of all AKU alleles.
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Affiliation(s)
- Andrea Soltysova
- grid.419303.c0000 0001 2180 9405Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia ,grid.7634.60000000109409708Faculty of Natural Sciences, Department of Molecular Biology, Comenius University, Bratislava, Slovakia
| | - Alexandr Kuzin
- grid.488825.bV.A.Nasonova Research Institute of Rheumatology, Moscow, Russia ,grid.465497.dRussian Medical Academy of Continuous Professional Education, Moscow, Russia
| | - Elena Samarkina
- grid.488825.bV.A.Nasonova Research Institute of Rheumatology, Moscow, Russia
| | - Andrea Zatkova
- grid.419303.c0000 0001 2180 9405Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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Karmakar M, Cicaloni V, Rodrigues CH, Spiga O, Santucci A, Ascher DB. HGDiscovery: An online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase. Curr Res Struct Biol 2022; 4:271-277. [PMID: 36118553 PMCID: PMC9471331 DOI: 10.1016/j.crstbi.2022.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/28/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in the body. Affected individuals lack functional levels of an enzyme required to breakdown HGA. Mutations in the homogentisate 1,2-dioxygenase (HGD) gene cause AKU and they are responsible for deficient levels of functional HGD, which, in turn, leads to excess levels of HGA. Although HGA is rapidly cleared from the body by the kidneys, in the long term it starts accumulating in various tissues, especially cartilage. Over time (rarely before adulthood), it eventually changes the color of affected tissue to slate blue or black. Here we report a comprehensive mutation analysis of 111 pathogenic and 190 non-pathogenic HGD missense mutations using protein structural information. Using our comprehensive suite of graph-based signature methods, mCSM complemented with sequence-based tools, we studied the functional and molecular consequences of each mutation on protein stability, interaction and evolutionary conservation. The scores generated from the structure and sequence-based tools were used to train a supervised machine learning algorithm with 89% accuracy. The empirical classifier was used to generate the variant phenotype for novel HGD missense mutations. All this information is deployed as a user friendly freely available web server called HGDiscovery (https://biosig.lab.uq.edu.au/hgdiscovery/). Functional and phenotypic consequences of HGD non-synonymous variations. Biophysical, structural and evolutionary analysis of novel and known clinical variants. Pathogenic mutations affected protein stability and conformational flexibility. Pathogenic mutations associated with deleterious scores for sequence-based features. HGDiscovery (http://biosig.unimelb.edu.au/hgdiscovery/) – webserver.
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Affiliation(s)
- Malancha Karmakar
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Vittoria Cicaloni
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Carlos H.M. Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - David B. Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biology, University of Queensland, Brisbane, Queensland, Australia
- Corresponding author. Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
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15
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A molecular spectroscopy approach for the investigation of early phase ochronotic pigment development in Alkaptonuria. Sci Rep 2021; 11:22562. [PMID: 34799606 PMCID: PMC8605014 DOI: 10.1038/s41598-021-01670-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Alkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in organs due to a deficiency in functional levels of the enzyme homogentisate 1,2-dioxygenase (HGD), required for the breakdown of HGA, because of mutations in the HGD gene. Over time, HGA accumulation causes the formation of the ochronotic pigment, a dark deposit that leads to tissue degeneration and organ malfunction. Such behaviour can be observed also in vitro for HGA solutions or HGA-containing biofluids (e.g. urine from AKU patients) upon alkalinisation, although a comparison at the molecular level between the laboratory and the physiological conditions is lacking. Indeed, independently from the conditions, such process is usually explained with the formation of 1,4-benzoquinone acetic acid (BQA) as the product of HGA chemical oxidation, mostly based on structural similarity between HGA and hydroquinone that is known to be oxidized to the corresponding para-benzoquinone. To test such correlation, a comprehensive, comparative investigation on HGA and BQA chemical behaviours was carried out by a combined approach of spectroscopic techniques (UV spectrometry, Nuclear Magnetic Resonance, Electron Paramagnetic Resonance, Dynamic Light Scattering) under acid/base titration both in solution and in biofluids. New insights on the process leading from HGA to ochronotic pigment have been obtained, spotting out the central role of radical species as intermediates not reported so far. Such evidence opens the way for molecular investigation of HGA fate in cells and tissue aiming to find new targets for Alkaptonuria therapy.
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Lai CY, Tsai IJ, Chiu PC, Ascher DB, Chien YH, Huang YH, Lin YL, Hwu WL, Lee NC. A novel deep intronic variant strongly associates with Alkaptonuria. NPJ Genom Med 2021; 6:89. [PMID: 34686677 PMCID: PMC8536767 DOI: 10.1038/s41525-021-00252-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 10/04/2021] [Indexed: 11/08/2022] Open
Abstract
Alkaptonuria is a rare autosomal recessive inherited disorder of tyrosine metabolism, which causes ochronosis, arthropathy, cardiac valvular calcification, and urolithiasis. The epidemiology of alkaptonuria in East Asia is not clear. In this study, patients diagnosed with alkaptonuria from January 2010 to June 2020 were reviewed. Their clinical and molecular features were further compared with those of patients from other countries. Three patients were found to have alkaptonuria. Mutation analyses of the homogentisate 1,2-dioxygenase gene (HGD) showed four novel variants c.16-2063 A > C, p.(Thr196Ile), p.(Gly344AspfsTer25), and p.(Gly362Arg) in six mutated alleles (83.3%). RNA sequencing revealed that c.16-2063 A > C activates a cryptic exon, causing protein truncation p.(Tyr5_Ile6insValTer17). A literature search identified another 6 patients with alkaptonuria in East Asia; including our cases, 13 of the 18 mutated alleles have not been reported elsewhere in the world. Alkaptonuria is rare in Taiwan and East Asia, with HGD variants being mostly novel and private.
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Affiliation(s)
- Chien-Yi Lai
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - I-Jung Tsai
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
| | - Pao-Chin Chiu
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry, Bio21 Institute, University of Cambridge, Cambridge, UK
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
| | - Yu-Hsuan Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
- Department of Pediatrics, National Taiwan University Children Hospital, Taipei, Taiwan.
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Mwafi N, Alasmar A, Al-Momani M, Alazaydeh S, Alajoulin O, Alsalem M, Kalbouneh H. Alkaptonuria with extensive ochronotic degeneration of the Achilles tendon and its surgical treatment: a case report and literature review. ASIAN BIOMED 2021; 15:129-136. [PMID: 37551372 PMCID: PMC10388780 DOI: 10.2478/abm-2021-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background Alkaptonuria is a rare genetic metabolic disorder due to deficiency of homogentisate 1,2-dioxygenase (HGD), an enzyme catalyzing the conversion of homogentisate to 4-maleylacetoacetate in the pathway for the catabolism of phenylalanine and tyrosine. HGD deficiency results in accumulation of homogentisic acid and its pigmented polymer. Ochronosis is a bluish-black discoloration due to the deposition of the polymer in collagenous tissues. Extensive ochronotic involvement of the Achilles tendon in alkaptonuria and its surgical treatment is rarely reported. Case report A 43-year-old man presented to our clinic in March 2019 with sudden onset of left Achilles tendon pain with no history of prior trauma. Surgical exploration revealed a complete disruption of the tendon at its attachment to the calcaneus. Black pigmentation was extensive and reached the calcaneal tuberosity, extending about 7 cm from the insertion. Discussion Achilles reconstruction was performed using flexor hallucis longus tendon transfer. The patient experienced uncomplicated healing with satisfactory functional results. Conclusion Orthopedic surgeons should be aware of the progressive nature of alkaptonuria. Extensive degenerative changes of the ruptured tendon should be suspected so that physicians can plan tendon repair and facilitate prompt surgical intervention.
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Affiliation(s)
- Nesrin Mwafi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Mutah University, Alkarak61710, Jordan
| | - Ali Alasmar
- Department of Urology, Prince Hussein Urology Center, Jordanian Royal Medical Services, Amman11855, Jordan
| | - Monther Al-Momani
- Department of Radiology, Jordanian Royal Medical Services, Amman11855, Jordan
| | - Sattam Alazaydeh
- Department of Orthopedics and Trauma, Jordanian Royal Medical Services, Amman11855, Jordan
| | - Omar Alajoulin
- Department of Orthopedics and Trauma, Jordanian Royal Medical Services, Amman11855, Jordan
| | - Mohammad Alsalem
- Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman11942, Jordan
| | - Heba Kalbouneh
- Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman11942, Jordan
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Kisa PT, Gunduz M, Dorum S, Uzun OU, Cakar NE, Yildirim GK, Erdol S, Hismi BO, Tugsal HY, Ucar U, Gorukmez O, Gulten ZA, Kucukcongar A, Bulbul S, Sari I, Arslan N. Alkaptonuria in Turkey: Clinical and molecular characteristics of 66 patients. Eur J Med Genet 2021; 64:104197. [PMID: 33746036 DOI: 10.1016/j.ejmg.2021.104197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/28/2021] [Accepted: 03/14/2021] [Indexed: 01/17/2023]
Abstract
Alkaptonuria (AKU) is an inborn error of metabolism caused by the deficiency of homogentisate 1,2-dioxygenase (HGD) as a result of a defect in the HGD gene. HGD enzyme deficiency results in accumulation of homogentisic acid (HGA) in the body, which in turn leads to multisystemic clinical symptoms. The present study aimed to investigate the presenting symptoms, age at diagnosis, and clinical and genetic characteristics of AKU patients followed-up in different centers in Turkey. In this cross-sectional, multicenter, descriptive study, medical records of 66 AKU patients were retrospectively evaluated. Patients' data regarding demographic, clinical and genetic characteristics were recorded. HGD database (http://hgddatabase.cvtisr.sk/) was used to identify HGD gene variants. Of the patients, 37 (56.1%) presented with isolated dark urine and 29 (43.9%) were diagnosed based on the clinical symptoms or family screening. One of these patients was on follow-up for 2 years due to Parkinsonism and was diagnosed with AKU on further analyses. Signs of ochronosis such as joint pain, low back pain and renal stones developed in childhood in 7 patients. Eight patients were diagnosed with depression via psychiatric evaluation. There were 14 (21.2%) patients operated on for ochronosis. The most frequent mutation observed in the patients was c.175delA, which was followed by c.674G > A and c.1007-2A > T mutations. Four novel mutations (c.189G > A, c.549+1G > T, c.1188+1G > A, and c.334 T > G) were identified in the patients included in the study. In addition to the known signs such as dark urine and skin pigmentation, symptoms involving different systems such as neurological findings and depression can also be encountered in AKU patients. The presence of a change in urine color needs to be questioned in patients presenting with different symptoms such as arthralgia/arthritis, renal stones or low-back pain, particularly in childhood, when skin ochronosis is not pronounced, and further examination should be performed.
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Affiliation(s)
- Pelin Teke Kisa
- Department of Pediatric Metabolism and Nutrition, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Mehmet Gunduz
- Department of Pediatric Metabolism and Nutrition, Ministry of Health Ankara City Hospital, Ankara, Turkey
| | - Sevil Dorum
- Department of Pediatric Metabolism and Nutrition, Bursa Yuksek Ihtisas Training and Research Hospital, Bursa, Turkey
| | - Ozlem Unal Uzun
- Department of Pediatric Metabolism and Nutrition, Ministry of Health Ankara City Hospital, Ankara, Turkey
| | - Nafiye Emel Cakar
- Department of Pediatric Metabolism and Nutrition, Okmeydani Training and Research Hospital, Istanbul, Turkey
| | - Gonca Kilic Yildirim
- Department of Pediatric Metabolism and Nutrition, Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Sahin Erdol
- Department of Pediatric Metabolism and Nutrition, Uludag University Faculty of Medicine, Bursa, Turkey
| | - Burcu Ozturk Hismi
- Department of Pediatric Metabolism and Nutrition, Marmara University Faculty of Medicine, Istanbul, Turkey
| | | | - Ulku Ucar
- Department of Rheumatology, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| | - Ozlem Gorukmez
- Department of Medical Genetics, Bursa Yuksek Ihtisas Training and Research Hospital, Bursa, Turkey
| | - Zumrut Arslan Gulten
- Department of Pediatric Metabolism and Nutrition, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Aynur Kucukcongar
- Department of Pediatric Metabolism and Nutrition, Ministry of Health Ankara City Hospital, Ankara, Turkey
| | - Selda Bulbul
- Department of Pediatric Metabolism and Nutrition, Kirikkale University Faculty of Medicine, Kirikkale, Turkey
| | - Ismail Sari
- Department of Rheumatology, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey
| | - Nur Arslan
- Department of Pediatric Metabolism and Nutrition, Dokuz Eylul University Faculty of Medicine, Izmir, Turkey; Izmir Biomedicine and Genome Center, Izmir, Turkey.
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Variant Analysis of Alkaptonuria Families with Significant Founder Effect in Jordan. BIOMED RESEARCH INTERNATIONAL 2021; 2021:1515641. [PMID: 34235214 PMCID: PMC8216811 DOI: 10.1155/2021/1515641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/30/2021] [Accepted: 02/19/2021] [Indexed: 12/04/2022]
Abstract
Background Metabolic disorder alkaptonuria is an autosomal recessive disorder caused by mutations in the HGD gene, and a deficiency HGD enzyme activity results in an accumulation of homogentisic acid (HGA), ochronosis, and destruction of connective tissue. Methods We clinically evaluated 18 alkaptonuria patients (age range, 3 to 60 years) from four unrelated families. Furthermore, 11 out of 18 alkaptonuria patients and 7 unaffected members were enrolled for molecular investigations by utilizing Sanger sequencing to identify variants of the 14 exons of HGD gene. Results We found that the seven patients from the 4 unrelated families carried a recurrent pathogenic missense variant (c.365C>T, p. Ala122Val) in exon 6 of HGD gene. The variant was fully segregated with the disease in affected family members while the other unaffected family members were heterozygous carriers for this variant. Additionally, the clinical features were fully predicted with alkaptonuria disorder. Conclusion In this study, we confirmed that the most common variants in Jordanian AKU patients was c.365C>T, p. Ala122Val in exon 6 of HGD gene. Additionally, we correlated the clinical and genetic features of AKU patients at various ages (3-60 years).
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Mwafi NR, Ali DA, Khalil RW, Alsbou' IN, Saraireh AM. Novel R225C variant identified in the <i>HGD</i> gene in Jordanian patients with alkaptonuria. AIMS MOLECULAR SCIENCE 2021. [DOI: 10.3934/molsci.2021005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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21
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Dai J, Yu X, Han Y, Chai L, Liao Y, Zhong P, Xie R, Sun X, Huang Q, Wang J, Yin Z, Zhang Y, Lv Z, Jia C. TMT-labeling Proteomics of Papillary Thyroid Carcinoma Reveal Invasive Biomarkers. J Cancer 2020; 11:6122-6132. [PMID: 32922552 PMCID: PMC7477402 DOI: 10.7150/jca.47290] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/16/2020] [Indexed: 01/23/2023] Open
Abstract
Background and Aim: Invasion and metastasis are critical events in papillary thyroid carcinoma (PTC) progression. Protein markers specific to this process may avoid over-treatment and urgently needed. Methods: TMT-labeled mass spectrometry-based proteomics were carried out on PTC and invasive phenotype (iPTC) (3 pairs per group) and cross validate differentially expressed proteins (DEPs) (FC>1.5 and <0.67 and p<0.05) with GEO and TCGA datasets and the correlation genes of DEPs were also analyzed. Results: We identified and quantified 4607 proteins identical to PTC and iPTC groups. Among which 12 DEPs in PTC and 179 DEPs in iPTCs were found. Cross-validation with GSE60542 and TCGA database revealed 10 DEPs that all significant correlated with metastasis and staging. Upregulated SLC27A6 showed negative correlation with 6 out of 9 downregulated DEPs including HGD, CA4, COL23A1, SLC26A7, FHL1 and TPO. Conclusion: The panel of 7 genes (SLC27A6 and 6 downregulated DEPs) could have ideal prediction value to improve our understanding of invasiveness of PTC.
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Affiliation(s)
- Jiaqi Dai
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Xiaqing Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Yali Han
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Li Chai
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Yina Liao
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Peng Zhong
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Ruting Xie
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Xuechen Sun
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Qingqing Huang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Jian Wang
- Department of Nuclear Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, P. R. China
| | - Zhiqiang Yin
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Yun Zhang
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
| | - Zhongwei Lv
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China.,Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Chengyou Jia
- Shanghai Research Center for Thyroid Diseases, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, P. R. China
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Transient pockets as mediators of gas molecules routes inside proteins: The case study of dioxygen pathway in homogentisate 1,2-dioxygenase and its implication in Alkaptonuria development. Comput Biol Chem 2020; 88:107356. [PMID: 32823072 DOI: 10.1016/j.compbiolchem.2020.107356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/10/2020] [Accepted: 08/03/2020] [Indexed: 11/20/2022]
Abstract
Alkaptonuria (AKU) is an ultra-rare disease caused by mutations in homogentisate 1,2-dioxygenase (HGD) enzyme, characterized by the loss of enzymatic activity and the accumulation of its substrate, homogentisic acid (HGA) in different tissues, leading to ochronosis and organ degeneration. Although the pathological effects of HGD mutations are largely studied, less is known about the structure of the enzyme, in particular the pathways for dioxygen diffusion to the active site, required for the enzymatic reaction, are still uninvestigated. In the present project, the combination of two in silico techniques, Molecular Dynamics (MD) simulation and Implicit Ligand Sampling (ILS), was used to delineate gas diffusion routes in HGD enzyme. A route from the central opening of the hexameric structure of the enzyme to the back of the active site trough the protein moiety was identified as the path for dioxygen diffusion, also overlapping with a transient pocket, which then assumes an important role in dioxygen diffusion. Along the route the sequence location of the missense variant E401Q, responsible for AKU development, was also found, suggesting such mutation to be conducive of enzymatic activity loss by altering the flow dynamics of dioxygen. Our in silico approach allowed also to delineate the route of HGA substrate to the active site, until now only supposed.
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Hughes JH, Liu K, Plagge A, Wilson PJM, Sutherland H, Norman BP, Hughes AT, Keenan CM, Milan AM, Sakai T, Ranganath LR, Gallagher JA, Bou-Gharios G. Conditional targeting in mice reveals that hepatic homogentisate 1,2-dioxygenase activity is essential in reducing circulating homogentisic acid and for effective therapy in the genetic disease alkaptonuria. Hum Mol Genet 2020; 28:3928-3939. [PMID: 31600782 PMCID: PMC7073386 DOI: 10.1093/hmg/ddz234] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 11/14/2022] Open
Abstract
Alkaptonuria is an inherited disease caused by homogentisate 1,2-dioxygenase (HGD) deficiency. Circulating homogentisic acid (HGA) is elevated and deposits in connective tissues as ochronotic pigment. In this study, we aimed to define developmental and adult HGD tissue expression and determine the location and amount of gene activity required to lower circulating HGA and rescue the alkaptonuria phenotype. We generated an alkaptonuria mouse model using a knockout-first design for the disruption of the HGD gene. Hgd tm1a −/− mice showed elevated HGA and ochronosis in adulthood. LacZ staining driven by the endogenous HGD promoter was localised to only liver parenchymal cells and kidney proximal tubules in adulthood, commencing at E12.5 and E15.5 respectively. Following removal of the gene trap cassette to obtain a normal mouse with a floxed 6th HGD exon, a double transgenic was then created with Mx1-Cre which conditionally deleted HGD in liver in a dose dependent manner. 20% of HGD mRNA remaining in liver did not rescue the disease, suggesting that we need more than 20% of liver HGD to correct the disease in gene therapy. Kidney HGD activity which remained intact reduced urinary HGA, most likely by increased absorption, but did not reduce plasma HGA nor did it prevent ochronosis. In addition, downstream metabolites of exogenous 13C6-HGA, were detected in heterozygous plasma, revealing that hepatocytes take up and metabolise HGA. This novel alkaptonuria mouse model demonstrated the importance of targeting liver for therapeutic intervention, supported by our observation that hepatocytes take up and metabolise HGA.
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Affiliation(s)
- Juliette H Hughes
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Ke Liu
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Antonius Plagge
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, UK
| | - Peter J M Wilson
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Hazel Sutherland
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Brendan P Norman
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Andrew T Hughes
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK.,Liverpool Clinical Laboratories, Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospitals Trust, Liverpool, L7 8XP, UK
| | - Craig M Keenan
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - Anna M Milan
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK.,Liverpool Clinical Laboratories, Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospitals Trust, Liverpool, L7 8XP, UK
| | - Takao Sakai
- Institute of Translational Medicine, University of Liverpool, Liverpool, L69 3GA, UK
| | - Lakshminarayan R Ranganath
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK.,Liverpool Clinical Laboratories, Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospitals Trust, Liverpool, L7 8XP, UK
| | - James A Gallagher
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
| | - George Bou-Gharios
- Institute of Ageing and Chronic disease, University of Liverpool, Liverpool, L7 8TX, UK
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Founder effects of the homogentisate 1,2-dioxygenase (HGD) gene in a gypsy population and mutation spectrum in the gene among alkaptonuria patients from India. Clin Rheumatol 2020; 39:2743-2749. [PMID: 32212000 DOI: 10.1007/s10067-020-05020-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/23/2020] [Accepted: 02/28/2020] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Alkaptonuria (AKU) is a rare metabolic disease. The global incidence is 1:100,000 to 1:250,000. However, identification of a founder mutation in a gypsy population from India prompted us to study the prevalence of AKU in this population and to do molecular typing in referred cases of AKU from the rest of India. OBJECTIVE To determine the prevalence of AKU in the gypsy population predominantly residing in the seven districts of Tamil Nadu. To determine the molecular characteristic of AKU cases referred to our clinic from various parts of India. METHOD Urine spot test to detect homogentisic acid followed by quantitative estimation using high-performance liquid chromatography in 499 participants from the gypsy population and confirming the founder mutation in those with high levels by sequencing. Sequence the homogentisate 1,2-dioxygenase (HGD) gene to identify mutations and variants in 29 AKU non-gypsy cases. RESULTS The founder mutation was detected in homozygous state in 41/499 AKU-affected individuals of the gypsy community giving a high prevalence of 8.4%. Low back pain, knee pain, and eye and ear pigmentation were the most common symptoms and signs respectively. The commonest mutation identified in the non-gypsy AKU cases was p.Ala122Val. CONCLUSION High prevalence of AKU in the inbred gypsy population at 8.4% was detected confirming the founder effect. Urine screening provided a cost-effective method to detect the disease early. Mutation spectrum is varied in the rest of the Indian population. This study identified maximum number of mutations in exon 6 of the HGD gene. Key Points • High prevalence (8.4%) of alkaptonuria (AKU) in the gypsy population due to founder mutation in the HGD gene. • Inbreeding exemplifies the founder effects of this rare genetic disorder. • Urinary screening is a cost-effective method in this community for early detection of AKU and intervention. • The mutation spectrum causing AKU is diverse in the rest of the Indian population.
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Akbaba AI, Ozgül RK, Dursun A. Presentation of 14 alkaptonuria patients from Turkey. J Pediatr Endocrinol Metab 2020; 33:289-294. [PMID: 31927521 DOI: 10.1515/jpem-2019-0163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 11/19/2019] [Indexed: 11/15/2022]
Abstract
Background Alkaptonuria (OMIM: 203500) is an inborn error of metabolism due to homogentisate 1,2-dioxygenase homogentisic acid 1,2 dioxygenase (HGD) enzyme deficiency. Due to the enzyme deficiency, homogentisic acid cannot be converted to maleylacetoacetate and it accumulates in body fluids. Increased homogentisic acid is converted to benzoquinones, the resulting benzoquinones are converted to melanin-like pigments, and these pigments are deposited in collagen - this process is called ochronosis. In patients with alkaptonuria, the urine is darkened, which is misinterpreted as hematuria, the incidences of renal stones, arthritis and cardiac valve calcification are increased, and spontaneous tendon ruptures, prostatitis and prostate stones can be encountered. The present study aimed to evaluate the HGD gene mutations in 14 patients with alkaptonuria. Methods Fourteen patients diagnosed with alkaptonuria and followed up from 1990 to 2014 were retrospectively evaluated. Their demographic, clinical and treatment-related data were retrieved from hospital files. For mutation analysis, genomic DNAs of the patients were isolated from their peripheral blood samples. Variations in the HGD gene were scanned on the HGD-mutation database (http://hgddatabase.cvtisr.sk). Results Among 14 patients, the female/male ratio was 1/1 and the median age was 9 years (range, 6-59 years). All patients were symptomatic at their first visit and the most common symptom was dark urine (71%) followed by arthralgia. Independent of the urinary homogentisic acid concentrations, patients with the presenting symptom of arthralgia were elder. Nine different mutations including p.Ser59AlafsX52, p.Gly161Arg, p.Asn219Ser, p.Gly251Asp, p.Pro274Leu, p.Arg330Ser, p.Gly372Ala, c.656_657insAATCAA and a novel mutation of p.Val316Ile were detected. All of the pediatric-age patients (n = 13) were treated with ascorbic acid at a dose of 250-1000 mg/day. Conclusions Nine different HGD gene mutations with a novel one, p.Val316Ile, were detected. The most common mutation was p.Ser59AlafsX52 for the HGD gene followed by p.Gly161Arg and p.asn219Ser, which can be considered specific to the Turkish population.
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Affiliation(s)
- Alper Ilker Akbaba
- Department of Pediatrics, Hacettepe University Faculty of Medicine, Gevher Nesibe Cd., Altındağ, 06230, Ankara, Turkey, Phone: +90 505 329 4554
| | - Rıza Köksal Ozgül
- Department of Pediatric Metabolism, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Ali Dursun
- Department of Pediatric Metabolism, Hacettepe University Faculty of Medicine, Ankara, Turkey
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Zatkova A, Ranganath L, Kadasi L. Alkaptonuria: Current Perspectives. APPLICATION OF CLINICAL GENETICS 2020; 13:37-47. [PMID: 32158253 PMCID: PMC6986890 DOI: 10.2147/tacg.s186773] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022]
Abstract
The last 15 years have been the most fruitful in the history of research on the metabolic disorder alkaptonuria (AKU). AKU is caused by a deficiency of homogentisate dioxygenase (HGD), the enzyme involved in metabolism of tyrosine, and is characterized by the presence of dark ochronotic pigment in the connective tissue that is formed, due to high levels of circulating homogentisic acid. Almost 120 years ago, Sir Archibald Garrod used AKU to illustrate the concept of Mendelian inheritance in man. In January 2019, the phase III clinical study SONIA 2 was completed, which tested the effectiveness and safety of nitisinone in the treatment of AKU. Results were positive, and they will serve as the basis for the application for registration of nitisinone for treatment of AKU at the European Medicines Agency. Therefore, AKU might become a rare disease for which a cure will be found by 2020. We understand the natural history of the disease and the process of ochronosis much more, but at the same time there are still unanswered questions. One of them is the issue of the factors influencing the varying severity of the disease, since our recent genotype–phenotype study did not show that differences in residual homogentisic acid activity caused by the different mutations was responsible. Although nitisinone has proved to arrest the process of ochronosis, it has some unwanted effects and does not cure the disease completely. As such, enzyme replacement or gene therapy might become a new focus of AKU research, for which a novel suitable mouse model of AKU is available already. We believe that the story of AKU is also a story of effective collaboration between scientists and patients that might serve as an example for other rare diseases.
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Affiliation(s)
- Andrea Zatkova
- Department of Human Genetics, Biomedical Research Center, Slovak Academy of Sciences, Institute of Clinical and Translational Research, Bratislava, Slovakia
| | | | - Ludevit Kadasi
- Department of Human Genetics, Biomedical Research Center, Slovak Academy of Sciences, Institute of Clinical and Translational Research, Bratislava, Slovakia.,Faculty of Natural Sciences, Department of Molecular Biology, Comenius University, Bratislava, Slovakia
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Homogentisate 1,2-dioxygenase (HGD) gene variants, their analysis and genotype-phenotype correlations in the largest cohort of patients with AKU. Eur J Hum Genet 2019; 27:888-902. [PMID: 30737480 DOI: 10.1038/s41431-019-0354-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 01/12/2019] [Accepted: 01/24/2019] [Indexed: 11/08/2022] Open
Abstract
Alkaptonuria (AKU) is a rare metabolic disorder caused by a deficient enzyme in the tyrosine degradation pathway, homogentisate 1,2-dioxygenase (HGD). In 172 AKU patients from 39 countries, we identified 28 novel variants of the HGD gene, which include three larger genomic deletions within this gene discovered via self-designed multiplex ligation-dependent probe amplification (MLPA) probes. In addition, using a reporter minigene assay, we provide evidence that three of eight tested variants potentially affecting splicing cause exon skipping or cryptic splice-site activation. Extensive bioinformatics analysis of novel missense variants, and of the entire HGD monomer, confirmed mCSM as an effective computational tool for evaluating possible enzyme inactivation mechanisms. For the first time for AKU, a genotype-phenotype correlation study was performed for the three most frequent HGD variants identified in the Suitability Of Nitisinone in Alkaptonuria 2 (SONIA2) study. We found a small but statistically significant difference in urinary homogentisic acid (HGA) excretion, corrected for dietary protein intake, between variants leading to 1% or >30% residual HGD activity. There was, interestingly, no difference in serum levels or absolute urinary excretion of HGA, or clinical symptoms, indicating that protein intake is more important than differences in HGD variants for the amounts of HGA that accumulate in the body of AKU patients.
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28
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A new integrated and interactive tool applicable to inborn errors of metabolism: Application to alkaptonuria. Comput Biol Med 2018; 103:1-7. [DOI: 10.1016/j.compbiomed.2018.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 11/23/2022]
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Abstract
Alkaptonuria is a rare inborn error of metabolism with autosomal recessive inheritance with a mutation in homogentisate 1,2-dioxygenase. It results in accumulation of homogentisic acid in connective tissues (ochronosis). Most common ocular manifestations are bluish-black discoloration of the conjunctiva, cornea, and sclera. In this case report, a 39-year-old Indian male patient with additional ocular features in the retina is described.
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Affiliation(s)
- Nirupama Damarla
- Department of Ophthalmology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, Telangana, India
| | - Prathima Linga
- Department of Ophthalmology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, Telangana, India
| | - Mallika Goyal
- Department of Ophthalmology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, Telangana, India
| | - Sanjay Reddy Tadisina
- Department of Ophthalmology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, Telangana, India
| | - G Satyanarayana Reddy
- Department of Ophthalmology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, Telangana, India
| | - Hymavathi Bommisetti
- Department of Ophthalmology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, Telangana, India
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Albanaz ATS, Rodrigues CHM, Pires DEV, Ascher DB. Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opin Drug Discov 2017; 12:553-563. [PMID: 28490289 DOI: 10.1080/17460441.2017.1322579] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Mutations introduce diversity into genomes, leading to selective changes and driving evolution. These changes have contributed to the emergence of many of the current major health concerns of the 21st century, from the development of genetic diseases and cancers to the rise and spread of drug resistance. The experimental systematic testing of all mutations in a system of interest is impractical and not cost-effective, which has created interest in the development of computational tools to understand the molecular consequences of mutations to aid and guide rational experimentation. Areas covered: Here, the authors discuss the recent development of computational methods to understand the effects of coding mutations to protein function and interactions, particularly in the context of the 3D structure of the protein. Expert opinion: While significant progress has been made in terms of innovative tools to understand and quantify the different range of effects in which a mutation or a set of mutations can give rise to a phenotype, a great gap still exists when integrating these predictions and drawing causality conclusions linking variants. This often requires a detailed understanding of the system being perturbed. However, as part of the drug development process it can be used preemptively in a similar fashion to pharmacokinetics predictions, to guide development of therapeutics to help guide the design and analysis of clinical trials, patient treatment and public health policy strategies.
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Affiliation(s)
- Amanda T S Albanaz
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Carlos H M Rodrigues
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Douglas E V Pires
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil
| | - David B Ascher
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,c Department of Biochemistry , University of Cambridge , Cambridge , Cambridgeshire , UK.,d Department of Biochemistry and Molecular Biology , University of Melbourne , Melbourne , Victoria , Australia
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Spiga O, Cicaloni V, Bernini A, Zatkova A, Santucci A. ApreciseKUre: an approach of Precision Medicine in a Rare Disease. BMC Med Inform Decis Mak 2017; 17:42. [PMID: 28410607 PMCID: PMC5391600 DOI: 10.1186/s12911-017-0438-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 04/01/2017] [Indexed: 11/23/2022] Open
Abstract
Background Alkaptonuria (AKU; OMIM:203500) is a classic Mendelian genetic disorder described by Garrod already in 1902. It causes urine to turn black upon exposure to air and also leads to ochronosis as well as early osteoarthritis. Main body of the abstract Our objective is the implementation of a Precision Medicine (PM) approach to AKU. We present here a novel ApreciseKUre database facilitating the collection, integration and analysis of patient data in order to create an AKU-dedicated “PM Ecosystem” in which genetic, biochemical and clinical resources can be shared among registered researchers. In order to exploit the ApreciseKUre database, we developed an analytic method based on Pearson’s correlation coefficient and P value that generates as refreshable correlation matrix. A complete statistical analysis is obtained by associating every pair of parameters to examine the dependence between multiple variables at the same time. Short conclusions Employing this analytic approach, we showed that some clinically used biomarkers are not suitable as prognostic biomarkers in AKU for a more reliable patients’ clinical monitoring. We believe this database could be a good starting point for the creation of a new clinical management tool in AKU, which will lead to the development of a deeper knowledge network on the disease and will advance its treatment. Moreover, our approach can serve as a personalization model paradigm for other inborn errors of metabolism or rare diseases in general. Electronic supplementary material The online version of this article (doi:10.1186/s12911-017-0438-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
| | - Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.,Toscana Life Sciences Foundation, Siena, Italy
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - Andrea Zatkova
- Institute for Clinical and Translational Research Biomedical Research Center, Slovak Academy of Sciences Bratislava, Bratislava, Slovakia
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
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A Founder Effect for the HGD G360R Mutation in Italy: Implications for a Regional Screening of Alkaptonuria. JIMD Rep 2016. [PMID: 26960557 DOI: 10.1007/8904_2016_534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] Open
Abstract
We sought to establish rapid and specific genotyping methods for G360R mutation and for seven tightly linked markers in the homogentisate dioxygenase gene to address the question of whether G360R is a mutational hot spot or the result of a founder effect, as it has been repeatedly found in alkaptonuric patients from a geographic isolate in Italy.For G360R and single nucleotide polymorphism genotyping, high-resolution melting analysis was performed. Microsatellites were analysed by multiplex PCR and capillary electrophoresis. To investigate the natural history of the G360R mutation, we genotyped markers in 52 controls and in 8 unrelated patients from the UK and USA, who also segregated the G360R mutation, and calculated its age using DMLE+2.3 software.A distinct G360R-bearing haplotype was identified in all patients of Caucasian descent. Estimated mutation age was 545 generations (95% credible set, 402-854), suggesting that G360R arose in an ancestor who lived 8,000-10,000 years BC. Archaeological, historical and demographic data support that a G360R carrier has settled the remote valley where present-day population might have a heterozygote frequency of at least 6%.Given the late health-threatening complications of alkaptonuria and a cure within reach, inhabitants of this isolate would benefit from screening and genetic counselling.
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Braconi D, Millucci L, Bernardini G, Santucci A. Oxidative stress and mechanisms of ochronosis in alkaptonuria. Free Radic Biol Med 2015; 88:70-80. [PMID: 25733348 DOI: 10.1016/j.freeradbiomed.2015.02.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/29/2015] [Accepted: 02/19/2015] [Indexed: 12/16/2022]
Abstract
Alkaptonuria (AKU) is a rare metabolic disease due to a deficient activity of the enzyme homogentisate 1,2-dioxygenase (HGD), involved in Phe and Tyr catabolism. Due to such a deficiency, AKU patients undergo accumulation of the metabolite homogentisic acid (HGA), which is prone to oxidation/polymerization reactions causing the production of a melanin-like pigment. Once the pigment is deposited onto connective tissues (mainly in joints, spine, and cardiac valves), a classical bluish-brown discoloration is imparted, leading to a phenomenon known as "ochronosis", the hallmark of AKU. A clarification of the molecular mechanisms for the production and deposition of the ochronotic pigment in AKU started only recently with a range of in vitro and ex vivo human models used for the study of HGA-induced effects. Thanks to redox-proteomic analyses, it was found that HGA could induce significant oxidation of a number of serum and chondrocyte proteins. Further investigations allowed highlighting how HGA-induced proteome alteration, lipid peroxidation, thiol depletion, and amyloid production could contribute to oxidative stress generation and protein oxidation in AKU. This review briefly summarizes the most recent findings on HGA-induced oxidative stress in AKU, helping in the clarification of the molecular mechanisms of ochronosis and potentially providing the basis for its pharmacological treatment. Future work should be undertaken in order to validate in vivo the results so far obtained in in vitro AKU models.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy
| | - Lia Millucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy
| | - Annalisa Santucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy.
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Twelve novel HGD gene variants identified in 99 alkaptonuria patients: focus on 'black bone disease' in Italy. Eur J Hum Genet 2015; 24:66-72. [PMID: 25804398 DOI: 10.1038/ejhg.2015.60] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/05/2015] [Accepted: 02/24/2015] [Indexed: 11/09/2022] Open
Abstract
Alkaptonuria (AKU) is an autosomal recessive disorder caused by mutations in homogentisate-1,2-dioxygenase (HGD) gene leading to the deficiency of HGD enzyme activity. The DevelopAKUre project is underway to test nitisinone as a specific treatment to counteract this derangement of the phenylalanine-tyrosine catabolic pathway. We analysed DNA of 40 AKU patients enrolled for SONIA1, the first study in DevelopAKUre, and of 59 other AKU patients sent to our laboratory for molecular diagnostics. We identified 12 novel DNA variants: one was identified in patients from Brazil (c.557T>A), Slovakia (c.500C>T) and France (c.440T>C), three in patients from India (c.469+6T>C, c.650-85A>G, c.158G>A), and six in patients from Italy (c.742A>G, c.614G>A, c.1057A>C, c.752G>A, c.119A>C, c.926G>T). Thus, the total number of potential AKU-causing variants found in 380 patients reported in the HGD mutation database is now 129. Using mCSM and DUET, computational approaches based on the protein 3D structure, the novel missense variants are predicted to affect the activity of the enzyme by three mechanisms: decrease of stability of individual protomers, disruption of protomer-protomer interactions or modification of residues in the region of the active site. We also present an overview of AKU in Italy, where so far about 60 AKU cases are known and DNA analysis has been reported for 34 of them. In this rather small group, 26 different HGD variants affecting function were described, indicating rather high heterogeneity. Twelve of these variants seem to be specific for Italy.
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Usher JL, Ascher DB, Pires DEV, Milan AM, Blundell TL, Ranganath LR. Analysis of HGD Gene Mutations in Patients with Alkaptonuria from the United Kingdom: Identification of Novel Mutations. JIMD Rep 2015; 24:3-11. [PMID: 25681086 PMCID: PMC4582018 DOI: 10.1007/8904_2014_380] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 10/23/2014] [Accepted: 11/03/2014] [Indexed: 12/24/2022] Open
Abstract
Alkaptonuria (AKU) is a rare autosomal recessive disorder with incidence ranging from 1:100,000 to 1:250,000. The disorder is caused by a deficiency of the enzyme homogentisate 1,2-dioxygenase (HGD), which results from defects in the HGD gene. This enzyme converts homogentisic acid to maleylacetoacetate and has a major role in the catabolism of phenylalanine and tyrosine. To elucidate the mutation spectrum of the HGD gene in patients with alkaptonuria from 42 patients attending the National Alkaptonuria Centre, 14 exons of the HGD gene and the intron-exon boundaries were analysed by PCR-based sequencing. A total of 34 sequence variants was observed, confirming the genetic heterogeneity of AKU. Of these mutations, 26 were missense substitutions and four splice site mutations. There were two deletions and one duplication giving rise to frame shifts and one substitution abolishing the translation termination codon (no stop). Nine of the mutations were previously unreported novel variants. Using computational approaches based on the 3D structure, these novel mutations are predicted to affect the activity of the protein complex through destabilisation of the individual protomer structure or through disruption of protomer-protomer interactions.
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Affiliation(s)
- Jeannette L Usher
- Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospital Trust, Duncan Building, Liverpool, L7 8XP, UK.
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Douglas E V Pires
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Anna M Milan
- Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospital Trust, Duncan Building, Liverpool, L7 8XP, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lakshminarayan R Ranganath
- Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool and Broadgreen University Hospital Trust, Duncan Building, Liverpool, L7 8XP, UK
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Braconi D, Millucci L, Ghezzi L, Santucci A. Redox proteomics gives insights into the role of oxidative stress in alkaptonuria. Expert Rev Proteomics 2014; 10:521-35. [PMID: 24206226 DOI: 10.1586/14789450.2013.858020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Alkaptonuria (AKU) is an ultra-rare metabolic disorder of the catabolic pathway of tyrosine and phenylalanine that has been poorly characterized at molecular level. As a genetic disease, AKU is present at birth, but its most severe manifestations are delayed due to the deposition of a dark-brown pigment (ochronosis) in connective tissues. The reasons for such a delayed manifestation have not been clarified yet, though several lines of evidence suggest that the metabolite accumulated in AKU sufferers (homogentisic acid) is prone to auto-oxidation and induction of oxidative stress. The clarification of the pathophysiological molecular mechanisms of AKU would allow a better understanding of the disease, help find a cure for AKU and provide a model for more common rheumatic diseases. With this aim, we have shown how proteomics and redox proteomics might successfully overcome the difficulties of studying a rare disease such as AKU and the limitations of the hitherto adopted approaches.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, via Fiorentina 1, Università degli Studi di Siena, 53100 Siena, Italy
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Sakthivel S, Zatkova A, Nemethova M, Surovy M, Kadasi L, Saravanan MP. Mutation screening of the HGD gene identifies a novel alkaptonuria mutation with significant founder effect and high prevalence. Ann Hum Genet 2014; 78:155-64. [PMID: 24575791 DOI: 10.1111/ahg.12055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022]
Abstract
Alkaptonuria (AKU) is an autosomal recessive disorder; caused by the mutations in the homogentisate 1, 2-dioxygenase (HGD) gene located on Chromosome 3q13.33. AKU is a rare disorder with an incidence of 1: 250,000 to 1: 1,000,000, but Slovakia and the Dominican Republic have a relatively higher incidence of 1: 19,000. Our study focused on studying the frequency of AKU and identification of HGD gene mutations in nomads. HGD gene sequencing was used to identify the mutations in alkaptonurics. For the past four years, from subjects suspected to be clinically affected, we found 16 positive cases among a randomly selected cohort of 41 Indian nomads (Narikuravar) settled in the specific area of Tamil Nadu, India. HGD gene mutation analysis showed that 11 of these patients carry the same homozygous splicing mutation c.87 + 1G > A; in five cases, this mutation was found to be heterozygous, while the second AKU-causing mutation was not identified in these patients. This result indicates that the founder effect and high degree of consanguineous marriages have contributed to AKU among nomads. Eleven positive samples were homozygous for a novel mutation c.87 + 1G > A, that abolishes an intron 2 donor splice site and most likely causes skipping of exon 2. The prevalence of AKU observed earlier seems to be highly increased in people of nomadic origin.
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Affiliation(s)
- Srinivasan Sakthivel
- Department of Biotechnology & Genetic Engineering, Bharathidasan University, Tiruchirapalli, Tamil Nadu, India
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Zatkova A. An update on molecular genetics of Alkaptonuria (AKU). J Inherit Metab Dis 2011; 34:1127-36. [PMID: 21720873 DOI: 10.1007/s10545-011-9363-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/01/2011] [Accepted: 06/08/2011] [Indexed: 11/25/2022]
Abstract
Alkaptonuria (AKU) is an autosomal recessive disorder caused by a deficiency of homogentisate 1,2 dioxygenase (HGD) and characterized by homogentisic aciduria, ochronosis, and ochronotic arthritis. The defect is caused by mutations in the HGD gene, which maps to the human chromosome 3q21-q23. AKU shows a very low prevalence (1:100,000-250,000) in most ethnic groups, but there are countries such as Slovakia and the Dominican Republic in which the incidence of this disorder rises to as much as 1:19,000. In this work, we summarize the genetic aspects of AKU in general and the distribution of all known disease-causing mutations reported so far. We focus on special features of AKU in Slovakia, which is one of the countries with an increased incidence of this rare metabolic disorder.
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Affiliation(s)
- Andrea Zatkova
- Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlarska 5, 833 34, Bratislava, Slovakia.
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