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Minadakis G, Christodoulou K, Tsouloupas G, Spyrou GM. PathIN: an integrated tool for the visualization of pathway interaction networks. Comput Struct Biotechnol J 2022; 21:378-387. [PMID: 36618987 PMCID: PMC9798270 DOI: 10.1016/j.csbj.2022.12.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
PathIN is a web-service that provides an easy and flexible way for rapidly creating pathway-based networks at several functional biological levels: genes, compounds and reactions. The tool is supported by a database repository of reference pathway networks across a large set of species, developed through the freely available information included in the KEGG, Reactome and Wiki Pathways database repositories. PathIN provides networks by means of five diverse methodologies: (a) direct connections between pathways of interest, (b) direct connections as well as the first neighbours of the given pathways, (c) direct connections, the first neighbours and the connections in between them, and (d) two additional methodologies for creating complementary pathway-to-pathway networks that involve additional (missing) pathways that interfere in-between pathways of interest. PathIN is expected to be used as a simple yet informative reference tool for understanding networks of molecular mechanisms related to specific diseases.
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Affiliation(s)
- George Minadakis
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683, Nicosia, Cyprus,Correspondence to: George Minadakis, Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683, Nicosia, Cyprus.
| | - Kyproula Christodoulou
- Neurogenetics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683, Nicosia, Cyprus
| | - George Tsouloupas
- HPC Facility, The Cyprus Institute, 20 Konstantinou Kavafi Street, Aglantzia, 2121, Nicosia, Cyprus
| | - George M. Spyrou
- Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus
- PO Box 23462, 1683, Nicosia, Cyprus
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Costantini A, Laureti T, Pala MI, Colangeli M, Cavalieri S, Pozzi E, Brusco A, Salvarani S, Serrati C, Fancellu R. Long-term treatment with thiamine as possible medical therapy for Friedreich ataxia. J Neurol 2016; 263:2170-2178. [PMID: 27488863 DOI: 10.1007/s00415-016-8244-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 01/13/2023]
Abstract
Thiamine (vitamin B1) is a cofactor of fundamental enzymes of cell energetic metabolism; its deficiency causes disorders affecting both the peripheral and central nervous system. Previous studies reported low thiamine levels in cerebrospinal fluid and pyruvate dehydrogenase dysfunction in Friedreich ataxia (FRDA). We investigated the effect of long-term treatment with thiamine in FRDA, evaluating changes in neurological symptoms, echocardiographic parameters, and plasma FXN mRNA levels. Thirty-four consecutive FRDA patients have been continuously treated with intramuscular thiamine 100 mg twice a week and have been assessed with the Scale for the Assessment and Rating of Ataxia (SARA) at baseline, after 1 month, and then every 3 months during treatment. Thiamine administration ranged from 80 to 930 days and was effective in improving total SARA scores from 26.6 ± 7.7 to 21.5 ± 6.2 (p < 0.02). Moreover, deep tendon reflexes reappeared in 57 % of patients with areflexia at baseline, and swallowing improved in 63 % of dysphagic patients. Clinical improvement was stable in all patients, who did not show worsening even after 2 years of treatment. In a subgroup of 13 patients who performed echocardiogram before and during treatment, interventricular septum thickness reduced significantly (p < 0.02). Frataxin mRNA blood levels were modestly increased in one-half of treated patients. We suppose that a focal thiamine deficiency may contribute to a selective neuronal damage in the areas involved in FRDA. Further studies are mandatory to evaluate thiamine role on FXN regulation, to exclude placebo effect, to verify our clinical results, and to confirm restorative and neuroprotective action of thiamine in FRDA.
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Affiliation(s)
- Antonio Costantini
- Department of Neurological Rehabilitation, "Villa Immacolata" Clinic, Strada Sammartinese 65A, 01100, Viterbo, Italy
| | - Tiziana Laureti
- Department of Economics and Management, University of Tuscia, Via del Paradiso 47, 01100, Viterbo, Italy
| | - Maria Immacolata Pala
- Department of Neurological Rehabilitation, "Villa Immacolata" Clinic, Strada Sammartinese 65A, 01100, Viterbo, Italy
| | - Marco Colangeli
- University Studies Abroad Consortium, University of Tuscia, Via Santa Maria in Gradi 4, 01100, Viterbo, Italy
| | - Simona Cavalieri
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Elisa Pozzi
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Sandro Salvarani
- Unit of Neurology, ASL3 Villa Scassi Hospital, Corso O. Scassi 1, 16149, Genoa, Italy
| | - Carlo Serrati
- Unit of Neurology, IRCCS San Martino University Hospital IST, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Roberto Fancellu
- Unit of Neurology, ASL3 Villa Scassi Hospital, Corso O. Scassi 1, 16149, Genoa, Italy. .,Unit of Neurology, IRCCS San Martino University Hospital IST, Largo Rosanna Benzi 10, 16132, Genoa, Italy.
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Costantini A, Giorgi R, D'Agostino S, Pala MI. High-dose thiamine improves the symptoms of Friedreich's ataxia. BMJ Case Rep 2013; 2013:bcr-2013-009424. [PMID: 23704441 DOI: 10.1136/bcr-2013-009424] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Friedreich's ataxia (FRDA) is an autosomal recessive inherited disorder characterised by progressive gait and limb ataxia, dysarthria, areflexia, loss of position sense and a progressive motor weakness of central origin. Some observations indicate that all symptoms of FRDA ataxia could be the manifestation of a thiamine deficiency because of enzymatic abnormalities. Two patients with FRDA were under rehabilitative treatment from February 2012 to February 2013. The scale for assessment and rating of ataxia was performed. The patient began an intramuscular therapy with 100 mg of thiamine every 3-5 days. Injection of high-dose thiamine was effective in reversing the motor failure. From this clinical observation, it is reasonable to infer that a thiamine deficiency due to enzymatic abnormalities could cause a selective neuronal damage in the centres that are typically affected by this disease.
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Affiliation(s)
- Antonio Costantini
- Department of Neurological Rehabilitation, Villa Immacolata, Viterbo, Italy.
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Yan LJ, Thangthaeng N, Sumien N, Forster MJ. Serum Dihydrolipoamide Dehydrogenase Is a Labile Enzyme. JOURNAL OF BIOCHEMICAL AND PHARMACOLOGICAL RESEARCH 2013; 1:30-42. [PMID: 23646291 PMCID: PMC3641859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Dihydrolipoamide dehydrogenase (DLDH) is a multifunctional oxidoreductase and is well known as an essential component of four mammalian mitochondrial multienzyme complexes: pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, branched chain α-keto acid dehydrogenase, and the glycine cleavage system. However, existence of extracellular DLDH in mammals, if any, has not been clearly defined. The present article reports identification and biochemical characterization of serum DLDH. Proteomic analysis of rat serum using blue native polyacrylamide gel electrophoresis (BN-PAGE) and mass spectrometry peptide sequencing led to generation of 6 tryptic peptides in one band that matched to mitochondrial DLDH, indicating the existence of DLDH in rat serum. Measurement of enzymatic activity also indicated the existence of DLDH in human and mouse serum. Further biochemical analysis of rat serum DLDH revealed that this enzyme lacked diaphorase activity and could not be detected on Western blots probed with antibodies that recognized mitochondrial DLDH. Moreover, both ammonium sulfate fractioning and gel filtration of serum samples rendered a great loss in DLDH activity, indicating that the enzyme activity of this serum protein, unlike that of mitochondrial DLDH, is very labile. When DTT was supplemented in the buffer used for gel filtration, DLDH activity was found to be largely preserved; indicating that serum DLDH is susceptible to air-implicated inactivation. Results of the present study indicate that serum DLDH differs from mitochondrial DLDH in that it is a very labile enzyme.
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Affiliation(s)
- Liang-Jun Yan
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Nopporn Thangthaeng
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Nathalie Sumien
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Michael J. Forster
- Department of Pharmacology and Neuroscience and Institute for Aging and Alzheimer’s Disease Research, University of North Texas Health Science Center, Fort Worth, Texas, USA
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García-Giménez JL, Sanchis-Gomar F, Pallardó FV. Could thiazolidinediones increase the risk of heart failure in Friedreich's ataxia patients? Mov Disord 2011; 26:769-71. [DOI: 10.1002/mds.23711] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 02/09/2011] [Accepted: 02/17/2011] [Indexed: 11/11/2022] Open
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Santos R, Lefevre S, Sliwa D, Seguin A, Camadro JM, Lesuisse E. Friedreich ataxia: molecular mechanisms, redox considerations, and therapeutic opportunities. Antioxid Redox Signal 2010; 13:651-90. [PMID: 20156111 PMCID: PMC2924788 DOI: 10.1089/ars.2009.3015] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Revised: 02/08/2010] [Accepted: 02/14/2010] [Indexed: 12/14/2022]
Abstract
Mitochondrial dysfunction and oxidative damage are at the origin of numerous neurodegenerative diseases like Friedreich ataxia and Alzheimer and Parkinson diseases. Friedreich ataxia (FRDA) is the most common hereditary ataxia, with one individual affected in 50,000. This disease is characterized by progressive degeneration of the central and peripheral nervous systems, cardiomyopathy, and increased incidence of diabetes mellitus. FRDA is caused by a dynamic mutation, a GAA trinucleotide repeat expansion, in the first intron of the FXN gene. Fewer than 5% of the patients are heterozygous and carry point mutations in the other allele. The molecular consequences of the GAA triplet expansion is transcription silencing and reduced expression of the encoded mitochondrial protein, frataxin. The precise cellular role of frataxin is not known; however, it is clear now that several mitochondrial functions are not performed correctly in patient cells. The affected functions include respiration, iron-sulfur cluster assembly, iron homeostasis, and maintenance of the redox status. This review highlights the molecular mechanisms that underlie the disease phenotypes and the different hypothesis about the function of frataxin. In addition, we present an overview of the most recent therapeutic approaches for this severe disease that actually has no efficient treatment.
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Affiliation(s)
- Renata Santos
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Sophie Lefevre
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
- University Pierre et Marie Curie, Paris, France
| | - Dominika Sliwa
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Alexandra Seguin
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Jean-Michel Camadro
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
| | - Emmanuel Lesuisse
- Mitochondria, Metals and Oxidative Stress Laboratory, Institut Jacques Monod (UMR 7592 CNRS–University Paris-Diderot), Paris, France
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Bettendorff L, Mastrogiacomo F, LaMarche J, Dozić S, Kish SJ. Brain levels of thiamine and its phosphate esters in Friedreich's ataxia and spinocerebellar ataxia type 1. Mov Disord 1996; 11:437-9. [PMID: 8813226 DOI: 10.1002/mds.870110415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Decreased blood and cerebrospinal fluid levels of thiamine have been reported in patients with spinocerebellar ataxia disorders. To determine whether a thiamine deficiency is present in the brain, we measured levels of thiamine and its phosphate esters thiamine monophosphate (TMP) and thiamine diphosphate (TDP), in postmortem cerebellar and cerebral cortices of patients with Friedreich's ataxia (FA) and spinocerebellar ataxia type 1 (SCA1). Brain levels of free (nonphosphorylated) thiamine, TMP, TDP, and total thiamine in FA and SCA1 were, on average, not significantly different from control values. However, a nonsignificant trend was observed for slightly reduced levels of TDP and total thiamine in cerebellar cortex of the SCA1 patients, a finding that might be related to the severe neuronal damage in this brain area. We conclude that in FA, brain thiamine concentrations are normal, whereas in SCA1 the levels are, at most, only slightly reduced.
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Affiliation(s)
- L Bettendorff
- Laboratory of Neurochemistry, University of Liège, Belgium
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Abstract
Blood thiamine levels in ataxia patients were studied. No significant differences were found between 30 patients with Friedreich's ataxia and 29 patients with olivopontocerebellar atrophy (OPCA) compared with control subjects. Both OPCA and Friedreich's ataxia patients presented significantly lower cerebrospinal fluid thiamine levels than their controls (p less than 0.001 and p less than 0.04 respectively). These results, discussed in terms of the high degree of cerebellar atrophy on CT scans in OPCA v Friedreich's ataxia patients, seem to correlate with cerebellar thiamine turnover and content.
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Affiliation(s)
- O L Pedraza
- Neurology Service, Hôtel-Dieu de Montréal, Quebec, Canada
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Affiliation(s)
- A Harding
- University Department of Clinical Neurology, Institute of Clinical Neurology, London
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Gray RG, Kumar D. Mitochondrial malic enzyme in Friedreich's ataxia: failure to demonstrate reduced activity in cultured fibroblasts. J Neurol Neurosurg Psychiatry 1985; 48:70-4. [PMID: 3973624 PMCID: PMC1028186 DOI: 10.1136/jnnp.48.1.70] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mitochondrial and cytosolic malic enzymes were assayed radiochemically in fibroblasts from six patients suffering from Friedreich's ataxia in order to verify earlier reports of abnormalities in these enzymes. No abnormalities could be detected in the activities of either enzyme. On cellulose acetate electrophoresis a band of enzyme activity corresponding to the mitochondrial isoenzyme was detectable contrary to earlier reports. Possible explanations for the disparity of results between different laboratories are discussed.
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Matthews W, Esiri M. Matthews and Esiri reply. Journal of Neurology, Neurosurgery and Psychiatry 1984. [DOI: 10.1136/jnnp.47.1.110-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
The author reviews the arguments for and against the four etiologic hypotheses in Friedreich's disease that have been proposed since 1974: the "pyruvate hypothesis", the "lipid-membrane hypothesis", the "energy-defect hypothesis" and finally the "taurine hypothesis". While none of these hypotheses are mutually exclusive, the author shows that all of these mechanisms play some role in the pathophysiology of the symptoms, but that only the "taurine hypothesis" appears to be compatible with all the known facts and the biochemical abnormalities reported. The author proposed that the taurine retention defect (possibly due to a block in the high affinity-low capacity transport of taurine - The TH System) is a primary event in Friedreich's disease. Whether it is the primary genetic event still has to be determined.
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