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Subramanian C, Frank MW, Sukhun R, Henry CE, Wade A, Harden ME, Rao S, Tangallapally R, Yun MK, White SW, Lee RE, Sinha U, Rock CO, Jackowski S. Pantothenate Kinase Activation Restores Brain Coenzyme A in a Mouse Model of Pantothenate Kinase-Associated Neurodegeneration. J Pharmacol Exp Ther 2024; 388:171-180. [PMID: 37875310 DOI: 10.1124/jpet.123.001919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
Pantothenate kinase-associated neurodegeneration (PKAN) is characterized by a motor disorder with combinations of dystonia, parkinsonism, and spasticity, leading to premature death. PKAN is caused by mutations in the PANK2 gene that result in loss or reduction of PANK2 protein function. PANK2 is one of three kinases that initiate and regulate coenzyme A biosynthesis from vitamin B5, and the ability of BBP-671, an allosteric activator of pantothenate kinases, to enter the brain and elevate coenzyme A was investigated. The metabolic stability, protein binding, and membrane permeability of BBP-671 all suggest that it has the physical properties required to cross the blood-brain barrier. BBP-671 was detected in plasma, liver, cerebrospinal fluid, and brain following oral administration in rodents, demonstrating the ability of BBP-671 to penetrate the brain. The pharmacokinetic and pharmacodynamic properties of orally administered BBP-671 evaluated in cannulated rats showed that coenzyme A (CoA) concentrations were elevated in blood, liver, and brain. BBP-671 elevation of whole-blood acetyl-CoA served as a peripheral pharmacodynamic marker and provided a suitable method to assess target engagement. BBP-671 treatment elevated brain coenzyme A concentrations and improved movement and body weight in a PKAN mouse model. Thus, BBP-671 crosses the blood-brain barrier to correct the brain CoA deficiency in a PKAN mouse model, resulting in improved locomotion and survival and providing a preclinical foundation for the development of BBP-671 as a potential treatment of PKAN. SIGNIFICANCE STATEMENT: The blood-brain barrier represents a major hurdle for drugs targeting brain metabolism. This work describes the pharmacokinetic/pharmacodynamic properties of BBP-671, a pantothenate kinase activator. BBP-671 crosses the blood-brain barrier to correct the neuron-specific coenzyme A (CoA) deficiency and improve motor function in a mouse model of pantothenate kinase-associated neurodegeneration. The central role of CoA and acetyl-CoA in intermediary metabolism suggests that pantothenate kinase activators may be useful in modifying neurological metabolic disorders.
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Affiliation(s)
- Chitra Subramanian
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Matthew W Frank
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Rajaa Sukhun
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Christopher E Henry
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Anna Wade
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Mallory E Harden
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Satish Rao
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Rajendra Tangallapally
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Mi-Kyung Yun
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Stephen W White
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Richard E Lee
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Uma Sinha
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Charles O Rock
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
| | - Suzanne Jackowski
- Departments of Infectious Diseases (C.S., M.W.F., C.O.R., S.J.), Chemical Biology and Therapeutics (R.T., R.E.L.), Structural Biology (M.-K.Y., S.W.W.), and St. Jude Graduate School of Biomedical Sciences (S.W.W.), St. Jude Children's Research Hospital, Memphis, Tennessee; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee (S.W.W., C.O.R.); and CoA Therapeutics, Inc., a BridgeBio Pharma, Inc. Company, Palo Alto, California (R.S., C.E.H., A.W., M.E.H., S.R., U.S.)
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Fodder K, de Silva R, Warner TT, Bettencourt C. The contribution of DNA methylation to the (dys)function of oligodendroglia in neurodegeneration. Acta Neuropathol Commun 2023; 11:106. [PMID: 37386505 PMCID: PMC10311741 DOI: 10.1186/s40478-023-01607-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Neurodegenerative diseases encompass a heterogeneous group of conditions characterised by the progressive degeneration of the structure and function of the central or peripheral nervous systems. The pathogenic mechanisms underlying these diseases are not fully understood. However, a central feature consists of regional aggregation of proteins in the brain, such as the accumulation of β-amyloid plaques in Alzheimer's disease (AD), inclusions of hyperphosphorylated microtubule-binding tau in AD and other tauopathies, or inclusions containing α-synuclein in Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Various pathogenic mechanisms are thought to contribute to disease, and an increasing number of studies implicate dysfunction of oligodendrocytes (the myelin producing cells of the central nervous system) and myelin loss. Aberrant DNA methylation, the most widely studied epigenetic modification, has been associated with many neurodegenerative diseases, including AD, PD, DLB and MSA, and recent findings highlight aberrant DNA methylation in oligodendrocyte/myelin-related genes. Here we briefly review the evidence showing that changes to oligodendrocytes and myelin are key in neurodegeneration, and explore the relevance of DNA methylation in oligodendrocyte (dys)function. As DNA methylation is reversible, elucidating its involvement in pathogenic mechanisms of neurodegenerative diseases and in dysfunction of specific cell-types such as oligodendrocytes may bring opportunities for therapeutic interventions for these diseases.
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Affiliation(s)
- Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Rohan de Silva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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Li Y, Steinberg J, Coleman Z, Wang S, Subramanian C, Li Y, Patay Z, Akers W, Rock CO, Jackowski S, Bagga P. Proton magnetic resonance spectroscopy detects cerebral metabolic derangement in a mouse model of brain coenzyme a deficiency. J Transl Med 2022; 20:103. [PMID: 35197056 PMCID: PMC8867880 DOI: 10.1186/s12967-022-03304-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/09/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pantothenate kinase (PANK) is the first and rate-controlling enzymatic step in the only pathway for cellular coenzyme A (CoA) biosynthesis. PANK-associated neurodegeneration (PKAN), formerly known as Hallervorden–Spatz disease, is a rare, life-threatening neurologic disorder that affects the CNS and arises from mutations in the human PANK2 gene. Pantazines, a class of small molecules containing the pantazine moiety, yield promising therapeutic effects in an animal model of brain CoA deficiency. A reliable technique to identify the neurometabolic effects of PANK dysfunction and to monitor therapeutic responses is needed. Methods We applied 1H magnetic resonance spectroscopy as a noninvasive technique to evaluate the therapeutic effects of the newly developed Pantazine BBP-671. Results 1H MRS reliably quantified changes in cerebral metabolites, including glutamate/glutamine, lactate, and N-acetyl aspartate in a neuronal Pank1 and Pank2 double-knockout (SynCre+Pank1,2 dKO) mouse model of brain CoA deficiency. The neuronal SynCre+Pank1,2 dKO mice had distinct decreases in Glx/tCr, NAA/tCr, and lactate/tCr ratios compared to the wildtype matched control mice that increased in response to BBP-671 treatment. Conclusions BBP-671 treatment completely restored glutamate/glutamine levels in the brains of the mouse model, suggesting that these metabolites are promising clinically translatable biomarkers for future therapeutic trials. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03304-y.
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Affiliation(s)
- Yanan Li
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey Steinberg
- Center for In Vivo Imaging and Therapeutics (CIVIT), St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zane Coleman
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shubo Wang
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yimei Li
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Zoltan Patay
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Walter Akers
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Puneet Bagga
- Department of Diagnostic Imaging, St. Jude Children's Research Hospital, Memphis, TN, USA.
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Iron-regulatory genes are associated with Neuroimaging measures in HIV infection. Brain Imaging Behav 2021; 14:2037-2049. [PMID: 31273671 DOI: 10.1007/s11682-019-00153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The pathogenesis of HIV-associated neurocognitive impairment (NCI) may involve iron dysregulation. In 243 HIV-seropositive adults without severe comorbidities, we therefore genotyped 250 variants in 20 iron-related genes and evaluated their associations with magnetic resonance imaging measures of brain structure and metabolites, including measures previously linked to NCI. Multivariable regression analyses examined associations between genetic variants and neuroimaging measures, adjusting for relevant covariates and multiple testing. Exploratory analyses stratified by NCI (Global Deficit Score ≥ 0.5 vs. <0.5), virus detectability in plasma, and comorbidity levels were also performed. Of 27 variants (in 12 iron-regulatory genes) associated with neuroimaging measures after correction for the 37 haplotype blocks represented, 3 variants survived additional correction for the 21 neuroimaging measures evaluated and demonstrated biologically plausible associations. SLC11A1 rs7576974_T was significantly associated with higher frontal gray matter N-acetylaspartate (p = 3.62e-5). Among individuals with detectable plasma virus, TFRC rs17091382_A was associated with smaller subcortical gray matter volume (p = 3.23e-5), and CP rs4974389_A (p = 3.52e-5) was associated with higher basal ganglia Choline in persons with mild comorbidities. Two other strong associations were observed for variants in SLC40A1 and ACO2 but were not robust due to low minor-allele frequencies in the study sample. Variants in iron metabolism and transport genes are associated with structural and metabolite neuroimaging measures in HIV-seropositive adults, regardless of virus suppression on antiretroviral therapy. These variants may confer susceptibility to HIV-related brain injury and NCI. Further studies are needed to determine the specificity of these findings to HIV infection and explore potential underlying mechanisms.
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Bagwe-Parab S, Kaur G. Molecular targets and therapeutic interventions for iron induced neurodegeneration. Brain Res Bull 2020; 156:1-9. [DOI: 10.1016/j.brainresbull.2019.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 01/17/2023]
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Subramanian C, Yao J, Frank MW, Rock CO, Jackowski S. A pantothenate kinase-deficient mouse model reveals a gene expression program associated with brain coenzyme a reduction. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165663. [PMID: 31918006 DOI: 10.1016/j.bbadis.2020.165663] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/12/2019] [Accepted: 12/29/2019] [Indexed: 12/12/2022]
Abstract
Pantothenate kinase (PanK) is the first enzyme in the coenzyme A (CoA) biosynthetic pathway. The differential expression of the four-active mammalian PanK isoforms regulates CoA levels in different tissues and PANK2 mutations lead to Pantothenate Kinase Associated Neurodegeneration (PKAN). The molecular mechanisms that potentially underlie PKAN pathophysiology are investigated in a mouse model of CoA deficiency in the central nervous system (CNS). Both PanK1 and PanK2 contribute to brain CoA levels in mice and so a mouse model with a systemic deletion of Pank1 together with neuronal deletion of Pank2 was generated. Neuronal Pank2 expression in double knockout mice decreased starting at P9-11 triggering a significant brain CoA deficiency. The depressed brain CoA in the mice correlates with abnormal forelimb flexing and weakness that, in turn, contributes to reduced locomotion and abnormal gait. Biochemical analysis reveals a reduction in short-chain acyl-CoAs, including acetyl-CoA and succinyl-CoA. Comparative gene expression analysis reveals that the CoA deficiency in brain is associated with a large elevation of Hif3a transcript expression and significant reduction of gene transcripts in heme and hemoglobin synthesis. Reduction of brain heme levels is associated with the CoA deficiency. The data suggest a response to oxygen/glucose deprivation and indicate a disruption of oxidative metabolism arising from a CoA deficiency in the CNS.
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Affiliation(s)
| | - Jiangwei Yao
- St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Matthew W Frank
- St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Charles O Rock
- St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
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Iron and Sphingolipids as Common Players of (Mal)Adaptation to Hypoxia in Pulmonary Diseases. Int J Mol Sci 2020; 21:ijms21010307. [PMID: 31906427 PMCID: PMC6981703 DOI: 10.3390/ijms21010307] [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: 12/06/2019] [Revised: 12/24/2019] [Accepted: 12/31/2019] [Indexed: 12/11/2022] Open
Abstract
Hypoxia, or lack of oxygen, can occur in both physiological (high altitude) and pathological conditions (respiratory diseases). In this narrative review, we introduce high altitude pulmonary edema (HAPE), acute respiratory distress syndrome (ARDS), Chronic Obstructive Pulmonary Disease (COPD), and Cystic Fibrosis (CF) as examples of maladaptation to hypoxia, and highlight some of the potential mechanisms influencing the prognosis of the affected patients. Among the specific pathways modulated in response to hypoxia, iron metabolism has been widely explored in recent years. Recent evidence emphasizes hepcidin as highly involved in the compensatory response to hypoxia in healthy subjects. A less investigated field in the adaptation to hypoxia is the sphingolipid (SPL) metabolism, especially through Ceramide and sphingosine 1 phosphate. Both individually and in concert, iron and SPL are active players of the (mal)adaptation to physiological hypoxia, which can result in the pathological HAPE. Our aim is to identify some pathways and/or markers involved in the physiological adaptation to low atmospheric pressures (high altitudes) that could be involved in pathological adaptation to hypoxia as it occurs in pulmonary inflammatory diseases. Hepcidin, Cer, S1P, and their interplay in hypoxia are raising growing interest both as prognostic factors and therapeutical targets.
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Zhang J, Ju S. Identifying genuine protein-protein interactions within communities of gene co-expression networks using a deconvolution method. IET Syst Biol 2019; 13:290-296. [PMID: 31778125 PMCID: PMC8687158 DOI: 10.1049/iet-syb.2019.0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/24/2019] [Accepted: 07/09/2019] [Indexed: 11/20/2022] Open
Abstract
Direct relationships between biological molecules connected in a gene co-expression network tend to reflect real biological activities such as gene regulation, protein-protein interactions (PPIs), and metabolisation. As correlation-based networks contain numerous indirect connections, those direct relationships are always 'hidden' in them. Compared with the global network, network communities imply more biological significance on predicting protein function, detecting protein complexes and studying network evolution. Therefore, identifying direct relationships in communities is a pervasive and important topic in the biological sciences. Unfortunately, this field has not been well studied. A major thrust of this study is to apply a deconvolution algorithm on communities stemming from different gene co-expression networks, which are constructed by fixing different thresholds for robustness analysis. Using the fifth Dialogue on Reverse Engineering Assessment and Methods challenge (DREAM5) framework, the authors demonstrate that nearly all new communities extracted from a 'deconvolution filter' contain more genuine PPIs than before deconvolution.
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Affiliation(s)
- Jin Zhang
- School of Information Science and Engineering, University of Jinan, Jinan 250022, People's Republic of China.
| | - Shan Ju
- School of International Trade and Economics, Shandong University of Finance and Economics, Jinan 250014, People's Republic of China
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Neurodegeneration with Brain Iron Accumulation Disorders: Valuable Models Aimed at Understanding the Pathogenesis of Iron Deposition. Pharmaceuticals (Basel) 2019; 12:ph12010027. [PMID: 30744104 PMCID: PMC6469182 DOI: 10.3390/ph12010027] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 02/07/2023] Open
Abstract
Neurodegeneration with brain iron accumulation (NBIA) is a set of neurodegenerative disorders, which includes very rare monogenetic diseases. They are heterogeneous in regard to the onset and the clinical symptoms, while the have in common a specific brain iron deposition in the region of the basal ganglia that can be visualized by radiological and histopathological examinations. Nowadays, 15 genes have been identified as causative for NBIA, of which only two code for iron-proteins, while all the other causative genes codify for proteins not involved in iron management. Thus, how iron participates to the pathogenetic mechanism of most NBIA remains unclear, essentially for the lack of experimental models that fully recapitulate the human phenotype. In this review we reported the recent data on new models of these disorders aimed at highlight the still scarce knowledge of the pathogenesis of iron deposition.
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Sharma LK, Subramanian C, Yun MK, Frank MW, White SW, Rock CO, Lee RE, Jackowski S. A therapeutic approach to pantothenate kinase associated neurodegeneration. Nat Commun 2018; 9:4399. [PMID: 30352999 PMCID: PMC6199309 DOI: 10.1038/s41467-018-06703-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/20/2018] [Indexed: 12/17/2022] Open
Abstract
Pantothenate kinase (PANK) is a metabolic enzyme that regulates cellular coenzyme A (CoA) levels. There are three human PANK genes, and inactivating mutations in PANK2 lead to pantothenate kinase associated neurodegeneration (PKAN). Here we performed a library screen followed by chemical optimization to produce PZ-2891, an allosteric PANK activator that crosses the blood brain barrier. PZ-2891 occupies the pantothenate pocket and engages the dimer interface to form a PANK•ATP•Mg2+•PZ-2891 complex. The binding of PZ-2891 to one protomer locks the opposite protomer in a catalytically active conformation that is refractory to acetyl-CoA inhibition. Oral administration of PZ-2891 increases CoA levels in mouse liver and brain. A knockout mouse model of brain CoA deficiency exhibited weight loss, severe locomotor impairment and early death. Knockout mice on PZ-2891 therapy gain weight, and have improved locomotor activity and life span establishing pantazines as novel therapeutics for the treatment of PKAN.
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Affiliation(s)
- Lalit Kumar Sharma
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Nurix, Inc, 1700 Owens Street, Suite 205, San Francisco, CA, 94158, USA
| | - Chitra Subramanian
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew W Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephen W White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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11
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Links Between Iron and Lipids: Implications in Some Major Human Diseases. Pharmaceuticals (Basel) 2018; 11:ph11040113. [PMID: 30360386 PMCID: PMC6315991 DOI: 10.3390/ph11040113] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Maintenance of iron homeostasis is critical to cellular health as both its excess and insufficiency are detrimental. Likewise, lipids, which are essential components of cellular membranes and signaling mediators, must also be tightly regulated to hinder disease progression. Recent research, using a myriad of model organisms, as well as data from clinical studies, has revealed links between these two metabolic pathways, but the mechanisms behind these interactions and the role these have in the progression of human diseases remains unclear. In this review, we summarize literature describing cross-talk between iron and lipid pathways, including alterations in cholesterol, sphingolipid, and lipid droplet metabolism in response to changes in iron levels. We discuss human diseases correlating with both iron and lipid alterations, including neurodegenerative disorders, and the available evidence regarding the potential mechanisms underlying how iron may promote disease pathogenesis. Finally, we review research regarding iron reduction techniques and their therapeutic potential in treating patients with these debilitating conditions. We propose that iron-mediated alterations in lipid metabolic pathways are involved in the progression of these diseases, but further research is direly needed to elucidate the mechanisms involved.
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12
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Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging. Sci Rep 2017; 7:16890. [PMID: 29203886 PMCID: PMC5715102 DOI: 10.1038/s41598-017-17322-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/22/2017] [Indexed: 11/23/2022] Open
Abstract
Aging is a biologically universal event, and yet the key events that drive aging are still poorly understood. One approach to generate new hypotheses about aging is to use unbiased methods to look at change across lifespan. Here, we have examined gene expression in the human dorsolateral frontal cortex using RNA- Seq to populate a whole gene co-expression network analysis. We show that modules of co-expressed genes enriched for those encoding synaptic proteins are liable to change with age. We extensively validate these age-dependent changes in gene expression across several datasets including the publically available GTEx resource which demonstrated that gene expression associations with aging vary between brain regions. We also estimated the extent to which changes in cellular composition account for age associations and find that there are independent signals for cellularity and aging. Overall, these results demonstrate that there are robust age-related alterations in gene expression in the human brain and that genes encoding for neuronal synaptic function may be particularly sensitive to the aging process.
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13
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Salpietro V, Efthymiou S, Manole A, Maurya B, Wiethoff S, Ashokkumar B, Cutrupi MC, Dipasquale V, Manti S, Botia JA, Ryten M, Vandrovcova J, Bello OD, Bettencourt C, Mankad K, Mukherjee A, Mutsuddi M, Houlden H. A loss-of-function homozygous mutation in DDX59 implicates a conserved DEAD-box RNA helicase in nervous system development and function. Hum Mutat 2017; 39:187-192. [PMID: 29127725 PMCID: PMC5814734 DOI: 10.1002/humu.23368] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 12/12/2022]
Abstract
We report on a homozygous frameshift deletion in DDX59 (c.185del: p.Phe62fs*13) in a family presenting with orofaciodigital syndrome phenotype associated with a broad neurological involvement characterized by microcephaly, intellectual disability, epilepsy, and white matter signal abnormalities associated with cortical and subcortical ischemic events. DDX59 encodes a DEAD‐box RNA helicase and its role in brain function and neurological diseases is unclear. We showed a reduction of mutant cDNA and perturbation of SHH signaling from patient‐derived cell lines; furthermore, analysis of human brain gene expression provides evidence that DDX59 is enriched in oligodendrocytes and might act within pathways of leukoencephalopathies‐associated genes. We also characterized the neuronal phenotype of the Drosophila model using mutant mahe, the homolog of human DDX59, and showed that mahe loss‐of‐function mutant embryos exhibit impaired development of peripheral and central nervous system. Taken together, our results support a conserved role of this DEAD‐box RNA helicase in neurological function.
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Affiliation(s)
- Vincenzo Salpietro
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Andreea Manole
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Bhawana Maurya
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi, India
| | - Sarah Wiethoff
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Balasubramaniem Ashokkumar
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | | | | | - Sara Manti
- Department of Paediatrics, University of Messina, Messina, Italy
| | - Juan A Botia
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,Department of Information and Communications Engineering, University of Murcia University of Murcia, Murcia, Spain
| | - Mina Ryten
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Jana Vandrovcova
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Oscar D Bello
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK
| | - Conceicao Bettencourt
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK.,Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK
| | - Kshitij Mankad
- Department of Neuroradiology, Great Ormond Street Hospital for Children, London, UK
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Banaras Hindu University, Varanasi, India
| | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
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14
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The effects of graded levels of calorie restriction: VII. Topological rearrangement of hypothalamic aging networks. Aging (Albany NY) 2017; 8:917-32. [PMID: 27115072 PMCID: PMC4931844 DOI: 10.18632/aging.100944] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/31/2016] [Indexed: 12/31/2022]
Abstract
Connectivity in a gene-gene network declines with age, typically within gene clusters. We explored the effect of short-term (3 months) graded calorie restriction (CR) (up to 40 %) on network structure of aging-associated genes in the murine hypothalamus by using conditional mutual information. The networks showed a topological rearrangement when exposed to graded CR with a higher relative within cluster connectivity at 40CR. We observed changes in gene centrality concordant with changes in CR level, with Ppargc1a, and Ppt1 having increased centrality and Etfdh, Traf3 and Abcc1 decreased centrality as CR increased. This change in gene centrality in a graded manner with CR, occurred in the absence of parallel changes in gene expression levels. This study emphasizes the importance of augmenting traditional differential gene expression analyses to better understand structural changes in the transcriptome. Overall our results suggested that CR induced changes in centrality of biological relevant genes that play an important role in preventing the age-associated loss of network integrity irrespective of their gene expression levels.
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15
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Tello C, Darling A, Lupo V, Pérez-Dueñas B, Espinós C. On the complexity of clinical and molecular bases of neurodegeneration with brain iron accumulation. Clin Genet 2017; 93:731-740. [PMID: 28542792 DOI: 10.1111/cge.13057] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/04/2017] [Accepted: 05/18/2017] [Indexed: 02/06/2023]
Abstract
Neurodegeneration with brain iron accumulation (NBIA) is a group of inherited heterogeneous neurodegenerative rare disorders. These patients present with dystonia, spasticity, parkinsonism and neuropsychiatric disturbances, along with brain magnetic resonance imaging (MRI) evidence of iron accumulation. In sum, they are devastating disorders and to date, there is no specific treatment. Ten NBIA genes are accepted: PANK2, PLA2G6, C19orf12, COASY, FA2H, ATP13A2, WDR45, FTL, CP, and DCAF17; and nonetheless, a relevant percentage of patients remain without genetic diagnosis, suggesting that other novel NBIA genes remain to be discovered. Overlapping complex clinical pictures render an accurate differential diagnosis difficult. Little is known about the pathophysiology of NBIAs. The reported NBIA genes take part in a variety of pathways: CoA synthesis, lipid and iron metabolism, autophagy, and membrane remodeling. The next-generation sequencing revolution has achieved relevant advances in genetics of Mendelian diseases and provide new genes for NBIAs, which are investigated according to 2 main strategies: genes involved in disorders with similar phenotype and genes that play a role in a pathway of interest. To achieve an effective therapy for NBIA patients, a better understanding of the biological process underlying disease is crucial, moving toward a new age of precision medicine.
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Affiliation(s)
- C Tello
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - A Darling
- Department of Neuropediatrics, Hospital Sant Joan de Déu, Barcelona, Spain.,Unit U703, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - V Lupo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - B Pérez-Dueñas
- Department of Neuropediatrics, Hospital Sant Joan de Déu, Barcelona, Spain.,Unit U703, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - C Espinós
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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16
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Pflieger LT, Dansithong W, Paul S, Scoles DR, Figueroa KP, Meera P, Otis TS, Facelli JC, Pulst SM. Gene co-expression network analysis for identifying modules and functionally enriched pathways in SCA2. Hum Mol Genet 2017; 26:3069-3080. [PMID: 28525545 PMCID: PMC5886232 DOI: 10.1093/hmg/ddx191] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/22/2017] [Accepted: 05/11/2017] [Indexed: 12/22/2022] Open
Abstract
Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the ATXN2 gene. The repeat resides in an encoded region of the gene resulting in polyglutamine (polyQ) expansion which has been assumed to result in gain of function, predominantly, for the ATXN2 protein. We evaluated temporal cerebellar expression profiles by RNA sequencing of ATXN2Q127 mice versus wild-type (WT) littermates. ATXN2Q127 mice are characterized by a progressive motor phenotype onset, and have progressive cerebellar molecular and neurophysiological (Purkinje cell firing frequency) phenotypes. Our analysis revealed previously uncharacterized early and progressive abnormal patterning of cerebellar gene expression. Weighted Gene Coexpression Network Analysis revealed four gene modules that were significantly correlated with disease status, composed primarily of genes associated with GTPase signaling, calcium signaling and cell death. Of these genes, few overlapped with differentially expressed cerebellar genes that we identified in Atxn2-/- knockout mice versus WT littermates, suggesting that loss-of-function is not a significant component of disease pathology. We conclude that SCA2 is a disease characterized by gain of function for ATXN2.
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Affiliation(s)
| | - Warunee Dansithong
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel R. Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Karla P. Figueroa
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Pratap Meera
- Department of Neurobiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thomas S. Otis
- Department of Neurobiology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Stefan M. Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
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17
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Chen L, Mukerjee G, Dorfman R, Moghadas SM. Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores. Front Genet 2017; 8:29. [PMID: 28326099 PMCID: PMC5339255 DOI: 10.3389/fgene.2017.00029] [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: 10/24/2016] [Accepted: 02/22/2017] [Indexed: 11/18/2022] Open
Abstract
Much effort has been devoted to assess disease risk based on large-scale protein-protein network and genotype-phenotype associations. However, the challenge of risk prediction for complex diseases remains unaddressed. Here, we propose a framework to quantify the risk based on a Voronoi tessellation network analysis, taking into account the disease association scores of both genes and variants. By integrating ClinVar, SNPnexus, and DISEASES databases, we introduce a gene-variant map that is based on the pairwise disease-associated gene-variant scores. This map is clustered using Voronoi tessellation and network analysis with a threshold obtained from fitting the background Voronoi cell density distribution. We define the relative risk of disease that is inferred from the scores of the data points within the related clusters on the gene-variant map. We identify autoimmune-associated clusters that may interact at the system-level. The proposed framework can be used to determine the clusters that are specific to a subtype or contribute to multiple subtypes of complex diseases.
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Affiliation(s)
- Lin Chen
- Agent-Based Modelling Laboratory, York University Toronto, ON, Canada
| | | | | | - Seyed M Moghadas
- Agent-Based Modelling Laboratory, York University Toronto, ON, Canada
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18
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Orellana DI, Santambrogio P, Rubio A, Yekhlef L, Cancellieri C, Dusi S, Giannelli SG, Venco P, Mazzara PG, Cozzi A, Ferrari M, Garavaglia B, Taverna S, Tiranti V, Broccoli V, Levi S. Coenzyme A corrects pathological defects in human neurons of PANK2-associated neurodegeneration. EMBO Mol Med 2016; 8:1197-1211. [PMID: 27516453 PMCID: PMC5048368 DOI: 10.15252/emmm.201606391] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pantothenate kinase‐associated neurodegeneration (PKAN) is an early onset and severely disabling neurodegenerative disease for which no therapy is available. PKAN is caused by mutations in PANK2, which encodes for the mitochondrial enzyme pantothenate kinase 2. Its function is to catalyze the first limiting step of Coenzyme A (CoA) biosynthesis. We generated induced pluripotent stem cells from PKAN patients and showed that their derived neurons exhibited premature death, increased ROS production, mitochondrial dysfunctions—including impairment of mitochondrial iron‐dependent biosynthesis—and major membrane excitability defects. CoA supplementation prevented neuronal death and ROS formation by restoring mitochondrial and neuronal functionality. Our findings provide direct evidence that PANK2 malfunctioning is responsible for abnormal phenotypes in human neuronal cells and indicate CoA treatment as a possible therapeutic intervention.
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Affiliation(s)
- Daniel I Orellana
- Proteomics of Iron Metabolism Unit, Division of Neuroscience San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Santambrogio
- Proteomics of Iron Metabolism Unit, Division of Neuroscience San Raffaele Scientific Institute, Milan, Italy
| | - Alicia Rubio
- Stem Cells and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Latefa Yekhlef
- Neuroimmunology Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Cinzia Cancellieri
- Stem Cells and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Sabrina Dusi
- Molecular Neurogenetics Unit, Foundation IRCCS-Neurological Institute "Carlo Besta", Milan, Italy
| | - Serena G Giannelli
- Stem Cells and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Paola Venco
- Molecular Neurogenetics Unit, Foundation IRCCS-Neurological Institute "Carlo Besta", Milan, Italy
| | - Pietro G Mazzara
- Stem Cells and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Anna Cozzi
- Proteomics of Iron Metabolism Unit, Division of Neuroscience San Raffaele Scientific Institute, Milan, Italy
| | - Maurizio Ferrari
- Genomic Unit for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy Vita-Salute San Raffaele University, Milan, Italy
| | - Barbara Garavaglia
- Molecular Neurogenetics Unit, Foundation IRCCS-Neurological Institute "Carlo Besta", Milan, Italy
| | - Stefano Taverna
- Neuroimmunology Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Tiranti
- Molecular Neurogenetics Unit, Foundation IRCCS-Neurological Institute "Carlo Besta", Milan, Italy
| | - Vania Broccoli
- Stem Cells and Neurogenesis Unit, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy Institute of Neuroscience, National Research Council, Milan, Italy
| | - Sonia Levi
- Proteomics of Iron Metabolism Unit, Division of Neuroscience San Raffaele Scientific Institute, Milan, Italy Vita-Salute San Raffaele University, Milan, Italy
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19
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Santos JS, Alvarenga Brizola VR, Granato D. High-throughput assay comparison and standardization for metal chelating capacity screening: A proposal and application. Food Chem 2016; 214:515-522. [PMID: 27507505 DOI: 10.1016/j.foodchem.2016.07.091] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/12/2016] [Accepted: 07/12/2016] [Indexed: 12/31/2022]
Abstract
Aiming to standardize the experimental protocols to assess the ability to chelate Fe(2+) and Cu(2+) using 96-well microplates, we analyzed Brazilian coffees (n=20) as a study-case in relation to their antioxidant activity using conventional methods (DPPH and FRAP assays) and correlated the results with the total phenolic content (TPC) using bivariate and multivariate statistical approaches. Complementarily, we assessed the repeatability, reproducibility, recovery, and linearity of both methods. Data showed that the proposed assays presented a good repeatability and reproducibility (<7% RSD) and mean recovery values of 96.66% and 98.91% for the iron and copper assays, respectively. Both methods were linear in the range of 0-100mg EDTA equivalents/L. Cu(2+)-chelating ability was significantly correlated to FRAP, DPPH, and TPC, while sparse (p<0.05) correlations were obtained with Fe(2+)-chelating ability. Overall, both micro assays can be used to assess the ability of plant-based extracts to chelate Fe(2+) and Cu(2+)in vitro.
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Affiliation(s)
- Jânio Sousa Santos
- Food Science and Technology Graduate Program, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Uvaranas Campus, Ponta Grossa, PR, Brazil
| | - Vitor Rafael Alvarenga Brizola
- Department of Food Engineering, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Uvaranas Campus, Ponta Grossa, PR, Brazil
| | - Daniel Granato
- Food Science and Technology Graduate Program, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Uvaranas Campus, Ponta Grossa, PR, Brazil; Department of Food Engineering, State University of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Uvaranas Campus, Ponta Grossa, PR, Brazil.
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20
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Heidari M, Gerami SH, Bassett B, Graham RM, Chua ACG, Aryal R, House MJ, Collingwood JF, Bettencourt C, Houlden H, Ryten M, Olynyk JK, Trinder D, Johnstone DM, Milward EA. Pathological relationships involving iron and myelin may constitute a shared mechanism linking various rare and common brain diseases. Rare Dis 2016; 4:e1198458. [PMID: 27500074 PMCID: PMC4961263 DOI: 10.1080/21675511.2016.1198458] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/02/2016] [Accepted: 06/01/2016] [Indexed: 12/18/2022] Open
Abstract
We previously demonstrated elevated brain iron levels in myelinated structures and associated cells in a hemochromatosis Hfe−/−xTfr2mut mouse model. This was accompanied by altered expression of a group of myelin-related genes, including a suite of genes causatively linked to the rare disease family ‘neurodegeneration with brain iron accumulation’ (NBIA). Expanded data mining and ontological analyses have now identified additional myelin-related transcriptome changes in response to brain iron loading. Concordance between the mouse transcriptome changes and human myelin-related gene expression networks in normal and NBIA basal ganglia testifies to potential clinical relevance. These analyses implicate, among others, genes linked to various rare central hypomyelinating leukodystrophies and peripheral neuropathies including Pelizaeus-Merzbacher-like disease and Charcot-Marie-Tooth disease as well as genes linked to other rare neurological diseases such as Niemann-Pick disease. The findings may help understand interrelationships of iron and myelin in more common conditions such as hemochromatosis, multiple sclerosis and various psychiatric disorders.
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Affiliation(s)
- Moones Heidari
- School of Biomedical Sciences and Pharmacy, The University of Newcastle , Callaghan, NSW, Australia
| | - Sam H Gerami
- School of Biomedical Sciences and Pharmacy, The University of Newcastle , Callaghan, NSW, Australia
| | - Brianna Bassett
- School of Biomedical Sciences and Pharmacy, The University of Newcastle , Callaghan, NSW, Australia
| | - Ross M Graham
- School of Biomedical Sciences & Curtin Health Innovation Research Institute - Biosciences, Curtin University of Technology , Bentley, WA, Australia
| | - Anita C G Chua
- School of Medicine and Pharmacology, University of Western Australia, Fiona Stanley Hospital, Murdoch, WA, Australia; Harry Perkins Institute of Medical Research, Murdoch, WA, Australia
| | - Ritambhara Aryal
- School of Biomedical Sciences and Pharmacy, The University of Newcastle , Callaghan, NSW, Australia
| | - Michael J House
- School of Physics, University of Western Australia , Crawley, WA, Australia
| | - Joanna F Collingwood
- Warwick Engineering in Biomedicine, School of Engineering, University of Warwick , Coventry, UK
| | - Conceição Bettencourt
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology , London, UK
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - John K Olynyk
- School of Biomedical Sciences & Curtin Health Innovation Research Institute - Biosciences, Curtin University of Technology, Bentley, WA, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia; Department of Gastroenterology and Hepatology, Fiona Stanley Hospital, Murdoch, WA, Australia; Department of Gastroenterology and Hepatology, Fremantle Hospital, Fremantle, WA, Australia
| | - Debbie Trinder
- School of Medicine and Pharmacology, University of Western Australia, Fiona Stanley Hospital, Murdoch, WA, Australia; Harry Perkins Institute of Medical Research, Murdoch, WA, Australia
| | - Daniel M Johnstone
- Bosch Institute and Discipline of Physiology, University of Sydney , Sydney, NSW, Australia
| | - Elizabeth A Milward
- School of Biomedical Sciences and Pharmacy, The University of Newcastle , Callaghan, NSW, Australia
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