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Milella MS, Geminiani M, Trezza A, Visibelli A, Braconi D, Santucci A. Alkaptonuria: From Molecular Insights to a Dedicated Digital Platform. Cells 2024; 13:1072. [PMID: 38920699 PMCID: PMC11201470 DOI: 10.3390/cells13121072] [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: 05/22/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Alkaptonuria (AKU) is a genetic disorder that affects connective tissues of several body compartments causing cartilage degeneration, tendon calcification, heart problems, and an invalidating, early-onset form of osteoarthritis. The molecular mechanisms underlying AKU involve homogentisic acid (HGA) accumulation in cells and tissues. HGA is highly reactive, able to modify several macromolecules, and activates different pathways, mostly involved in the onset and propagation of oxidative stress and inflammation, with consequences spreading from the microscopic to the macroscopic level leading to irreversible damage. Gaining a deeper understanding of AKU molecular mechanisms may provide novel possible therapeutical approaches to counteract disease progression. In this review, we first describe inflammation and oxidative stress in AKU and discuss similarities with other more common disorders. Then, we focus on HGA reactivity and AKU molecular mechanisms. We finally describe a multi-purpose digital platform, named ApreciseKUre, created to facilitate data collection, integration, and analysis of AKU-related data.
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Affiliation(s)
- Maria Serena Milella
- ONE-HEALTH Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (M.S.M.); (A.T.); (A.V.); (D.B.); (A.S.)
| | - Michela Geminiani
- ONE-HEALTH Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (M.S.M.); (A.T.); (A.V.); (D.B.); (A.S.)
- SienabioACTIVE-SbA, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Alfonso Trezza
- ONE-HEALTH Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (M.S.M.); (A.T.); (A.V.); (D.B.); (A.S.)
| | - Anna Visibelli
- ONE-HEALTH Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (M.S.M.); (A.T.); (A.V.); (D.B.); (A.S.)
| | - Daniela Braconi
- ONE-HEALTH Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (M.S.M.); (A.T.); (A.V.); (D.B.); (A.S.)
| | - Annalisa Santucci
- ONE-HEALTH Lab, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (M.S.M.); (A.T.); (A.V.); (D.B.); (A.S.)
- SienabioACTIVE-SbA, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- ARTES 4.0, Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
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Piras IS, DiStefano JK. Comprehensive meta-analysis reveals distinct gene expression signatures of MASLD progression. Life Sci Alliance 2024; 7:e202302517. [PMID: 38565287 PMCID: PMC10987979 DOI: 10.26508/lsa.202302517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), pose significant risks of severe fibrosis, cirrhosis, and hepatocellular carcinoma. Despite their widespread prevalence, the molecular mechanisms underlying the development and progression of these common chronic hepatic conditions are not fully understood. Here, we conducted the most extensive meta-analysis of hepatic gene expression datasets from liver biopsy samples to date, integrating 10 RNA-sequencing and microarray datasets (1,058 samples). Using a random-effects meta-analysis model, we compared over 12,000 shared genes across datasets. We identified 685 genes differentially expressed in MASLD versus normal liver, 1,870 in MASH versus normal liver, and 3,284 in MASLD versus MASH. Integrating these results with genome-wide association studies and coexpression networks, we identified two functionally relevant, validated coexpression modules mainly driven by SMOC2, ITGBL1, LOXL1, MGP, SOD3, and TAT, HGD, SLC25A15, respectively, the latter not previously associated with MASLD and MASH. Our findings provide a comprehensive and robust analysis of hepatic gene expression alterations associated with MASLD and MASH and identify novel key drivers of MASLD progression.
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Affiliation(s)
- Ignazio S Piras
- https://ror.org/02hfpnk21 Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Johanna K DiStefano
- https://ror.org/02hfpnk21 Diabetes and Metabolic Disease Research Unit, Translational Genomics Research Institute, Phoenix, AZ, USA
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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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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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Li JQ, Wang HJ. [Research advances in pharmacotherapy for rare diseases in children]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2023; 25:759-766. [PMID: 37529960 PMCID: PMC10414178 DOI: 10.7499/j.issn.1008-8830.2302048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/15/2023] [Indexed: 08/03/2023]
Abstract
There are more than 7 000 rare diseases and approximately 475 million individuals with rare diseases globally, with children accounting for two-thirds of this population. Due to a relatively small patient population and limited financial resources allocated for drug research and development in pharmaceutical enterprises, there are still no drugs approved for the treatment of several thousands of these rare diseases. At present, there are no drugs for 95% of the patients with rare diseases, and consequently, the therapeutic drugs for rare diseases have been designated as orphan drugs. In order to guide pharmaceutical enterprises to strengthen the research and development of orphan drugs, various nations have enacted the acts for rare disease drugs, promoted and simplified the patent application process for orphan drugs, and provided scientific recommendations and guidance for the research and development of orphan drugs. Since there is a relatively high incidence rate of rare diseases in children, this article reviews the latest research on pharmacotherapy for children with rare diseases.
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Affiliation(s)
- Jia-Qi Li
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Hui-Jun Wang
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai 201102, China
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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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Vöcking O, Famulski JK. A temporal single cell transcriptome atlas of zebrafish anterior segment development. Sci Rep 2023; 13:5656. [PMID: 37024546 PMCID: PMC10079958 DOI: 10.1038/s41598-023-32212-4] [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: 11/02/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
Anterior segment dysgenesis (ASD), resulting in vision impairment, stems from maldevelopment of anterior segment (AS) tissues. Incidence of ASD has been linked to malfunction of periocular mesenchyme cells (POM). POM cells specify into anterior segment mesenchyme (ASM) cells which colonize and produce AS tissues. In this study we uncover ASM developmental trajectories associated with formation of the AS. Using a transgenic line of zebrafish that fluorescently labels the ASM throughout development, Tg[foxc1b:GFP], we isolated GFP+ ASM cells at several developmental timepoints (48-144 hpf) and performed single cell RNA sequencing. Clustering analysis indicates subdifferentiation of ASM as early as 48 hpf and subsequent diversification into corneal epithelium/endothelium/stroma, or annular ligament (AL) lineages. Tracking individual clusters reveals common developmental pathways, up to 72 hpf, for the AL and corneal endothelium/stroma and distinct pathways for corneal epithelium starting at 48 hpf. Spatiotemporal validation of over 80 genes found associated with AS development demonstrates a high degree of conservation with mammalian trabecular meshwork and corneal tissues. In addition, we characterize thirteen novel genes associated with annular ligament and seven with corneal development. Overall, the data provide a molecular verification of the long-standing hypothesis that POM derived ASM give rise to AS tissues and highlight the high degree of conservation between zebrafish and mammals.
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Affiliation(s)
- Oliver Vöcking
- Department of Biology, University of Kentucky, Lexington, USA
| | - J K Famulski
- Department of Biology, University of Kentucky, Lexington, USA.
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Liu Y, Zhao W, Lu Y, Zhao Y, Zhang Y, Dai M, Hai S, Ge N, Zhang S, Huang M, Liu X, Li S, Yue J, Lei P, Dong B, Dai L, Dong B. Systematic metabolic characterization of mental disorders reveals age-related metabolic disturbances as potential risk factors for depression in older adults. MedComm (Beijing) 2022; 3:e165. [PMID: 36204590 PMCID: PMC9523679 DOI: 10.1002/mco2.165] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/01/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Mental disorders are associated with dysregulated metabolism, but comprehensive investigations of their metabolic similarities and differences and their clinical relevance are few. Here, based on the plasma metabolome and lipidome of subcohort1, comprising 100 healthy participants, 55 cases with anxiety, 52 persons with depression, and 41 individuals with comorbidity, which are from WCHAT, a perspective cohort study of community-dwelling older adults aged over 50, multiple metabolites as potential risk factors of mental disorders were identified. Furthermore, participants with mental illnesses were classified into three subtypes (S1, S2, and S3) by unsupervised classification with lipidomic data. Among them, S1 showed higher triacylglycerol and lower sphingomyelin, while S2 displayed opposite features. The metabolic profile of S3 was like that of the normal group. Compared with S3, individuals in S1 and S2 had worse quality of life, and suffered more from sleep and cognitive disorders. Notably, an assessment of 6,467 individuals from the WCHAT showed an age-related increase in the incidence of depression. Seventeen depression-related metabolites were significantly correlated with age, which were validated in an independent subcohort2. Collectively, this work highlights the clinical relevance of metabolic perturbation in mental disorders, and age-related metabolic disturbances may be a bridge-linking aging and depressive.
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Affiliation(s)
- Yu Liu
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Wanyu Zhao
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Ying Lu
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yunli Zhao
- Department of Health Research Methods, Evidence, and ImpactMcMaster UniversityHamiltonOntarioCanada
| | - Yan Zhang
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Miao Dai
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Shan Hai
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Ning Ge
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Shuting Zhang
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
| | - Mingjin Huang
- The Third Hospital of MianyangSichuan Mental Health CenterMianyangChina
| | - Xiaohui Liu
- School of Life SciencesTsinghua UniversityBeijingChina
| | - Shuangqing Li
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jirong Yue
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Peng Lei
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Biao Dong
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Birong Dong
- National Clinical Research Center for Geriatrics and Department of General PracticeState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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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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Mahdkhah A, Salehpour F, Lotfinia I, Riazi A, Mirzaee F, Kaleibar SA. Asymptomatic alkaptonuria and degenerative disc herniation report of two rare cases. INTERDISCIPLINARY NEUROSURGERY 2022. [DOI: 10.1016/j.inat.2021.101471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Visibelli A, Cicaloni V, Spiga O, Santucci A. Computational Approaches Integrated in a Digital Ecosystem Platform for a Rare Disease. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:827340. [PMID: 39086980 PMCID: PMC11285671 DOI: 10.3389/fmmed.2022.827340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/24/2022] [Indexed: 08/02/2024]
Abstract
Alkaptonuria (AKU) is an ultra-rare autosomal recessive disease caused by a mutation in the homogentisate 1,2-dioxygenase gene. One of the main obstacles in studying AKU and other ultra-rare diseases, is the lack of a standardized methodology to assess disease severity or response to treatment. Based on that, a multi-purpose digital platform, called ApreciseKUre, was implemented to facilitate data collection, integration and analysis for patients affected by AKU. It includes genetic, biochemical, histopathological, clinical, therapeutic resources and Quality of Life (QoL) scores that can be shared among registered researchers and clinicians to create a Precision Medicine Ecosystem. The combination of machine learning applications to analyse and re-interpret data available in the ApreciseKUre clearly indicated the potential direct benefits to achieve patients' stratification and the consequent tailoring of care and treatments to a specific subgroup of patients. In order to generate a comprehensive patient profile, computational modeling and database construction support the identification of potential new biomarkers, paving the way for more personalized therapy to maximize the benefit-risk ratio. In this work, different Machine Learning implemented approaches were described.
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Affiliation(s)
- Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
| | | | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
- Competence Center ARTES 4.0, Siena, Italy
- SienabioACTIVE—SbA, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy
- Competence Center ARTES 4.0, Siena, Italy
- SienabioACTIVE—SbA, Siena, Italy
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13
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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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14
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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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15
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Graceffa N, Sohet AS, Levecq L. [Ocular clinical findings in alkaptonuria: A case report]. J Fr Ophtalmol 2021; 44:e323-e325. [PMID: 33642058 DOI: 10.1016/j.jfo.2020.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/25/2022]
Affiliation(s)
- N Graceffa
- Service d'ophtalmologie, CHU UCL Namur, UCLouvain, avenue du Docteur-Thérasse, 1, 5530 Yvoir, Belgique
| | - A-S Sohet
- Service d'ophtalmologie, CHU UCL Namur, UCLouvain, avenue du Docteur-Thérasse, 1, 5530 Yvoir, Belgique
| | - L Levecq
- Service d'ophtalmologie, CHU UCL Namur, UCLouvain, avenue du Docteur-Thérasse, 1, 5530 Yvoir, Belgique.
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16
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Spiga O, Cicaloni V, Dimitri GM, Pettini F, Braconi D, Bernini A, Santucci A. Machine learning application for patient stratification and phenotype/genotype investigation in a rare disease. Brief Bioinform 2021; 22:6127149. [PMID: 33538294 DOI: 10.1093/bib/bbaa434] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/04/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Alkaptonuria (AKU, OMIM: 203500) is an autosomal recessive disorder caused by mutations in the Homogentisate 1,2-dioxygenase (HGD) gene. A lack of standardized data, information and methodologies to assess disease severity and progression represents a common complication in ultra-rare disorders like AKU. This is the reason why we developed a comprehensive tool, called ApreciseKUre, able to collect AKU patients deriving data, to analyse the complex network among genotypic and phenotypic information and to get new insight in such multi-systemic disease. By taking advantage of the dataset, containing the highest number of AKU patient ever considered, it is possible to apply more sophisticated computational methods (such as machine learning) to achieve a first AKU patient stratification based on phenotypic and genotypic data in a typical precision medicine perspective. Thanks to our sufficiently populated and organized dataset, it is possible, for the first time, to extensively explore the phenotype-genotype relationships unknown so far. This proof of principle study for rare diseases confirms the importance of a dedicated database, allowing data management and analysis and can be used to tailor treatments for every patient in a more effective way.
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Affiliation(s)
- Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, ITALY
| | | | - Giovanna Maria Dimitri
- Department of Computer Science, University of Cambridge, Cambridge, UK.,Department of Information Engineering and Mathematics, University of Siena, ITALY
| | | | - Daniela Braconi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, ITALY
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, ITALY
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, ITALY
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17
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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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18
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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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19
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Spiga O, Cicaloni V, Fiorini C, Trezza A, Visibelli A, Millucci L, Bernardini G, Bernini A, Marzocchi B, Braconi D, Prischi F, Santucci A. Machine learning application for development of a data-driven predictive model able to investigate quality of life scores in a rare disease. Orphanet J Rare Dis 2020; 15:46. [PMID: 32050984 PMCID: PMC7017449 DOI: 10.1186/s13023-020-1305-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/14/2020] [Indexed: 01/11/2023] Open
Abstract
Background Alkaptonuria (AKU) is an ultra-rare autosomal recessive disease caused by a mutation in the homogentisate 1,2-dioxygenase (HGD) gene. One of the main obstacles in studying AKU, and other ultra-rare diseases, is the lack of a standardized methodology to assess disease severity or response to treatment. Quality of Life scores (QoL) are a reliable way to monitor patients’ clinical condition and health status. QoL scores allow to monitor the evolution of diseases and assess the suitability of treatments by taking into account patients’ symptoms, general health status and care satisfaction. However, more comprehensive tools to study a complex and multi-systemic disease like AKU are needed. In this study, a Machine Learning (ML) approach was implemented with the aim to perform a prediction of QoL scores based on clinical data deposited in the ApreciseKUre, an AKU- dedicated database. Method Data derived from 129 AKU patients have been firstly examined through a preliminary statistical analysis (Pearson correlation coefficient) to measure the linear correlation between 11 QoL scores. The variable importance in QoL scores prediction of 110 ApreciseKUre biomarkers has been then calculated using XGBoost, with K-nearest neighbours algorithm (k-NN) approach. Due to the limited number of data available, this model has been validated using surrogate data analysis. Results We identified a direct correlation of 6 (age, Serum Amyloid A, Chitotriosidase, Advanced Oxidation Protein Products, S-thiolated proteins and Body Mass Index) out of 110 biomarkers with the QoL health status, in particular with the KOOS (Knee injury and Osteoarthritis Outcome Score) symptoms (Relative Absolute Error (RAE) 0.25). The error distribution of surrogate-model (RAE 0.38) was unequivocally higher than the true-model one (RAE of 0.25), confirming the consistency of our dataset. Our data showed that inflammation, oxidative stress, amyloidosis and lifestyle of patients correlates with the QoL scores for physical status, while no correlation between the biomarkers and patients’ mental health was present (RAE 1.1). Conclusions This proof of principle study for rare diseases confirms the importance of database, allowing data management and analysis, which can be used to predict more effective treatments.
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Affiliation(s)
- Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.
| | - Vittoria Cicaloni
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.,Toscana Life Sciences Foundation, Siena, Italy
| | | | - Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.,Department of Information Engineering and Mathematics, University of Siena, Siena, Italy
| | - Lia Millucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Giulia Bernardini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Barbara Marzocchi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy.,UOC Patologia Clinica, Azienda Ospedaliera Senese, Siena, Italy
| | - Daniela Braconi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A., 53100, Siena, Italy
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20
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Cicaloni V, Spiga O, Dimitri GM, Maiocchi R, Millucci L, Giustarini D, Bernardini G, Bernini A, Marzocchi B, Braconi D, Santucci A. Interactive alkaptonuria database: investigating clinical data to improve patient care in a rare disease. FASEB J 2019; 33:12696-12703. [PMID: 31462106 DOI: 10.1096/fj.201901529r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Alkaptonuria (AKU) is an ultrarare autosomal recessive disorder (MIM 203500) that is caused byby a complex set of mutations in homogentisate 1,2-dioxygenasegene and consequent accumulation of homogentisic acid (HGA), causing a significant protein oxidation. A secondary form of amyloidosis was identified in AKU and related to high circulating serum amyloid A (SAA) levels, which are linked with inflammation and oxidative stress and might contribute to disease progression and patients' poor quality of life. Recently, we reported that inflammatory markers (SAA and chitotriosidase) and oxidative stress markers (protein thiolation index) might be disease activity markers in AKU. Thanks to an international network, we collected genotypic, phenotypic, and clinical data from more than 200 patients with AKU. These data are currently stored in our AKU database, named ApreciseKUre. In this work, we developed an algorithm able to make predictions about the oxidative status trend of each patient with AKU based on 55 predictors, namely circulating HGA, body mass index, total cholesterol, SAA, and chitotriosidase. Our general aim is to integrate the data of apparently heterogeneous patients with AKUAKU by using specific bioinformatics tools, in order to identify pivotal mechanisms involved in AKU for a preventive, predictive, and personalized medicine approach to AKU.-Cicaloni, V., Spiga, O., Dimitri, G. M., Maiocchi, R., Millucci, L., Giustarini, D., Bernardini, G., Bernini, A., Marzocchi, B., Braconi, D., Santucci, A. Interactive alkaptonuria database: investigating clinical data to improve patient care in a rare disease.
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Affiliation(s)
- Vittoria Cicaloni
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy.,Toscana Life Sciences Foundation, Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | | | - Rebecca Maiocchi
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy.,Toscana Life Sciences Foundation, Siena, Italy
| | - Lia Millucci
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Daniela Giustarini
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Giulia Bernardini
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Andrea Bernini
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Barbara Marzocchi
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy.,Unità Operativa Complessa (UOC) Patologia Clinica, Azienda Ospedaliera Senese, Siena, Italy
| | - Daniela Braconi
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Siena, Italy
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21
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Yu X, Zhong P, Han Y, Huang Q, Wang J, Jia C, Lv Z. Key candidate genes associated with BRAF
V600E
in papillary thyroid carcinoma on microarray analysis. J Cell Physiol 2019; 234:23369-23378. [PMID: 31161615 DOI: 10.1002/jcp.28906] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaqing Yu
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, School of Medicine Tongji University Shanghai China
| | - Peng Zhong
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, School of Medicine Tongji University Shanghai China
| | - Yali Han
- Shanghai Center for Thyroid Disease, Shanghai Tenth People's Hospital School of Medicine, Tongji University Shanghai China
| | - Qingqing Huang
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, School of Medicine Tongji University Shanghai China
| | - Jian Wang
- Department of Nuclear Medicine, Sir Run Run Shaw Hospital, School of Medicine Zhejiang University Hangzhou China
| | - Chengyou Jia
- Shanghai Center for Thyroid Disease, Shanghai Tenth People's Hospital School of Medicine, Tongji University Shanghai China
| | - Zhongwei Lv
- Department of Nuclear Medicine, Shanghai Tenth People’s Hospital, School of Medicine Tongji University Shanghai China
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22
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Yang W, Ruan L, Tao J, Peng D, Zheng J, Sun M. Single Amino Acid Substitution in Homogentisate Dioxygenase Affects Melanin Production in Bacillus thuringiensis. Front Microbiol 2018; 9:2242. [PMID: 30364256 PMCID: PMC6193087 DOI: 10.3389/fmicb.2018.02242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/03/2018] [Indexed: 12/20/2022] Open
Abstract
Bacillus thuringiensis formulation losing its activity under field conditions due to UV radiation and photoprotection of B. thuringiensis based on melanin has attracted the attention of researchers for many years. Here, a single amino acid substitution (G272E) in homogentisate 1,2-dioxygenase was found to be responsible for pigment overproduction in B. thuringiensis BMB181, a derivative of BMB171. Disrupting the gene encoding homogentisate dioxygenase in BMB171 induced the accumulation of the homogentisic acid and provoked an increased pigment formation. To gain insights into homogentisate 1,2-dioxygenase in B. thuringiensis, we constructed a total of 14 mutations with a single amino acid substitution, and six of the mutant proteins were found to affect the melanin production when substituted by alanine. This study provides a new way to construct pigment-overproducing strains by impairing the homogentisate dioxygenase with a single mutation in B. thuringiensis, and the findings will facilitate a better understanding of this enzyme.
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Affiliation(s)
- Wenjun Yang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiangming Tao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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23
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Tanoğlu O, Arıcan G, Özmeriç A, Alemdaroğlu KB, Çaydere M. Calcaneal Avulsion of an Ochronotic Achilles Tendon: A Case Report. J Foot Ankle Surg 2018; 57:179-183. [PMID: 29113706 DOI: 10.1053/j.jfas.2017.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Indexed: 02/03/2023]
Abstract
Alkaptonuria is a hereditary disorder of phenylalanine and tyrosine, with an incidence of approximately 1/200,000 to 1/1,000,000. Ochronosis is the accumulation of homogentisic acid and its metabolites in connective tissues such as the tendons, cartilage, and skin. In the present case study, a 50-year-old male presented with a nontraumatic calcaneal avulsion without a previous diagnosis of ochronosis. To the best of our knowledge, little information has been reported of this pathology in the Achilles tendon and the surgical management.
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Affiliation(s)
- Oğuzhan Tanoğlu
- Specialist in Orthopaedics, Orthopaedics and Traumatology Clinics, Ankara Research and Training Hospital, Ankara, Turkey.
| | - Gökhun Arıcan
- Resident in Orthopaedics, Orthopaedics and Traumatology Clinics, Ankara Research and Training Hospital, Ankara, Turkey
| | - Ahmet Özmeriç
- Associate Professor in Orthopaedics, Orthopaedics and Traumatology Clinics, Ankara Research and Training Hospital, Ankara, Turkey
| | - Kadir Bahadır Alemdaroğlu
- Professor in Orthopaedics, Orthopaedics and Traumatology Clinics, Ankara Research and Training Hospital, Ankara, Turkey
| | - Muzaffer Çaydere
- Specialist in Pathology, Department of Pathology, Ankara Research and Training Hospital, Ankara, Turkey
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24
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Braconi D, Giustarini D, Marzocchi B, Peruzzi L, Margollicci M, Rossi R, Bernardini G, Millucci L, Gallagher JA, Le Quan Sang KH, Imrich R, Rovensky J, Al-Sbou M, Ranganath LR, Santucci A. Inflammatory and oxidative stress biomarkers in alkaptonuria: data from the DevelopAKUre project. Osteoarthritis Cartilage 2018; 26:1078-1086. [PMID: 29852277 DOI: 10.1016/j.joca.2018.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/30/2018] [Accepted: 05/03/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVE The aim of this work was to assess baseline serum levels of established biomarkers related to inflammation and oxidative stress in samples from alkaptonuric subjects enrolled in SONIA1 (n = 40) and SONIA2 (n = 138) clinical trials (DevelopAKUre project). METHODS Baseline serum levels of Serum Amyloid A (SAA), IL-6, IL-1β, TNFα, CRP, cathepsin D (CATD), IL-1ra, and MMP-3 were determined through commercial ELISA assays. Chitotriosidase activity was assessed through a fluorimetric method. Advanced Oxidation Protein Products (AOPP) were determined by spectrophotometry. Thiols, S-thiolated proteins and Protein Thiolation Index (PTI) were determined by spectrophotometry and HPLC. Patients' quality of life was assessed through validated questionnaires. RESULTS We found that SAA serum levels were significantly increased compared to reference threshold in 57.5% and 86% of SONIA1 and SONIA2 samples, respectively. Similarly, chitotriosidase activity was above the reference threshold in half of SONIA2 samples, whereas CRP levels were increased only in a minority of samples. CATD, IL-1β, IL-6, TNFα, MMP-3, AOPP, thiols, S-thiolated protein and PTI showed no statistically significant differences from control population. We provided evidence that alkaptonuric patients presenting with significantly higher SAA, chitotriosidase activity and PTI reported more often a decreased quality of life. This suggests that worsening of symptoms in alkaptonuria (AKU) is paralleled by increased inflammation and oxidative stress, which might play a role in disease progression. CONCLUSIONS Monitoring of SAA may be suggested in AKU to evaluate inflammation. Though further evidence is needed, SAA, chitotriosidase activity and PTI might be proposed as disease activity markers in AKU.
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Affiliation(s)
- D Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy.
| | - D Giustarini
- Dipartimento Scienze Mediche, Chirurgiche e Neuroscienze, Università degli Studi di Siena, Siena, Italy.
| | - B Marzocchi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy; UOC Patologia Clinica, Azienda Ospedaliera Senese, Siena, Italy.
| | - L Peruzzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy; UOC Medicina Molecolare e Genetica, Azienda Ospedaliera Senese, Siena, Italy.
| | - M Margollicci
- UOC Medicina Molecolare e Genetica, Azienda Ospedaliera Senese, Siena, Italy.
| | - R Rossi
- Dipartimento Scienze della Vita, Università degli Studi di Siena, Siena, Italy.
| | - G Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy.
| | - L Millucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy.
| | - J A Gallagher
- Department of Musculoskeletal Biology, University of Liverpool, Liverpool, UK.
| | | | - R Imrich
- Center for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - J Rovensky
- National Institute of Rheumatic Diseases, Piešťany, Slovakia.
| | - M Al-Sbou
- Department of Pharmacology, Alkaptonuria Research Office, Faculty of Medicine, Mutah University, Mutah, Karak, Jordan.
| | - L R Ranganath
- Department of Musculoskeletal Biology, University of Liverpool, Liverpool, UK; Department of Clinical Biochemistry and Metabolism, Royal Liverpool University Hospital, Liverpool, UK.
| | - A Santucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Siena, Italy.
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An Unusual Cause of Myelopathy: Ochronotic Spondyloarthropathy With Positive HLA B27. Am J Phys Med Rehabil 2017; 96:e206-e209. [PMID: 28240677 DOI: 10.1097/phm.0000000000000727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ochronosis is a late developing complication of alkaptonuria, a black brownish pigment in the fibrous and cartilaginous tissues. Although most previous studies reported alkaptonuria and back pain due to ochronosis, thoracic myelopathy is an extremely rare complication. In this report, a paraparetic patient who has ochronotic spondiloarthropathy with the presence of HLA B27 antigen is described. He had low back and leg pain and morning stiffness for 5 yrs. Last year, these were followed by tingling, numbness, and weakness the in lower extremities and he was operated on with preliminary diagnosis of prolapsed disc herniation and cord compression. Surgery is suggested for disc herniations related to ochronotic spondyloarthropathy if it is necessary or neurologic symptoms are present. However, his pain and weakness have partially recovered after the operation. After medical and physical treatment, he showed clinically significant improvements. This case report demonstrates that the management of ochronosis needs a multidisciplinary approach with physiologic, neurologic, and psychologic effects and proper treatment may significantly improve functional outcomes in these patients.
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Morrow G, Tanguay RM. Biochemical and Clinical Aspects of Hereditary Tyrosinemia Type 1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 959:9-21. [DOI: 10.1007/978-3-319-55780-9_2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Bryan LK, Weeks BR, Payne HR, Thompson LA, Mansell JL. Ochronosis-like condition in a cat. Vet Dermatol 2016; 27:311-e77. [DOI: 10.1111/vde.12326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Laura K. Bryan
- Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; 4467 TAMU College Station TX 77843-4467 USA
| | - Brad R. Weeks
- Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; 4467 TAMU College Station TX 77843-4467 USA
| | - Harold Ross Payne
- Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; 4467 TAMU College Station TX 77843-4467 USA
| | - Lori A. Thompson
- Animal Dermatology Clinic; 3901 East 82nd Street Indianapolis IN 46240 USA
| | - Joanne L. Mansell
- Department of Veterinary Pathobiology; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; 4467 TAMU College Station TX 77843-4467 USA
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28
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Bassily E, O'Dell MC, Homan B, Wasyliw C. Alkaptonuria. Orthopedics 2016; 39:e810-3. [PMID: 27158826 DOI: 10.3928/01477447-20160503-03] [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] [Indexed: 02/03/2023]
Abstract
A 50-year-old woman with a chronic polyarthropathy was seen by her orthopedist for long-standing back and shoulder and worsening hip pain. A lateral labral tear and chronic trochanteric bursitis were diagnosed on hip magnetic resonance imaging, which was otherwise unremarkable. Hip arthroscopy was performed revealing an unusual bluish-tinged femoral head articular surface. Computed tomography scans of the spine were also obtained.
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Gil JA, Wawrzynski J, Waryasz GR. Orthopedic Manifestations of Ochronosis: Pathophysiology, Presentation, Diagnosis, and Management. Am J Med 2016; 129:536.e1-6. [PMID: 26844634 DOI: 10.1016/j.amjmed.2016.01.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/09/2016] [Accepted: 01/13/2016] [Indexed: 11/17/2022]
Abstract
Ochronotic arthropathy occurs in patients with alkaptonuria, manifesting first in the intervertebral discs of the lumbar spine, with subsequent degeneration most often observed in the knee, hip, and shoulder joints. Efforts at treatment are targeted at minimizing the damaging effects of the underlying metabolic disorder on the articular cartilage. Vitamin E and N-acetyl cysteine are potential therapies because of their scavenging of free radicals and consequent limitation of oxidative damage to joint tissue. Arthroscopy has been found to be an effective diagnostic tool in cases of suspected ochronosis. Arthroplasty performed in patients with ochronotic arthropathy suggests that the procedure is effective in the alleviation of joint pain and the improvement of mobility. Perioperative management of these patients may require more careful consideration pertinent to the associated comorbidities of this disorder.
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Affiliation(s)
- Joseph A Gil
- Department of Orthopedic Surgery, Warren Alpert Medical School, Brown University, Providence, RI.
| | | | - Gregory R Waryasz
- Department of Orthopedic Surgery, Warren Alpert Medical School, Brown University, Providence, RI
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Mirzashahi B, Tafakhori A, Najafi A, Farzan M. Neglected Alkaptonuric Patient Presenting with Steppage Gait. THE ARCHIVES OF BONE AND JOINT SURGERY 2016; 4:188-191. [PMID: 27200402 PMCID: PMC4852050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 11/28/2015] [Indexed: 06/05/2023]
Abstract
Even though intervertebral disc degeneration can be found in the natural course of alkaptonuria, detection of the disease by black disc color change in a patient without any other presentation of alkaptonuria is an exceptionally rare condition. We have reported a very rare case of alkaptonuria presented with low back pain and steppage gait in a 51-year-old male with a complaint of chronic low-back pain and steppage gait who was operated on for prolapsed lumbar disc herniation. Intraoperatively his lumbar disk was discovered to be black. The alkaptonuria diagnosis was considered after histopathological examination of the black disc material and elevated urinary concentration of homogentisic acid confirmed the diagnosis. To our knowledge, this presentation has not been reported previously in literature.
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Affiliation(s)
- Babak Mirzashahi
- Joint Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Tafakhori
- Joint Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Arvin Najafi
- Joint Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Farzan
- Joint Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
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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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32
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Zatkova A, Nemethova M. Genetics of alkaptonuria – an overview. ACTA FACULTATIS PHARMACEUTICAE UNIVERSITATIS COMENIANAE 2015. [DOI: 10.1515/afpuc-2015-0021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Alkaptonuria (AKU) is the first described inborn error of metabolism and a classical example of rare autosomal recessive disease. AKU patients carry homozygous or compound heterozygous mutations of the gene coding for enzyme homogentisate dioxygenase (HGD) involved in metabolism of tyrosine. The metabolic block in AKU causes accumulation of homogentisic acid (HGA) that, with advancing age of the patient, leads to severe and painful ochronotic arthropathy. HGD gene was mapped to chromosome 3q13.3 and is composed of 14 exons. In about 400 patients, 142 pathogenic variants were reported that are listed in HGD mutations database (http://hgddatabase.cvtisr.sk/). In this review, we summarise different aspects of AKU genetics and impact of the HGD variants on enzyme function.
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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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35
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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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36
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Kraus VB. Rare osteoarthritis. Rheumatology (Oxford) 2015. [DOI: 10.1016/b978-0-323-09138-1.00185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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First report of a deletion encompassing an entire exon in the homogentisate 1,2-dioxygenase gene causing alkaptonuria. PLoS One 2014; 9:e106948. [PMID: 25233259 PMCID: PMC4169433 DOI: 10.1371/journal.pone.0106948] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/05/2014] [Indexed: 11/23/2022] Open
Abstract
Alkaptonuria is often diagnosed clinically with episodes of dark urine, biochemically by the accumulation of peripheral homogentisic acid and molecularly by the presence of mutations in the homogentisate 1,2-dioxygenase gene (HGD). Alkaptonuria is invariably associated with HGD mutations, which consist of single nucleotide variants and small insertions/deletions. Surprisingly, the presence of deletions beyond a few nucleotides among over 150 reported deleterious mutations has not been described, raising the suspicion that this gene might be protected against the detrimental mechanisms of gene rearrangements. The quest for an HGD mutation in a proband with AKU revealed with a SNP array five large regions of homozygosity (5–16 Mb), one of which includes the HGD gene. A homozygous deletion of 649 bp deletion that encompasses the 72 nucleotides of exon 2 and surrounding DNA sequences in flanking introns of the HGD gene was unveiled in a proband with AKU. The nature of this deletion suggests that this in-frame deletion could generate a protein without exon 2. Thus, we modeled the tertiary structure of the mutant protein structure to determine the effect of exon 2 deletion. While the two β-pleated sheets encoded by exon 2 were missing in the mutant structure, other β-pleated sheets are largely unaffected by the deletion. However, nine novel α-helical coils substituted the eight coils present in the native HGD crystal structure. Thus, this deletion results in a deleterious enzyme, which is consistent with the proband’s phenotype. Screening for mutations in the HGD gene, particularly in the Middle East, ought to include this exon 2 deletion in order to determine its frequency and uncover its origin.
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Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice. PLoS One 2014; 9:e102319. [PMID: 25029527 PMCID: PMC4100879 DOI: 10.1371/journal.pone.0102319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 06/18/2014] [Indexed: 12/25/2022] Open
Abstract
Computational models using metabolic reconstructions for in silico simulation of metabolic disorders such as type 2 diabetes mellitus (T2DM) can provide a better understanding of disease pathophysiology and avoid high experimentation costs. There is a limited amount of computational work, using metabolic reconstructions, performed in this field for the better understanding of T2DM. In this study, a new algorithm for generating tissue-specific metabolic models is presented, along with the resulting multi-confidence level (MCL) multi-tissue model. The effect of T2DM on liver, muscle, and fat in MKR mice was first studied by microarray analysis and subsequently the changes in gene expression of frank T2DM MKR mice versus healthy mice were applied to the multi-tissue model to test the effect. Using the first multi-tissue genome-scale model of all metabolic pathways in T2DM, we found out that branched-chain amino acids' degradation and fatty acids oxidation pathway is downregulated in T2DM MKR mice. Microarray data showed low expression of genes in MKR mice versus healthy mice in the degradation of branched-chain amino acids and fatty-acid oxidation pathways. In addition, the flux balance analysis using the MCL multi-tissue model showed that the degradation pathways of branched-chain amino acid and fatty acid oxidation were significantly downregulated in MKR mice versus healthy mice. Validation of the model was performed using data derived from the literature regarding T2DM. Microarray data was used in conjunction with the model to predict fluxes of various other metabolic pathways in the T2DM mouse model and alterations in a number of pathways were detected. The Type 2 Diabetes MCL multi-tissue model may explain the high level of branched-chain amino acids and free fatty acids in plasma of Type 2 Diabetic subjects from a metabolic fluxes perspective.
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Mistry JB, Bukhari M, Taylor AM. Alkaptonuria. Rare Dis 2013; 1:e27475. [PMID: 25003018 DOI: 10.4161/rdis.27475] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/26/2013] [Accepted: 12/09/2013] [Indexed: 12/15/2022] Open
Abstract
Alkaptonuria (AKU) is a rare disorder of autosomal recessive inheritance. It is caused by a mutation in a gene that results in the accumulation of homogentisic acid (HGA). Characteristically, the excess HGA means sufferers pass dark urine, which upon standing turns black. This is a feature present from birth. Over time patients develop other manifestations of AKU, due to deposition of HGA in collagenous tissues, namely ochronosis and ochronotic osteoarthropathy. Although this condition does not reduce life expectancy, it significantly affects quality of life. The natural history of this condition is becoming better understood, despite gaps in knowledge. Clinical assessment of the condition has also improved along with the development of a potentially disease-modifying therapy. Furthermore, recent developments in AKU research have led to new understanding of the disease, and further study of the AKU arthropathy has the potential to influence therapy in the management of osteoarthritis.
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Affiliation(s)
- Jemma B Mistry
- Lancaster Medical School; Faculty of Health & Medicine; Lancaster, UK
| | - Marwan Bukhari
- University Hospitals of Morecambe Bay NHS Foundation Trust; Royal Lancaster Infirmary; Lancaster, UK
| | - Adam M Taylor
- Lancaster Medical School; Faculty of Health & Medicine; Lancaster, UK
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40
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Yin F, Luo S, Cai J, Zhou W, Yuan F, Ma M, Wu Q. Knee Arthroplasty in Alkaptonuric Arthropathy: A Case Report. JBJS Case Connect 2013; 3:e60. [PMID: 29252216 DOI: 10.2106/jbjs.cc.l.00246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Feng Yin
- Department of Joint and Bone Disease, Shanghai East Hospital, Tongji University School of Medicine, 150 JiMo Road, PuDong New Area, Shanghai 200120, China.
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Pan YH, Zhang Y, Cui J, Liu Y, McAllan BM, Liao CC, Zhang S. Adaptation of phenylalanine and tyrosine catabolic pathway to hibernation in bats. PLoS One 2013; 8:e62039. [PMID: 23620802 PMCID: PMC3631164 DOI: 10.1371/journal.pone.0062039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 02/24/2013] [Indexed: 11/19/2022] Open
Abstract
Some mammals hibernate in response to harsh environments. Although hibernating mammals may metabolize proteins, the nitrogen metabolic pathways commonly activated during hibernation are not fully characterized. In contrast to the hypothesis of amino acid preservation, we found evidence of amino acid metabolism as three of five key enzymes, including phenylalanine hydroxylase (PAH), homogentisate 1,2-dioxygenase (HGD), fumarylacetoacetase (FAH), involved in phenylalanine and tyrosine catabolism were co-upregulated during hibernation in two distantly related species of bats, Myotis ricketti and Rhinolophus ferrumequinum. In addition, the levels of phenylalanine in the livers of these bats were significantly decreased during hibernation. Because phenylalanine and tyrosine are both glucogenic and ketogenic, these results indicate the role of this catabolic pathway in energy supply. Since any deficiency in the catabolism of these two amino acids can cause accumulations of toxic metabolites, these results also suggest the detoxification role of these enzymes during hibernation. A higher selective constraint on PAH, HPD, and HGD in hibernators than in non-hibernators was observed, and hibernators had more conserved amino acid residues in each of these enzymes than non-hibernators. These conserved amino acid residues are mostly located in positions critical for the structure and activity of the enzymes. Taken together, results of this work provide novel insights in nitrogen metabolism and removal of harmful metabolites during bat hibernation.
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Affiliation(s)
- Yi-Hsuan Pan
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Yijian Zhang
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Jie Cui
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Yang Liu
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
| | - Bronwyn M. McAllan
- Discipline of Physiology and Bosch Institute, School of Medical Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Chen-Chung Liao
- Proteomic Research Center, National Yang-Ming University, Taipei, Taiwan
- * E-mail: (SZ); (CL)
| | - Shuyi Zhang
- Laboratory of Molecular Ecology and Evolution, Institute for Advanced Studies in Multidisciplinary Science and Technology, East China Normal University, Shanghai, China
- * E-mail: (SZ); (CL)
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42
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Eslami M, Namazian M, Zare HR. Electrooxidation of homogentisic acid in aqueous and mixed solvent solutions: experimental and theoretical studies. J Phys Chem B 2013; 117:2757-63. [PMID: 23384055 DOI: 10.1021/jp3121325] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrochemical behavior of homogentisic acid (HGA) has been studied in both aqueous and mixed solvent solution of water-acetonitrile. Physicochemical parameters of the electrochemical reaction of HGA in these solutions are obtained experimentally by cyclic voltammetry method and are also calculated theoretically using accurate ab initio calculations (G3MP2//B3LYP). Solvation energies are calculated using the available solvation model of CPCM. The pH dependence of the redox activity of HGA in aqueous and the mixture solutions at different temperatures was used for the experimental determination of the standard reduction potential and changes of entropy, enthalpy, and Gibbs free energy for the studied reaction. The experimental standard redox potential of the compound in aqueous solution was obtained to be 0.636 V versus the standard hydrogen electrode. There is a good agreement between the theoretical and experimental values (0.702 and 0.636 V) for the standard electrode potential of HGA. The changes of thermodynamic functions of solvation are also calculated from the differences between the solution-phase experimental values and the gas-phase theoretical values. Finally, using the value of solvation energy of HGA in water and acetonitrile solvents which calculated by the CPCM model of energy, we proposed an equation for calculating the standard redox potential of HGA in mixture solution of water and acetonitrile. A good agreement between the result of electrode potential calculated by the proposed equation and the experimental value confirms the validity of the theoretical models used here and the accuracy of experimental methods.
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Affiliation(s)
- Marzieh Eslami
- Department of Chemistry, Yazd University, P. O. Box 89195-741, Yazd, Iran
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43
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Flydal MI, Chatfield CH, Zheng H, Gunderson FF, Aubi O, Cianciotto NP, Martinez A. Phenylalanine hydroxylase from Legionella pneumophila is a thermostable enzyme with a major functional role in pyomelanin synthesis. PLoS One 2012; 7:e46209. [PMID: 23049981 PMCID: PMC3458870 DOI: 10.1371/journal.pone.0046209] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/29/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Legionella pneumophila is a pathogenic bacterium that can cause Legionnaires' disease and other non-pneumonic infections in humans. This bacterium produces a pyomelanin pigment, a potential virulence factor with ferric reductase activity. In this work, we have investigated the role of phenylalanine hydroxylase from L. pneumophila (lpPAH), the product of the phhA gene, in the synthesis of the pyomelanin pigment and the growth of the bacterium in defined compositions. METHODOLOGY/PRINCIPAL FINDINGS Comparative studies of wild-type and phhA mutant corroborate that lpPAH provides the excess tyrosine for pigment synthesis. phhA and letA (gacA) appear transcriptionally linked when bacteria were grown in buffered yeast extract medium at 37°C. phhA is expressed in L. pneumophila growing in macrophages. We also cloned and characterized lpPAH, which showed many characteristics of other PAHs studied so far, including Fe(II) requirement for activity. However, it also showed many particular properties such as dimerization, a high conformational thermal stability, with a midpoint denaturation temperature (T(m)) = 79 ± 0.5°C, a high specific activity at 37°C (10.2 ± 0.3 µmol L-Tyr/mg/min) and low affinity for the substrate (K(m) (L-Phe) = 735 ± 50 µM. CONCLUSIONS/SIGNIFICANCE lpPAH has a major functional role in the synthesis of pyomelanin and promotes growth in low-tyrosine media. The high thermal stability of lpPAH might reflect the adaptation of the enzyme to withstand relatively high survival temperatures.
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Affiliation(s)
- Marte I. Flydal
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christa H. Chatfield
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Huaixin Zheng
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Felizza F. Gunderson
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Oscar Aubi
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Nicholas P. Cianciotto
- Department of Microbiology-Immunology, Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
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Magesh R, George Priya Doss C. Computational methods to work as first-pass filter in deleterious SNP analysis of alkaptonuria. ScientificWorldJournal 2012; 2012:738423. [PMID: 22606059 PMCID: PMC3349151 DOI: 10.1100/2012/738423] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 10/31/2011] [Indexed: 01/14/2023] Open
Abstract
A major challenge in the analysis of human genetic variation is to distinguish functional from nonfunctional SNPs. Discovering these functional SNPs is one of the main goals of modern genetics and genomics studies. There is a need to effectively and efficiently identify functionally important nsSNPs which may be deleterious or disease causing and to identify their molecular effects. The prediction of phenotype of nsSNPs by computational analysis may provide a good way to explore the function of nsSNPs and its relationship with susceptibility to disease. In this context, we surveyed and compared variation databases along with in silico prediction programs to assess the effects of deleterious functional variants on protein functions. In other respects, we attempted these methods to work as first-pass filter to identify the deleterious substitutions worth pursuing for further experimental research. In this analysis, we used the existing computational methods to explore the mutation-structure-function relationship in HGD gene causing alkaptonuria.
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Affiliation(s)
- R Magesh
- Department of Biotechnology, Faculty of Biomedical Sciences, Technology & Research, Sri Ramachandra University, Chennai, India
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45
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Genetic basis of cystinosis in Turkish patients: a single-center experience. Pediatr Nephrol 2012; 27:115-21. [PMID: 21786142 PMCID: PMC3501933 DOI: 10.1007/s00467-011-1942-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 04/28/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
We report the molecular findings for the CTNS gene in 12 Turkish cystinosis patients aged 7-29 years. All presented initially with severe failure to thrive, polyuria, and polydipsia. Cystinosis was diagnosed at age 1 month to 9 years. Seven patients reached end-stage renal failure at ages ranging from 6.5 to 15 years. Whereas three of the remaining five have renal Fanconi syndrome with proteinuria, two have had kidney failure of varying degrees. Molecular analyses involved an initial multiplex polymerase chain reaction (PCR) to determine the presence or absence of the 57-kb northern European founder deletion in CTNS, followed by sequencing of the ten coding exons of CTNS. Comprehensive mutation analysis verified that none of the 12 patients carried the common 57-kb deletion. We identified four previously reported nucleotide variations associated with cystinosis and five new variants: a 10-kb deletion, three missense variants, and a nucleotide substitution in a potential branch point site of intron 4. This study is the first molecular analysis of Turkish cystinosis patients and provides guidance for the molecular diagnosis of cystinosis in this population.
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46
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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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47
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Zatkova A, Sedlackova T, Radvansky J, Polakova H, Nemethova M, Aquaron R, Dursun I, Usher JL, Kadasi L. Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database. JIMD Rep 2011; 4:55-65. [PMID: 23430897 DOI: 10.1007/8904_2011_68] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/01/2011] [Accepted: 06/07/2011] [Indexed: 12/05/2022] Open
Abstract
Enzymatic loss in alkaptonuria (AKU), an autosomal recessive disorder, is caused by mutations in the homogentisate 1,2 dioxygenase (HGD) gene, which decrease or completely inactivate the function of the HGD protein to metabolize homogentisic acid (HGA). AKU shows a very low prevalence (1:100,000-250,000) in most ethnic groups, but there are countries with much higher incidence, such as Slovakia and the Dominican Republic. In this work, we report 11 novel HGD mutations identified during analysis of 36 AKU patients and 41 family members from 27 families originating from 9 different countries, mainly from Slovakia and France. In Slovak patients, we identified two additional mutations, thus a total number of HGD mutations identified in this small country is 12. In order to record AKU-causing mutations and variants of the HGD gene, we have created a HGD mutation database that is open for future submissions and is available online ( http://hgddatabase.cvtisr.sk/ ). It is founded on the Leiden Open (source) Variation Database (LOVD) system and includes data from the original AKU database ( http://www.alkaptonuria.cib.csic.es ) and also all so far reported variants and AKU patients. Where available, HGD-haplotypes associated with the mutations are also presented. Currently, this database contains 148 unique variants, of which 115 are reported pathogenic mutations. It provides a valuable tool for information exchange in AKU research and care fields and certainly presents a useful data source for genotype-phenotype correlations and also for future clinical trials.
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Affiliation(s)
- Andrea Zatkova
- Laboratory of Genetics, Institute of Molecular Physiology and Genetics, Slovak Academy of Sciences, Vlarska 5, 833 34, Bratislava, Slovakia,
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Ranganath L, Taylor AM, Shenkin A, Fraser WD, Jarvis J, Gallagher JA, Sireau N. Identification of alkaptonuria in the general population: a United Kingdom experience describing the challenges, possible solutions and persistent barriers. J Inherit Metab Dis 2011; 34:723-30. [PMID: 21311977 DOI: 10.1007/s10545-011-9282-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/12/2011] [Accepted: 01/13/2011] [Indexed: 12/19/2022]
Abstract
Progress in research into rare diseases is challenging. This paper discusses strategies to identify individuals with the rare genetic disease alkaptonuria (AKU) within the general population. Strategies used included a questionnaire survey of general practitioners, a dedicated website and patient network contact, targeted family screening and medical conference targeting. Primary care physicians of the UK were targeted by a postal survey that involved mailing 11,151 UK GPs; the response rate was 18.2%. We have identified 75 patients in the UK with AKU by the following means: postal survey (23), targeted family screening (11), patient networks and the website (41). Targeting medical conferences (AKU, rare diseases, rheumatology, clinical biochemistry, orthopaedics, general practitioners) did not lead to new identification in the UK but helped identify overseas cases. We are now aware of 626 patients worldwide including newly identified non-UK people with AKU in the following areas: Slovakia (208), the rest of Europe (including Turkey) (79), North America (including USA and Canada) (110), and the rest of the world (154). A mechanism for identifying individuals with AKU in the general population-not just in the UK but worldwide-has been established. Knowledge of patients with AKU, both in the UK and outside, is often confined to establishing their location in a particular GP practice or association with a particular medical professional. Mere identification, however, does not always lead to full engagement for epidemiological research purposes or targeting treatment since further barriers exist.
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Affiliation(s)
- L Ranganath
- Department of Clinical Biochemistry and Metabolic Medicine, Royal Liverpool University Hospital, Prescot Street, Liverpool L7 8XP, UK.
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Al-sbou M. Novel mutations in the homogentisate 1,2 dioxygenase gene identified in Jordanian patients with alkaptonuria. Rheumatol Int 2011; 32:1741-6. [PMID: 21437689 DOI: 10.1007/s00296-011-1868-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 02/18/2011] [Indexed: 11/29/2022]
Abstract
This study was conducted to identify mutations in the homogentisate 1,2 dioxygenase gene (HGD) in alkaptonuria patients among Jordanian population. Blood samples were collected from four alkaptonuria patients, four carriers, and two healthy volunteers. DNA was isolated from peripheral blood. All 14 exons of the HGD gene were amplified using the polymerase chain reaction (PCR) technique. The PCR products were then purified and analyzed by sequencing. Five mutations were identified in our samples. Four of them were novel C1273A, T1046G, 551-552insG, T533G and had not been previously reported, and one mutation T847C has been described before. The types of mutations identified were two missense mutations, one splice site mutation, one frameshift mutation, and one polymorphism. We present the first molecular study of the HGD gene in Jordanian alkaptonuria patients. This study provides valuable information about the molecular basis of alkaptonuria in Jordanian population.
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Affiliation(s)
- Mohammed Al-sbou
- Department of Pharmacology, Alkaptonuria Research Office, Faculty of Medicine, Mutah University, P.O. Box: (7), Mutah, karak, 61710, Jordan.
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50
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Laktasic-Zerjavic N, Curkovic B, Babic-Naglic D, Potocki K, Prutki M, Soldo-Juresa D. Akute Schulterschmerzen beidseits als Anfangssymptom einer Ochronose. Z Rheumatol 2010; 69:443-6. [DOI: 10.1007/s00393-010-0621-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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