1
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Bhalla K, Rosier K, Monnens Y, Meulemans S, Vervoort E, Thorrez L, Agostinis P, Meier DT, Rochtus A, Resnick JL, Creemers JWM. Similar metabolic pathways are affected in both Congenital Myasthenic Syndrome-22 and Prader-Willi Syndrome. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167175. [PMID: 38626828 DOI: 10.1016/j.bbadis.2024.167175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
Loss of prolyl endopeptidase-like (PREPL) encoding a serine hydrolase with (thio)esterase activity leads to the recessive metabolic disorder Congenital Myasthenic Syndrome-22 (CMS22). It is characterized by severe neonatal hypotonia, feeding problems, growth retardation, and hyperphagia leading to rapid weight gain later in childhood. The phenotypic similarities with Prader-Willi syndrome (PWS) are striking, suggesting that similar pathways are affected. The aim of this study was to identify changes in the hypothalamic-pituitary axis in mouse models for both disorders and to examine mitochondrial function in skin fibroblasts of patients and knockout cell lines. We have demonstrated that Prepl is downregulated in the brains of neonatal PWS-IC-p/+m mice. In addition, the hypothalamic-pituitary axis is similarly affected in both Prepl-/- and PWS-IC-p/+m mice resulting in defective orexigenic signaling and growth retardation. Furthermore, we demonstrated that mitochondrial function is altered in PREPL knockout HEK293T cells and can be rescued with the supplementation of coenzyme Q10. Finally, PREPL-deficient and PWS patient skin fibroblasts display defective mitochondrial bioenergetics. The mitochondrial dysfunction in PWS fibroblasts can be rescued by overexpression of PREPL. In conclusion, we provide the first molecular parallels between CMS22 and PWS, raising the possibility that PREPL substrates might become therapeutic targets for treating both disorders.
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Affiliation(s)
- Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Sandra Meulemans
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Ellen Vervoort
- Laboratory for Cell Death Research & Therapy, VIB, Department of Cellular and Molecular Medicine, Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lieven Thorrez
- Department of Development and Regeneration, KU Leuven Campus Kulak, 8500 Kortrijk, Belgium
| | - Patrizia Agostinis
- Laboratory for Cell Death Research & Therapy, VIB, Department of Cellular and Molecular Medicine, Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Daniel T Meier
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Anne Rochtus
- Department of Development and Regeneration, UZ Leuven, 3000 Leuven, Belgium
| | - James L Resnick
- Department of Molecular genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John W M Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium.
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2
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Gefen AM, Zaritsky JJ. Review of childhood genetic nephrolithiasis and nephrocalcinosis. Front Genet 2024; 15:1381174. [PMID: 38606357 PMCID: PMC11007102 DOI: 10.3389/fgene.2024.1381174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Nephrolithiasis (NL) is a common condition worldwide. The incidence of NL and nephrocalcinosis (NC) has been increasing, along with their associated morbidity and economic burden. The etiology of NL and NC is multifactorial and includes both environmental components and genetic components, with multiple studies showing high heritability. Causative gene variants have been detected in up to 32% of children with NL and NC. Children with NL and NC are genotypically heterogenous, but often phenotypically relatively homogenous, and there are subsequently little data on the predictors of genetic childhood NL and NC. Most genetic diseases associated with NL and NC are secondary to hypercalciuria, including those secondary to hypercalcemia, renal phosphate wasting, renal magnesium wasting, distal renal tubular acidosis (RTA), proximal tubulopathies, mixed or variable tubulopathies, Bartter syndrome, hyperaldosteronism and pseudohyperaldosteronism, and hyperparathyroidism and hypoparathyroidism. The remaining minority of genetic diseases associated with NL and NC are secondary to hyperoxaluria, cystinuria, hyperuricosuria, xanthinuria, other metabolic disorders, and multifactorial etiologies. Genome-wide association studies (GWAS) in adults have identified multiple polygenic traits associated with NL and NC, often involving genes that are involved in calcium, phosphorus, magnesium, and vitamin D homeostasis. Compared to adults, there is a relative paucity of studies in children with NL and NC. This review aims to focus on the genetic component of NL and NC in children.
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Affiliation(s)
- Ashley M. Gefen
- Phoenix Children’s Hospital, Department of Pediatrics, Division of Nephrology, Phoenix, AZ, United States
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3
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Kramer NJ, Prakash G, Isaac RS, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. Regulators of mitonuclear balance link mitochondrial metabolism to mtDNA expression. Nat Cell Biol 2023; 25:1575-1589. [PMID: 37770567 DOI: 10.1038/s41556-023-01244-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells requiring coordinated gene expression across organelles. To identify genes involved in dual-origin protein complex synthesis, we performed fluorescence-activated cell-sorting-based genome-wide screens analysing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of Complex IV. We identified genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6. We found that PREPL specifically impacts Complex IV biogenesis by acting at the intersection of mitochondrial lipid metabolism and protein synthesis, whereas NME6, an uncharacterized nucleoside diphosphate kinase, controls OXPHOS biogenesis through multiple mechanisms reliant on its NDPK domain. Firstly, NME6 forms a complex with RCC1L, which together perform nucleoside diphosphate kinase activity to maintain local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Secondly, NME6 modulates the activity of mitoribosome regulatory complexes, altering mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression.
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Affiliation(s)
- Nicholas J Kramer
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Boryana Petrova
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hope E Merens
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Naama Kanarek
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Ohno K, Ohkawara B, Shen XM, Selcen D, Engel AG. Clinical and Pathologic Features of Congenital Myasthenic Syndromes Caused by 35 Genes-A Comprehensive Review. Int J Mol Sci 2023; 24:ijms24043730. [PMID: 36835142 PMCID: PMC9961056 DOI: 10.3390/ijms24043730] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Congenital myasthenic syndromes (CMS) are a heterogeneous group of disorders characterized by impaired neuromuscular signal transmission due to germline pathogenic variants in genes expressed at the neuromuscular junction (NMJ). A total of 35 genes have been reported in CMS (AGRN, ALG14, ALG2, CHAT, CHD8, CHRNA1, CHRNB1, CHRND, CHRNE, CHRNG, COL13A1, COLQ, DOK7, DPAGT1, GFPT1, GMPPB, LAMA5, LAMB2, LRP4, MUSK, MYO9A, PLEC, PREPL, PURA, RAPSN, RPH3A, SCN4A, SLC18A3, SLC25A1, SLC5A7, SNAP25, SYT2, TOR1AIP1, UNC13A, VAMP1). The 35 genes can be classified into 14 groups according to the pathomechanical, clinical, and therapeutic features of CMS patients. Measurement of compound muscle action potentials elicited by repetitive nerve stimulation is required to diagnose CMS. Clinical and electrophysiological features are not sufficient to identify a defective molecule, and genetic studies are always required for accurate diagnosis. From a pharmacological point of view, cholinesterase inhibitors are effective in most groups of CMS, but are contraindicated in some groups of CMS. Similarly, ephedrine, salbutamol (albuterol), amifampridine are effective in most but not all groups of CMS. This review extensively covers pathomechanical and clinical features of CMS by citing 442 relevant articles.
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Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Correspondence: (K.O.); (A.G.E.)
| | - Bisei Ohkawara
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Xin-Ming Shen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Duygu Selcen
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew G. Engel
- Department of Neurology and Neuromuscular Research Laboratory, Mayo Clinic, Rochester, MN 55905, USA
- Correspondence: (K.O.); (A.G.E.)
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5
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Kramer NJ, Prakash G, Choquet K, Soto I, Petrova B, Merens HE, Kanarek N, Churchman LS. Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.11.528118. [PMID: 36798306 PMCID: PMC9934615 DOI: 10.1101/2023.02.11.528118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells, in which gene expression must be coordinated across organelles using distinct pools of ribosomes. How cells produce and maintain the accurate subunit stoichiometries for these OXPHOS complexes remains largely unknown. To identify genes involved in dual-origin protein complex synthesis, we performed FACS-based genome-wide screens analyzing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of cytochrome c oxidase (Complex IV). We identified novel genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6 . We found that PREPL specifically regulates Complex IV biogenesis by interacting with mitochondrial protein synthesis machinery, while NME6, an uncharacterized nucleoside diphosphate kinase (NDPK), controls OXPHOS complex biogenesis through multiple mechanisms reliant on its NDPK domain. First, NME6 maintains local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Second, through stabilizing interactions with RCC1L, NME6 modulates the activity of mitoribosome regulatory complexes, leading to disruptions in mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression. Finally, we present these screens as a resource, providing a catalog of genes involved in mitonuclear gene regulation and OXPHOS biogenesis.
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6
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Vaneynde P, Verbinnen I, Janssens V. The role of serine/threonine phosphatases in human development: Evidence from congenital disorders. Front Cell Dev Biol 2022; 10:1030119. [PMID: 36313552 PMCID: PMC9608770 DOI: 10.3389/fcell.2022.1030119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Reversible protein phosphorylation is a fundamental regulation mechanism in eukaryotic cell and organismal physiology, and in human health and disease. Until recently, and unlike protein kinases, mutations in serine/threonine protein phosphatases (PSP) had not been commonly associated with disorders of human development. Here, we have summarized the current knowledge on congenital diseases caused by mutations, inherited or de novo, in one of 38 human PSP genes, encoding a monomeric phosphatase or a catalytic subunit of a multimeric phosphatase. In addition, we highlight similar pathogenic mutations in genes encoding a specific regulatory subunit of a multimeric PSP. Overall, we describe 19 affected genes, and find that most pathogenic variants are loss-of-function, with just a few examples of gain-of-function alterations. Moreover, despite their widespread tissue expression, the large majority of congenital PSP disorders are characterised by brain-specific abnormalities, suggesting a generalized, major role for PSPs in brain development and function. However, even if the pathogenic mechanisms are relatively well understood for a small number of PSP disorders, this knowledge is still incomplete for most of them, and the further identification of downstream targets and effectors of the affected PSPs is eagerly awaited through studies in appropriate in vitro and in vivo disease models. Such lacking studies could elucidate the exact mechanisms through which these diseases act, and possibly open up new therapeutic avenues.
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Affiliation(s)
- Pieter Vaneynde
- Laboratory of Protein Phosphorylation and Proteomics, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
- Leuven Brain Institute (LBI), Leuven, Belgium
| | - Iris Verbinnen
- Laboratory of Protein Phosphorylation and Proteomics, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
- Leuven Brain Institute (LBI), Leuven, Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation and Proteomics, Department of Cellular and Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
- Leuven Brain Institute (LBI), Leuven, Belgium
- *Correspondence: Veerle Janssens,
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7
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Rosier K, McDevitt MT, Smet J, Floyd BJ, Verschoore M, Marcaida MJ, Bingman CA, Lemmens I, Dal Peraro M, Tavernier J, Cravatt BF, Gounko NV, Vints K, Monnens Y, Bhalla K, Aerts L, Rashan EH, Vanlander AV, Van Coster R, Régal L, Pagliarini DJ, Creemers JW. Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. iScience 2021; 24:103460. [PMID: 34888501 PMCID: PMC8634043 DOI: 10.1016/j.isci.2021.103460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiological substrates of PREPL remain largely unknown. In this study, we connect PREPL with mitochondrial gene expression and oxidative phosphorylation by analyzing its protein interactors. We demonstrate that the long PREPLL isoform localizes to mitochondria, whereas PREPLS remains cytosolic. Prepl KO mice showed reduced mitochondrial complex activities and disrupted mitochondrial gene expression. Furthermore, mitochondrial ultrastructure was abnormal in a PREPL-deficient patient and Prepl KO mice. In addition, we reveal that PREPL has (thio)esterase activity and inhibition of PREPL by Palmostatin M suggests a depalmitoylating function. We subsequently determined the crystal structure of PREPL, thereby providing insight into the mechanism of action. Taken together, PREPL is a (thio)esterase rather than a peptidase and PREPLL is involved in mitochondrial homeostasis.
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Affiliation(s)
- Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Molly T. McDevitt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joél Smet
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Brendan J. Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Maxime Verschoore
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Maria J. Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irma Lemmens
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jan Tavernier
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Benjamin F. Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia V. Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laetitia Aerts
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arnaud V. Vanlander
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Luc Régal
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Neurology and Metabolism, UZ Brussel, Brussels, Belgium
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Departments of Cell Biology and Physiology, Biochemistry and Molecular Biophysics, and Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John W.M. Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
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8
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Towheed A, Hietanen CL, Kamath VG, Singh LN, Ho A, Engelstad K, Cornett K, Montes J, De Vivo D. Hypotonia-cystinuria 2p21 deletion syndrome: Intrafamilial variability of clinical expression. Ann Clin Transl Neurol 2021; 8:2199-2204. [PMID: 34612606 PMCID: PMC8607452 DOI: 10.1002/acn3.51464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022] Open
Abstract
Two siblings presented similarly with congenital hypotonia, lactic acidosis, and failure to thrive. Later in childhood, the brother developed cystinuria and nephrolithiasis whereas the older sister suffered from cystinuria and chronic neurobehavioral disturbances. Biopsied muscle studies demonstrated deficient cytochrome c oxidase activities consistent with a mitochondrial disease. Whole exome sequencing (WES), however, revealed a homozygous 2p21 deletion involving two contiquous genes, SLC3A1 (deletion of exons 2‐10) and PREPL (deletion of exons 2‐14). The molecular findings were consistent with the hypotonia–cystinuria 2p21 deletion syndrome, presenting similarly in infancy with mitochondrial dysfunction but diverging later in childhood and displaying intrafamilial phenotypic variability.
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Affiliation(s)
- Atif Towheed
- Touro College of Osteopathic Medicine, Middletown, NY, 10940
| | | | | | - Larry N Singh
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, 19104
| | - Angela Ho
- Touro College of Osteopathic Medicine, Middletown, NY, 10940
| | - Kristin Engelstad
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032
| | - Kayla Cornett
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, 10032
| | - Jacqueline Montes
- Department of Rehabilitation and Regenerative Medicine (Physical Therapy), Columbia University Irving Medical Center, New York, NY, 10032
| | - Darryl De Vivo
- Department of Neurology and Pediatrics, Columbia University Irving Medical Center, New York, NY, 10032
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9
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Nano PR, Johnson TK, Kudo T, Mooney NA, Ni J, Demeter J, Jackson PK, Chen JK. Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains. PLoS One 2021; 16:e0251684. [PMID: 33999959 PMCID: PMC8128262 DOI: 10.1371/journal.pone.0251684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/01/2021] [Indexed: 11/24/2022] Open
Abstract
ARHGAP36 is an atypical Rho GTPase-activating protein (GAP) family member that drives both spinal cord development and tumorigenesis, acting in part through an N-terminal motif that suppresses protein kinase A and activates Gli transcription factors. ARHGAP36 also contains isoform-specific N-terminal sequences, a central GAP-like module, and a unique C-terminal domain, and the functions of these regions remain unknown. Here we have mapped the ARHGAP36 structure-activity landscape using a deep sequencing-based mutagenesis screen and truncation mutant analyses. Using this approach, we have discovered several residues in the GAP homology domain that are essential for Gli activation and a role for the C-terminal domain in counteracting an N-terminal autoinhibitory motif that is present in certain ARHGAP36 isoforms. In addition, each of these sites modulates ARHGAP36 recruitment to the plasma membrane or primary cilium. Through comparative proteomics, we also have identified proteins that preferentially interact with active ARHGAP36, and we demonstrate that one binding partner, prolyl oligopeptidase-like protein, is a novel ARHGAP36 antagonist. Our work reveals multiple modes of ARHGAP36 regulation and establishes an experimental framework that can be applied towards other signaling proteins.
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Affiliation(s)
- Patricia R. Nano
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Taylor K. Johnson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nancie A. Mooney
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jun Ni
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Janos Demeter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter K. Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - James K. Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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10
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Prot-Bertoye C, Daudon M, Tostivint I, Dousseaux MP, Defazio J, Traxer O, Knebelmann B, Courbebaisse M. [Cystinuria]. Nephrol Ther 2021; 17S:S100-S107. [PMID: 33910689 DOI: 10.1016/j.nephro.2020.03.001] [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: 01/28/2020] [Accepted: 03/01/2020] [Indexed: 10/21/2022]
Abstract
Cystinuria is the most common monogenic nephrolithiasis disorder. Because of its poor solubility at a typical urine pH of less than 7, cystine excretion results in recurrent urinary cystine stone formation. A high prevalence of high blood pressure and of chronic kidney disease has been reported in these patients. Alkaline hyperdiuresis remains the cornerstone of the preventive medical treatment. To reach a urine pH between 7.5 and 8 and a urine specific gravity less than or equal to 1.005 should be the goal of medical treatment. D-penicillamine and tiopronin, two cysteine-binding thiol agents, should be considered as second line treatments with frequent adverse events that should be closely monitored.
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Affiliation(s)
- Caroline Prot-Bertoye
- Service de physiologie - explorations fonctionnelles rénales et métaboliques, hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France.
| | - Michel Daudon
- Service de physiologie-explorations fonctionnelles, hôpital Tenon, 4, rue de la Chine, 75020 Paris, France
| | - Isabelle Tostivint
- Service de néphrologie, hôpital de la Pitié-Salpêtrière, 149, boulevard de l'Hôpital, 75013 Paris, France
| | - Marie-Paule Dousseaux
- Service de néphrologie, hôpital de la Pitié-Salpêtrière, 149, boulevard de l'Hôpital, 75013 Paris, France
| | - Jérôme Defazio
- Association pour l'information et la recherche sur les maladies génétiques (AIRG-France), BP 78, 75261 Paris cedex 06, France
| | - Olivier Traxer
- Service d'urologie, hôpital Tenon, 4, rue de la Chine, 75020 Paris, France
| | - Bertrand Knebelmann
- Service de néphrologie, hôpital Necker, 149, rue de Sèvres, 75015 Paris, France
| | - Marie Courbebaisse
- Service de physiologie - explorations fonctionnelles rénales et métaboliques, hôpital européen Georges-Pompidou, 20, rue Leblanc, 75015 Paris, France
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11
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Servais A, Thomas K, Dello Strologo L, Sayer JA, Bekri S, Bertholet-Thomas A, Bultitude M, Capolongo G, Cerkauskiene R, Daudon M, Doizi S, Gillion V, Gràcia-Garcia S, Halbritter J, Heidet L, van den Heijkant M, Lemoine S, Knebelmann B, Emma F, Levtchenko E. Cystinuria: clinical practice recommendation. Kidney Int 2020; 99:48-58. [PMID: 32918941 DOI: 10.1016/j.kint.2020.06.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 02/07/2023]
Abstract
Cystinuria (OMIM 220100) is an autosomal recessive hereditary disorder in which high urinary cystine excretion leads to the formation of cystine stones because of the low solubility of cystine at normal urinary pH. We developed clinical practice recommendation for diagnosis, surgical and medical treatment, and follow-up of patients with cystinuria. Elaboration of these clinical practice recommendations spanned from June 2018 to December 2019 with a consensus conference in January 2019. Selected topic areas were chosen by the co-chairs of the conference. Working groups focusing on specific topics were formed. Group members performed systematic literature review using MEDLINE, drafted the statements, and discussed them. They included geneticists, medical biochemists, pediatric and adult nephrologists, pediatric and adult urologists experts in cystinuria, and the Metabolic Nephropathy Joint Working Group of the European Reference Network for Rare Kidney Diseases (ERKNet) and eUROGEN members. Overall 20 statements were produced to provide guidance on diagnosis, genetic analysis, imaging techniques, surgical treatment (indication and modalities), conservative treatment (hydration, dietetic, alkalinization, and cystine-binding drugs), follow-up, self-monitoring, complications (renal failure and hypertension), and impact on quality of life. Because of the rarity of the disease and the poor level of evidence in the literature, these statements could not be graded. This clinical practice recommendation provides guidance on all aspects of the management of both adults and children with cystinuria, including diagnosis, surgery, and medical treatment.
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Affiliation(s)
- Aude Servais
- Nephrology and Transplantation Department, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, Paris, France.
| | - Kay Thomas
- Stone Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Luca Dello Strologo
- Renal Transplant Clinic, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne, UK; The Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, UK; NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
| | - Soumeya Bekri
- Department of Metabolic Biochemistry, Rouen University Hospital, Rouen, France
| | - Aurelia Bertholet-Thomas
- Centre de Référence des Maladies Rénales Rares, Filière ORKID, Service de Néphrologie, Rhumatologie et Dermatologie Pédiatriques, Hôpital Femme-Mère-Enfant, Hospices Civils de Lyon, Université Claude-Bernard Lyon 1, Lyon, France
| | | | - Giovanna Capolongo
- Unit of Nephrology, Department of Translational Medical Sciences, University of Campania "Luigi Vanvitelli," Naples, Italy
| | | | - Michel Daudon
- UMR S 1155 and Physiology Unit, AP-HP, Hôpital Tenon, Sorbonne Université and INSERM, Paris, France
| | - Steeve Doizi
- Sorbonne Université, GRC n°20, Groupe de Recherche Clinique sur la Lithiase Urinaire, Service d'Urologie, Hôpital Tenon, AP-HP, Paris, France
| | - Valentine Gillion
- Département de Néphrologie adulte, Cliniques universitaires Saint Luc, Bruxelles, Belgium
| | - Silvia Gràcia-Garcia
- Laboratory of Renal Lithiasis, Clinical Laboratories, Fundació Puigvert, Barcelona, Spain
| | - Jan Halbritter
- Division of Nephrology, Department of Endocrinology, Nephrology, and Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Laurence Heidet
- Néphrologie Pédiatrique, Centre de Référence MARHEA, Hôpital universitaire Necker-Enfants Malades, Paris, France
| | - Marleen van den Heijkant
- Pediatric Renal Center, University Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sandrine Lemoine
- Nephrology and Renal Function Unit, Edouard Herriot Hospital, Hospices Civils de Lyon, Lyon, France; University of Lyon, Lyon, France
| | - Bertrand Knebelmann
- Nephrology and Transplantation Department, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Necker Hospital, APHP, Université de Paris, Paris, France
| | - Francesco Emma
- Division of Nephrology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Elena Levtchenko
- Division of Pediatric Nephrology, University Hospitals Leuven, Leuven, Belgium; Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium
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12
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Curi RA, Pereira GL, Alvarez MVN, Baldassini WA, Machado Neto OR, Chardulo LAL. Exome analysis and functional classification of identified variants in racing Quarter Horses. Anim Genet 2020; 51:716-721. [PMID: 32696541 DOI: 10.1111/age.12976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 11/26/2022]
Abstract
The main objectives of this study were to identify and functionally classify SNPs and indels by exome sequencing of animals of the racing line of Quarter Horses. Based on the individual genomic estimated breeding values (GEBVs) for maximum speed index (SImax) obtained for 349 animals, two groups of 20 extreme animals were formed. Of these individuals, 20 animals with high GEBVs for SImax and 19 with low GEBVs for SImax had their exons and 5' and 3' UTRs sequenced. Considering SNPs and indels, 105 182 variants were identified in the expressed regions of the Quarter Horse genome. Of these, 72 166 variants were already known and 33 016 are new variants and were deposited in a database. The analysis of the set of gene variants significantly related (Padjusted < 0.05) to extreme animals in conjunction with the predicted impact of the changes and the physiological role of protein product pointed to two candidate genes potentially related to racing performance: SLC3A1 on ECA15 and CCN6 on ECA10.
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Affiliation(s)
- R A Curi
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - G L Pereira
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - M V N Alvarez
- Department of Parasitology, Institute of Biosciences, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - W A Baldassini
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - O R Machado Neto
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
| | - L A L Chardulo
- Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University, Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil
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13
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Shchagina O, Bessonova L, Bychkov I, Beskorovainaya T, Poliakov A. A Family Case of Congenital Myasthenic Syndrome-22 Induced by Different Combinations of Molecular Causes in Siblings. Genes (Basel) 2020; 11:genes11070821. [PMID: 32707643 PMCID: PMC7397044 DOI: 10.3390/genes11070821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 11/16/2022] Open
Abstract
Congenital myasthenic syndrome-22 (CMS22, OMIM 616224) is a very rare recessive hereditary disorder. At the moment, ten CMS22 patients are described, with the disorder caused by nine different Loss-of-Function mutations and 14 gross deletions in the PREPL gene. The materials for our study were DNA samples of five family members: two patients with myasthenia, their healthy sibling and parents. Clinical exome analysis was carried out for one patient, then the whole family was checked for target variants with Sanger sequencing, quantitative multiplex ligation-dependent probe amplification, and chromosome 2 microsatellite markers study. To determine the functional significance of the splicing variant, we applied the minigene assay. The cause of the proband's disorder is a compound heterozygous state of two previously non-described pathogenic PREPL variants: a c.1528C>T (p.(Arg510Ter)) nonsense mutation and a c.2094G>T pseudo-missense variant, which, simultaneously with a p.(Lys698Asn) amino acid substitution, affects splicing, leading to exon 14 skipping in mRNA. The second patient's disorder was caused by a homozygous nonsense c.1528C>T (p.(Arg510Ter)) mutation due to maternal uniparental disomy (UPD) of chromosome 2. In this study, we describe a unique case, in which two siblings with a rare disorder have different pathologic genotypes.
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Prolyl Endopeptidase-Like Facilitates the α-Synuclein Aggregation Seeding, and This Effect Is Reverted by Serine Peptidase Inhibitor PMSF. Biomolecules 2020; 10:biom10060962. [PMID: 32630529 PMCID: PMC7355856 DOI: 10.3390/biom10060962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
The aggregation of α-synuclein (α-Syn) is a characteristic of Parkinson’s disease (PD). α-Syn oligomerization/aggregation is accelerated by the serine peptidase, prolyl oligopeptidase (POP). Factors that affect POP conformation, including most of its inhibitors and an impairing mutation in its active site, influence the acceleration of α-Syn aggregation resulting from the interaction of these proteins. It is noteworthy, however, that α-Syn is not cleaved by POP. Prolyl endopeptidase-like (PREPL) protein is structurally related to the serine peptidases belonging to the POP family. Based on the α-Syn–POP studies and knowing that PREPL may contribute to the regulation of synaptic vesicle exocytosis, when this protein can encounter α-Syn, we investigated the α-Syn–PREPL interaction. The binding of these two human proteins was observed with an apparent affinity constant of about 5.7 μM and, as in the α-Syn assays with POP, the presence of PREPL accelerated the oligomerization/aggregation events, with no α-Syn cleavage. Furthermore, despite this lack of hydrolytic cleavage, the serine peptidase active site inhibitor phenylmethylsulfonyl fluoride (PMSF) abolished the enhancement of the α-Syn aggregation by PREPL. Therefore, given the attention to POP inhibitors as potential drugs to treat synucleinopathies, the present data point to PREPL as another potential target to be explored for this purpose.
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15
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Moussa M, Papatsoris AG, Abou Chakra M, Moussa Y. Update on cystine stones: current and future concepts in treatment. Intractable Rare Dis Res 2020; 9:71-78. [PMID: 32494553 PMCID: PMC7263987 DOI: 10.5582/irdr.2020.03006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Cystine stones are relatively uncommon compared with other stone compositions, constituting just 1% to 2% of adult urinary tract stone diseases, and accounting for up to 10% of pediatric stone diseases. Two responsible genes of cystinuria have been identified, the SLC3A1 and the SLC7A9. Cystinuria is diagnosed by family history, stone analysis, or by measurement of urine cystine excretion. Current treatments for cystinuria include increased fluid intake to increase cystine solubility by maintaining daily urine volume of greater than 3 Liter (L). Limiting sodium and protein intake can decrease cystine excretion. When conservative therapy fails, then pharmacologic therapy may be effective. Alkaline urine pH in the 7.0-7.5 range will reduce cystine solubility and can be achieved by the addition of alkali therapy. If these measures fail, cystine-binding thiol drugs such as tiopronin and D-penicillamine are considered. These compounds bind cysteine and prevent the formation of less soluble cystine. These drugs, however, have poor patient compliance due to adverse effects. Captopril can be useful in the treatment of cystine stones but the drug has not been tested in rigorous clinical trials. Novel potential therapies such as alpha-lipoic acid and crystal growth inhibitors (L-cystine dimethyl ester (L-CDME) and L-cystine methyl ester (L-CME)) were developed and tested in animals. Those therapies showed promising results. Compliance with treatment was associated with a lower rate of cystine stone formation.
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Affiliation(s)
- Mohamad Moussa
- Urology Department, Zahraa Hospital, University Medical Center, Lebanese University, Beirut, Lebanon
| | - Athanasios G. Papatsoris
- 2nd Department of Urology, School of Medicine, Sismanoglio Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Mohamad Abou Chakra
- Faculty of Medical Sciences, Department of Urology, Lebanese University, Beirut, Lebanon
- Address correspondence to:Mohamad Abou Chakra, Faculty of Medical Sciences, Department of Urology, Lebanese University. Beirut, Lebanon. E-mail:
| | - Yasmin Moussa
- Clinic of Dermatology, Dr. Brinkmann, Schult & Samimi-Fard. Gladbeck, Germany
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16
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Yang Q, Hua R, Qian J, Yi S, Shen F, Zhang Q, Li M, Yi S, Luo J, Fan X. PREPL Deficiency: A Homozygous Splice Site PREPL Mutation in a Patient With Congenital Myasthenic Syndrome and Absence of Ovaries and Hypoplasia of Uterus. Front Genet 2020; 11:198. [PMID: 32218803 PMCID: PMC7078161 DOI: 10.3389/fgene.2020.00198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Abstract
Prolyl endopeptidase-like (PREPL) deficiency (MIM 616224) is a very rare congenital disorder characterized by neonatal hypotonia and feeding difficulties, ptosis, neuromuscular symptoms, cognitive impairments, growth hormone deficiency, short stature, and hypergonadotropic hypogonadism. This syndrome is an autosomal recessive disease resulting from mutations in the PREPL gene. Previous reports have associated PREPL deficiency with only one nucleotide substitution, the deletion of four nucleotides, and eight small microdeletions in the PREPL gene In this study, we used whole exome sequencing (WES) to identify a novel homozygous splicing mutation (c.616 + 1G > T) in a 14-year-old Chinese girl with PREPL deficiency. Sequencing of the RT-PCR products from the patient’s blood sample revealed that the c.616 + 1G > T variant disrupted normal splicing in intron 4 leading to an aberrant inclusion of 43 nucleotides in intron, a frameshift, and premature termination codon. Our patient exhibited several of the common phenotypes, including severe neonatal hypotonia, growth impairment and cognitive problems. However, we also observed several unusual phenotypic characteristics: absence of the ovaries, hypoplasia of the uterus, microcephaly and a short neck in patient is alsoobserved. These results provide further evidence for the involvement of PREPL development of the ovaries and uterus. Our findings may provide further insight into the relationship between the genotype and phenotype in collagen-associated diseases and improve the clinical diagnosis of Prolyl endopeptidase-like deficiency.
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Affiliation(s)
- Qi Yang
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Rong Hua
- The Guangxi Zhang Autonomous Region Reproductive Hospital, Nanning, China
| | - Jiale Qian
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Shang Yi
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Fei Shen
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Qiang Zhang
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Mengting Li
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Sheng Yi
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Xin Fan
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
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17
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Zhang P, Wu B, Lu Y, Ni Q, Liu R, Zhou W, Wang H. First maternal uniparental disomy for chromosome 2 with PREPL novel frameshift mutation of congenital myasthenic syndrome 22 in an infant. Mol Genet Genomic Med 2020; 8:e1144. [PMID: 31985178 PMCID: PMC7057094 DOI: 10.1002/mgg3.1144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/07/2020] [Indexed: 11/11/2022] Open
Abstract
Background Congenital myasthenic syndrome 22 (CMS22) is a rare autosomal recessive disorder due to isolated PREPL deficiency and characterized by neonatal hypotonia, muscular weakness, and feeding difficulties. Eight such cases have already been reported, while maternal uniparental disomy with a PREPL pathogenic mutation has never been involved. Methods Trio whole‐exome sequencing (WES), comparative genomic hybridization microarray (arry‐CGH), and Sanger sequencing were performed on a 6‐month‐old girl with severe neonatal hypotonia and feeding difficulties. Also, the phenotype and genotype of reported CMS22 patients were reviewed. Results In this female infant, we identified a novel homozygous frameshift mutation in PREPL (c.1282_1285delTTTG, p.Phe428Argfs*18) by trio‐WES. Sanger sequencing confirmed that her mother was heterozygous and her father was normal. Trio‐WES data showed that 96.70% (1668/1725) variants on chromosome 2 were homozygous and maternally inherited, suggesting maternal uniparental disomy of chromosome 2 [UPD(2)mat]. Array‐CGH did not show copy number variants (CNVs) but revealed complete UPD(2). Conclusion To date, nine patients with CMS22 have been reported including our patient, and we report the youngest and the first UPD(2)mat with PREPL novel homozygous pathogenic mutation case, which expand the mutation spectrum of PREPL gene.
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Affiliation(s)
- Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.,Department of Neonates, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
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Yahyaoui R, Pérez-Frías J. Amino Acid Transport Defects in Human Inherited Metabolic Disorders. Int J Mol Sci 2019; 21:ijms21010119. [PMID: 31878022 PMCID: PMC6981491 DOI: 10.3390/ijms21010119] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/12/2019] [Accepted: 12/18/2019] [Indexed: 02/07/2023] Open
Abstract
Amino acid transporters play very important roles in nutrient uptake, neurotransmitter recycling, protein synthesis, gene expression, cell redox balance, cell signaling, and regulation of cell volume. With regard to transporters that are closely connected to metabolism, amino acid transporter-associated diseases are linked to metabolic disorders, particularly when they involve different organs, cell types, or cell compartments. To date, 65 different human solute carrier (SLC) families and more than 400 transporter genes have been identified, including 11 that are known to include amino acid transporters. This review intends to summarize and update all the conditions in which a strong association has been found between an amino acid transporter and an inherited metabolic disorder. Many of these inherited disorders have been identified in recent years. In this work, the physiological functions of amino acid transporters will be described by the inherited diseases that arise from transporter impairment. The pathogenesis, clinical phenotype, laboratory findings, diagnosis, genetics, and treatment of these disorders are also briefly described. Appropriate clinical and diagnostic characterization of the underlying molecular defect may give patients the opportunity to avail themselves of appropriate therapeutic options in the future.
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Affiliation(s)
- Raquel Yahyaoui
- Laboratory of Metabolic Disorders and Newborn Screening Center of Eastern Andalusia, Málaga Regional University Hospital, 29011 Málaga, Spain
- Grupo Endocrinología y Nutrición, Diabetes y Obesidad, Instituto de Investigación Biomédica de Málaga-IBIMA, 29010 Málaga, Spain
- Correspondence:
| | - Javier Pérez-Frías
- Grupo Multidisciplinar de Investigación Pediátrica, Instituto de Investigación Biomédica de Málaga-IBIMA, 29010 Málaga, Spain;
- Departamento de Farmacología y Pediatría, Facultad de Medicina, Universidad de Málaga, 29010 Málaga, Spain
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19
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Watanabe Y, Abe Y, Sakamoto S, Morimoto E, Taki Y, Hibino S, Fukagai T, Watanabe S. Pediatric Cystinuria Patient With Novel Mutation in SLC3A1. Glob Pediatr Health 2019; 6:2333794X19862441. [PMID: 31367653 PMCID: PMC6643165 DOI: 10.1177/2333794x19862441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/17/2019] [Indexed: 12/02/2022] Open
Affiliation(s)
- Yoshitaka Watanabe
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Yoshifusa Abe
- Children Medical Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | - Shinichi Sakamoto
- Department of Urology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Eiji Morimoto
- Clinical Laboratory, Showa University Hospital, Tokyo, Japan
| | | | - Satoshi Hibino
- Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, Aichi, Japan
| | - Takashi Fukagai
- Department of Urology, Showa University Koto Toyosu Hospital, Tokyo, Japan
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20
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Taroni F, Capone V, Berrettini A, De Marco EA, Manzoni GA, Montini G. A Case of Hypotonia-Cystinuria Syndrome With Genito-Urinary Malformations and Extrarenal Involvement. Front Pediatr 2019; 7:127. [PMID: 31024870 PMCID: PMC6465885 DOI: 10.3389/fped.2019.00127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/18/2019] [Indexed: 01/26/2023] Open
Abstract
Hypotonia-Cystinuria syndrome (HCS) is a rare disease, caused by a mutation in two contiguous genes (SLC3A1 and PREPL) localized on chromosome 2p21, and it is characterized by both renal involvement with cystine stones and nervous involvement with hypotonia. We here describe a 2 years old child with HCS associated with other clinical features as congenital anomalies of kidney and urinary tract (primary obstructed megaureter, POM), cryptorchidism and cardiac involvement (patent foramen ovale with atrial septum aneurysm). To the best of our knowledge, cryporchidism and POM have never been reported before in patients with HCS. Moreover, a cardiac involvement has been described only in another case of HCS that, interestingly, presents the same genetic abnormalities as our patient. The diagnosis of HCS can be difficult because neurological signs are aspecific and kidney stones are commonly absent during the first months of life. A better understanding of the complete clinical scenario associated with HCS can help clinicians suspect, diagnose and treat HCS earlier with a positive influence on both neurological and renal outcome.
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Affiliation(s)
- Francesca Taroni
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Capone
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Alfredo Berrettini
- Pediatric Urology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Erika Adalgisa De Marco
- Pediatric Urology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Gian Antonio Manzoni
- Pediatric Urology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Montini
- Pediatric Nephrology, Dialysis and Transplant Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.,Giuliana and Bernardo Caprotti Chair of Pediatrics, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
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21
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Kılıç M, Ceylan AC, Örün UA, Kılıç E. First cardiac manifestation of hypotonia-cystinuria syndrome. Metab Brain Dis 2018; 33:1375-1379. [PMID: 29627929 DOI: 10.1007/s11011-018-0226-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/27/2018] [Indexed: 02/03/2023]
Abstract
Hypotonia-cystinuria syndrome is a very rare autosomal recessive contiguous gene deletion syndrome of PREPL and SLC3A1 at 2p21 with neuromuscular and neuroendocrinologic presentation. We report a two-year-six-month-old affected female infant and her five-month-old affected brother with a novel homozygous deletion in SLC3A1 and PREPL gene. Both of siblings had mild facial dysmorphism, hypotonia, feeding problems, failure to thrive, developmental delay. She also had dilated cardiomyopathy which differ from other reported patients. Therefore cardiomyopathy may also be considered one of the features of hypotonia-cystinuria syndrome. With this case report, we present cardiac manifestation of hypotonia-cystinuria syndrome for the first time. Because of two siblings had hyperechogenic bowel in prenatal sonography, it might be a prenatal marker for HCS.
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Affiliation(s)
- Mustafa Kılıç
- Sami Ulus Children Hospital, Metabolism Unit, Babur cad, No: 44, 06080, Altındağ, Ankara, Turkey.
| | - Ahmet Cevdet Ceylan
- Atatürk Training and Research Hospital, Department of Genetics, Yıldırım Beyazıt University, Ankara, Turkey
| | - Utku Arman Örün
- Pediatric Cardiology Unit, Sami Ulus Children Hospital, Ankara, Turkey
| | - Esra Kılıç
- Pediatric Hematology-Oncology Training and Research Hospital, Pediatric Genetic Unit, Ankara, Turkey
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22
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Ferreira CR, van Karnebeek CDM, Vockley J, Blau N. A proposed nosology of inborn errors of metabolism. Genet Med 2018; 21:102-106. [PMID: 29884839 PMCID: PMC6286709 DOI: 10.1038/s41436-018-0022-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 01/13/2023] Open
Abstract
Purpose We propose a nosology for inborn errors of metabolism that builds on their recent redefinition. Methods We established a strict definition of criteria in order to develop a self-consistent schema for inclusion of a disorder into the nosology. Results We identified 1,015 well-characterized inborn errors of metabolism described in the literature. In addition, there are 111 less well-characterized conditions that may be inborn errors but do not meet strict criteria for inclusion in the current nosology. Conclusion We provide a master list of all currently recognized inborn errors of metabolism grouped according to their pathophysiological basis, with the hope of setting a standard against which new errors should be defined, as well as to promote awareness and foster collaboration in the area. With the rapid advances in the field of genetics in recent years, it is likely that this nosology will need to be updated in the near future, a process that will benefit from broader input and collaboration of experts in the field in order to improve future versions of the proposed classification.
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Affiliation(s)
- Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA. .,Division of Genetics and Metabolism, Children's National Health System, Washington, DC, USA.
| | - Clara D M van Karnebeek
- Departments of Pediatrics and Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands.,Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Department of Human Genetics, Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Nenad Blau
- Dietmar-Hopp Metabolic Center, University Children's Hospital, Heidelberg, Germany
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23
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Rodríguez Cruz PM, Palace J, Beeson D. The Neuromuscular Junction and Wide Heterogeneity of Congenital Myasthenic Syndromes. Int J Mol Sci 2018; 19:ijms19061677. [PMID: 29874875 PMCID: PMC6032286 DOI: 10.3390/ijms19061677] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/17/2018] [Accepted: 05/21/2018] [Indexed: 01/16/2023] Open
Abstract
Congenital myasthenic syndromes (CMS) are genetic disorders characterised by impaired neuromuscular transmission. This review provides an overview on CMS and highlights recent advances in the field, including novel CMS causative genes and improved therapeutic strategies. CMS due to mutations in SLC5A7 and SLC18A3, impairing the synthesis and recycling of acetylcholine, have recently been described. In addition, a novel group of CMS due to mutations in SNAP25B, SYT2, VAMP1, and UNC13A1 encoding molecules implicated in synaptic vesicles exocytosis has been characterised. The increasing number of presynaptic CMS exhibiting CNS manifestations along with neuromuscular weakness demonstrate that the myasthenia can be only a small part of a much more extensive disease phenotype. Moreover, the spectrum of glycosylation abnormalities has been increased with the report that GMPPB mutations can cause CMS, thus bridging myasthenic disorders with dystroglycanopathies. Finally, the discovery of COL13A1 mutations and laminin α5 deficiency has helped to draw attention to the role of extracellular matrix proteins for the formation and maintenance of muscle endplates. The benefit of β2-adrenergic agonists alone or combined with pyridostigmine or 3,4-Dyaminopiridine is increasingly being reported for different subtypes of CMS including AChR-deficiency and glycosylation abnormalities, thus expanding the therapeutic repertoire available.
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Affiliation(s)
- Pedro M Rodríguez Cruz
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.
- Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford OX3 9DS, UK.
| | - Jacqueline Palace
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.
| | - David Beeson
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.
- Neurosciences Group, Weatherall Institute of Molecular Medicine, University of Oxford, The John Radcliffe Hospital, Oxford OX3 9DS, UK.
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24
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Silva S, Miyake N, Tapia C, Matsumoto N. The second point mutation in PREPL: a case report and literature review. J Hum Genet 2018; 63:677-681. [PMID: 29483676 DOI: 10.1038/s10038-018-0426-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 12/13/2022]
Abstract
Prolyl endopeptidase-like (PREPL) deficiency (MIM# 616224) is a rare autosomal recessive inherited congenital myasthenic syndrome characterized by neonatal hypotonia, feeding problems, mild dysmorphism, and neuromuscular symptoms, followed by hyperphagia and obesity in later childhood. Some patients also exhibit growth deficits, sexual hormone deficiency, and cognitive impairments. This syndrome is caused by biallelic mutations in PREPL. To date, only one nucleotide deletion and seven small microdeletions in PREPL have been reported. Here we report a female patient with a novel homozygous frameshift mutation in PREPL (NM_006036.4, c.342delA:p.Val115Leufs*39). Her clinical features are similar to those of previously reported cases. The mutation is the first homozygous point mutation reported in humans.
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Affiliation(s)
- Sebastian Silva
- Servicio de Pediatría, Hospital de Puerto Montt, 5507798, Puerto Montt, Chile
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
| | - Carolina Tapia
- Instituto de Rehabilitación Teletón, 5502446, Puerto Montt, Chile
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan.
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25
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Engel AG, Shen XM, Selcen D. The unfolding landscape of the congenital myasthenic syndromes. Ann N Y Acad Sci 2018; 1413:25-34. [PMID: 29355968 DOI: 10.1111/nyas.13539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/28/2017] [Accepted: 10/02/2017] [Indexed: 12/14/2022]
Abstract
Congenital myasthenic syndromes (CMS) are heterogeneous disorders in which the safety margin of neuromuscular transmission is impaired by one or more specific mechanisms. Since the advent of next-generation sequencing methods, the discovery of novel CMS targets and phenotypes has proceeded at an accelerated rate. Here, we review the current classification of CMS and describe our findings in five of these targets identified and investigated in our laboratory in the past 5 years. Defects in LRP4 hinder synaptic development and maintenance; the defects in PREPL are predicted to diminish filling of the synaptic vesicle with acetylcholine; and defects in SNAP25, Munc13-1, and synaptotbrevin-1 impede synaptic vesicle exocytosis.
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Affiliation(s)
- Andrew G Engel
- Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Xin-Ming Shen
- Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Duygu Selcen
- Department of Neurology, Mayo Clinic, Rochester, Minnesota
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26
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Panneman DM, Smeitink JA, Rodenburg RJ. Mining for mitochondrial mechanisms: Linking known syndromes to mitochondrial function. Clin Genet 2017; 93:943-951. [PMID: 28686290 DOI: 10.1111/cge.13094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/28/2022]
Abstract
Mitochondrial disorders (MDs) are caused by defects in 1 or multiple complexes of the oxidative phosphorylation (OXPHOS) machinery. MDs are associated with a broad range of clinical signs and symptoms, and have considerable clinical overlap with other neuromuscular syndromes. This overlap might be due to involvement of mitochondrial pathways in some of these non-mitochondrial syndromes. Here, we give an overview of around 25 non-mitochondrial syndromes, diagnosed in patients who were initially suspected to have a MD on the basis of clinical and biochemical parameters. In addition, we highlight the mitochondrial connections of 6 of these non-mitochondrial syndromes (eg, Rett syndrome and Dravet syndrome) diagnosed in multiple patients. Further research to unravel the interplay between these genes and mitochondria may help to increase knowledge on these syndromes. Additionally, it may open new avenues for research on pathways interacting with mitochondrial function in order to find new targets for therapeutics to treat MDs. The data presented in this review underline the importance of careful assessment of clinical, genetic, and biochemical data in all patients suspected of a neuromuscular syndrome, and highlights the importance of the role of clinical geneticists, physicians, and clinical biochemists in recognizing the possible mitochondrial connection of non-mitochondrial syndromes.
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Affiliation(s)
- D M Panneman
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - J A Smeitink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - R J Rodenburg
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
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27
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Lemoine S, Cochat P, Bertholet-Thomas A, Levi C, Bonnefoy C, Sellier-Leclerc AL, Bacchetta J. Néphrologie pédiatrique : que doit savoir un néphrologue d’adulte sur ces pathologies ? Nephrol Ther 2017; 13:495-504. [DOI: 10.1016/j.nephro.2017.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/25/2022]
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28
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Régal L, Mårtensson E, Maystadt I, Voermans N, Lederer D, Burlina A, Juan Fita MJ, Hoogeboom AJM, Olsson Engman M, Hollemans T, Schouten M, Meulemans S, Jonson T, François I, Gil Ortega D, Kamsteeg EJ, Creemers JWM. PREPL deficiency: delineation of the phenotype and development of a functional blood assay. Genet Med 2017; 20:109-118. [PMID: 28726805 DOI: 10.1038/gim.2017.74] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/17/2017] [Indexed: 12/13/2022] Open
Abstract
PurposePREPL deficiency causes neonatal hypotonia, ptosis, neonatal feeding difficulties, childhood obesity, xerostomia, and growth hormone deficiency. Different recessive contiguous gene deletion syndromes involving PREPL and a variable combination of SLC3A1 (hypotonia-cystinuria syndrome), CAMKMT (atypical hypotonia-cystinuria syndrome), and PPM1B (2p21 deletion syndrome) have been described. In isolated PREPL deficiency, previously described only once, the absence of cystinuria complicates the diagnosis. Therefore, we developed a PREPL blood assay and further delineated the phenotype.MethodsClinical features of new subjects with PREPL deficiency were recorded. The presence of PREPL in lymphocytes and its reactivity with an activity-based probe were evaluated by western blot.ResultsFive subjects with isolated PREPL deficiency, three with hypotonia-cystinuria syndrome, and two with atypical hypotonia-cystinuria syndrome had nine novel alleles. Their IQs ranged from 64 to 112. Adult neuromuscular signs included ptosis, nasal dysarthria, facial weakness, and variable proximal and neck flexor weakness. Autonomic features are prevalent. PREPL protein and reactivity were absent in lymphocytes from subjects with PREPL deficiency, but normal in the clinically similar Prader-Willi syndrome.ConclusionPREPL deficiency causes neuromuscular, autonomic, cognitive, endocrine, and dysmorphic clinical features. PREPL is not deficient in Prader-Willi syndrome. The novel blood test should facilitate the confirmation of PREPL deficiency.
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Affiliation(s)
- Luc Régal
- Laboratory of Biochemical Neuroendocrinology, Department of Human Genetics, University of Leuven, Leuven, Belgium.,Pediatric Neurology and Metabolism, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | - Emma Mårtensson
- Department of Clinical Genetics, Region Skåne and Lund University, Lund, Sweden
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Nicol Voermans
- Department of Neurology, RadboudUMC Nijmegen, Nijmegen, The Netherlands
| | - Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et Génétique, Charleroi, Belgium
| | - Alberto Burlina
- Division of Inherited Metabolic Diseases, Department of Pediatrics, University Hospital Padova, Padova, Italy
| | - María Jesús Juan Fita
- Unidad de Metabolopatías, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - A Jeannette M Hoogeboom
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Tess Hollemans
- Pediatric Neurology and Metabolism, Department of Pediatrics, UZ Brussel, Brussels, Belgium
| | - Meyke Schouten
- Department of Clinical Genetics, RadboudUMC Nijmegen, Nijmegen, The Netherlands
| | - Sandra Meulemans
- Laboratory of Biochemical Neuroendocrinology, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Tord Jonson
- Department of Clinical Genetics, Region Skåne and Lund University, Lund, Sweden
| | - Inge François
- Department of Pediatric Endocrinology, UZ Leuven, Leuven, Belgium
| | - David Gil Ortega
- Unidad de Metabolopatías, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Erik-Jan Kamsteeg
- Department of Clinical Genetics, RadboudUMC Nijmegen, Nijmegen, The Netherlands
| | - John W M Creemers
- Laboratory of Biochemical Neuroendocrinology, Department of Human Genetics, University of Leuven, Leuven, Belgium
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29
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Gaildrat P, Lebbah S, Tebani A, Sudrié-Arnaud B, Tostivint I, Bollee G, Tubeuf H, Charles T, Bertholet-Thomas A, Goldenberg A, Barbey F, Martins A, Saugier-Veber P, Frébourg T, Knebelmann B, Bekri S. Clinical and molecular characterization of cystinuria in a French cohort: relevance of assessing large-scale rearrangements and splicing variants. Mol Genet Genomic Med 2017; 5:373-389. [PMID: 28717662 PMCID: PMC5511796 DOI: 10.1002/mgg3.294] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 03/27/2017] [Accepted: 04/06/2017] [Indexed: 02/04/2023] Open
Abstract
Background Cystinuria is an autosomal recessive disorder of dibasic amino acid transport in the kidney and the intestine leading to increased urinary cystine excretion and nephrolithiasis. Two genes, SLC3A1 and SLC7A9, coding respectively for rBAT and b0,+AT, account for the genetic basis of cystinuria. Methods This study reports the clinical and molecular characterization of a French cohort including 112 cystinuria patients and 25 relatives from 99 families. Molecular screening was performed using sequencing and Quantitative Multiplex PCR of Short Fluorescent Fragments analyses. Functional minigene‐based assays have been used to characterize splicing variants. Results Eighty‐eight pathogenic nucleotide changes were identified in SLC3A1 (63) and SLC7A9 (25) genes, of which 42 were novel. Interestingly, 17% (15/88) and 11% (10/88) of the total number of variants correspond, respectively, to large‐scale rearrangements and splicing mutations. Functional minigene‐based assays were performed for six variants located outside the most conserved sequences of the splice sites; three variants affect splice sites, while three others modify exonic splicing regulatory elements (ESR), in good agreement with a new in silico prediction based on ΔtESRseq values. Conclusion This report expands the spectrum of SLC3A1 and SLC7A9 variants and supports that digenic inheritance is unlikely. Furthermore, it highlights the relevance of assessing large‐scale rearrangements and splicing mutations to fully characterize cystinuria patients at the molecular level.
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Affiliation(s)
- Pascaline Gaildrat
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance
| | - Said Lebbah
- Department of NephrologyNecker HospitalParisFrance
| | - Abdellah Tebani
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of Metabolic BiochemistryRouen University HospitalRouenFrance
| | | | | | | | - Hélène Tubeuf
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Interactive BiosoftwareRouenFrance
| | | | | | | | - Frederic Barbey
- Department of TransplantationCHUV Department of PediatricsLausanne University HospitalLausanneSwitzerland
| | - Alexandra Martins
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance
| | - Pascale Saugier-Veber
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of GeneticsRouen University HospitalRouenFrance
| | - Thierry Frébourg
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of GeneticsRouen University HospitalRouenFrance
| | | | - Soumeya Bekri
- Inserm U1245UNIROUENNormandie UnivNormandy Centre for Genomic and Personalized MedicineRouenFrance.,Department of Metabolic BiochemistryRouen University HospitalRouenFrance
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30
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Legati A, Reyes A, Nasca A, Invernizzi F, Lamantea E, Tiranti V, Garavaglia B, Lamperti C, Ardissone A, Moroni I, Robinson A, Ghezzi D, Zeviani M. New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1326-1335. [PMID: 26968897 DOI: 10.1016/j.bbabio.2016.02.022] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/17/2016] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Abstract
Next Generation Sequencing (NGS) technologies are revolutionizing the diagnostic screening for rare disease entities, including primary mitochondrial disorders, particularly those caused by nuclear gene defects. NGS approaches are able to identify the causative gene defects in small families and even single individuals, unsuitable for investigation by traditional linkage analysis. These technologies are contributing to fill the gap between mitochondrial disease cases defined on the basis of clinical, neuroimaging and biochemical readouts, which still outnumber by approximately 50% the cases for which a molecular-genetic diagnosis is attained. We have been using a combined, two-step strategy, based on targeted genes panel as a first NGS screening, followed by whole exome sequencing (WES) in still unsolved cases, to analyze a large cohort of subjects, that failed to show mutations in mtDNA and in ad hoc sets of specific nuclear genes, sequenced by the Sanger's method. Not only this approach has allowed us to reach molecular diagnosis in a significant fraction (20%) of these difficult cases, but it has also revealed unexpected and conceptually new findings. These include the possibility of marked variable penetrance of recessive mutations, the identification of large-scale DNA rearrangements, which explain spuriously heterozygous cases, and the association of mutations in known genes with unusual, previously unreported clinical phenotypes. Importantly, WES on selected cases has unraveled the presence of pathogenic mutations in genes encoding non-mitochondrial proteins (e.g. the transcription factor E4F1), an observation that further expands the intricate genetics of mitochondrial disease and suggests a new area of investigation in mitochondrial medicine. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Andrea Legati
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Aurelio Reyes
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK
| | - Alessia Nasca
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Federica Invernizzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Eleonora Lamantea
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Barbara Garavaglia
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Costanza Lamperti
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy
| | - Anna Ardissone
- Unit of Child Neurology, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Isabella Moroni
- Unit of Child Neurology, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20133 Milan, Italy
| | - Alan Robinson
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK
| | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', 20126 Milan, Italy.
| | - Massimo Zeviani
- Mitochondrial Biology Unit, Medical Research Council, Cambridge CB2 0XY, UK.
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31
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He F, Li Y, Tang YH, Ma J, Zhu H. Identifying micro-inversions using high-throughput sequencing reads. BMC Genomics 2016; 17 Suppl 1:4. [PMID: 26818118 PMCID: PMC4895285 DOI: 10.1186/s12864-015-2305-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The identification of inversions of DNA segments shorter than read length (e.g., 100 bp), defined as micro-inversions (MIs), remains challenging for next-generation sequencing reads. It is acknowledged that MIs are important genomic variation and may play roles in causing genetic disease. However, current alignment methods are generally insensitive to detect MIs. Here we develop a novel tool, MID (Micro-Inversion Detector), to identify MIs in human genomes using next-generation sequencing reads. RESULTS The algorithm of MID is designed based on a dynamic programming path-finding approach. What makes MID different from other variant detection tools is that MID can handle small MIs and multiple breakpoints within an unmapped read. Moreover, MID improves reliability in low coverage data by integrating multiple samples. Our evaluation demonstrated that MID outperforms Gustaf, which can currently detect inversions from 30 bp to 500 bp. CONCLUSIONS To our knowledge, MID is the first method that can efficiently and reliably identify MIs from unmapped short next-generation sequencing reads. MID is reliable on low coverage data, which is suitable for large-scale projects such as the 1000 Genomes Project (1KGP). MID identified previously unknown MIs from the 1KGP that overlap with genes and regulatory elements in the human genome. We also identified MIs in cancer cell lines from Cancer Cell Line Encyclopedia (CCLE). Therefore our tool is expected to be useful to improve the study of MIs as a type of genetic variant in the human genome. The source code can be downloaded from: http://cqb.pku.edu.cn/ZhuLab/MID .
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Affiliation(s)
- Feifei He
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, and Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Yang Li
- Department of Bioengineering, University of Illinois, Urbana, IL, 61801, USA.
| | - Yu-Hang Tang
- Division of Applied Mathematics, Brown University, Providence, RI, 02912, USA.
| | - Jian Ma
- Department of Bioengineering, University of Illinois, Urbana, IL, 61801, USA. .,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, and Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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32
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Haziza S, Magnani R, Lan D, Keinan O, Saada A, Hershkovitz E, Yanay N, Cohen Y, Nevo Y, Houtz RL, Sheffield VC, Golan H, Parvari R. Calmodulin Methyltransferase Is Required for Growth, Muscle Strength, Somatosensory Development and Brain Function. PLoS Genet 2015; 11:e1005388. [PMID: 26247364 PMCID: PMC4527749 DOI: 10.1371/journal.pgen.1005388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/23/2015] [Indexed: 01/11/2023] Open
Abstract
Calmodulin lysine methyl transferase (CaM KMT) is ubiquitously expressed and highly conserved from plants to vertebrates. CaM is frequently trimethylated at Lys-115, however, the role of CaM methylation in vertebrates has not been studied. CaM KMT was found to be homozygously deleted in the 2P21 deletion syndrome that includes 4 genes. These patients present with cystinuria, severe intellectual disabilities, hypotonia, mitochondrial disease and facial dysmorphism. Two siblings with deletion of three of the genes included in the 2P21 deletion syndrome presented with cystinuria, hypotonia, a mild/moderate mental retardation and a respiratory chain complex IV deficiency. To be able to attribute the functional significance of the methylation of CaM in the mouse and the contribution of CaM KMT to the clinical presentation of the 2p21deletion patients, we produced a mouse model lacking only CaM KMT with deletion borders as in the human 2p21deletion syndrome. No compensatory activity for CaM methylation was found. Impairment of complexes I and IV, and less significantly III, of the mitochondrial respiratory chain was more pronounced in the brain than in muscle. CaM KMT is essential for normal body growth and somatosensory development, as well as for the proper functioning of the adult mouse brain. Developmental delay was demonstrated for somatosensory function and for complex behavior, which involved both basal motor function and motivation. The mutant mice also had deficits in motor learning, complex coordination and learning of aversive stimuli. The mouse model contributes to the evaluation of the role of methylated CaM. CaM methylation appears to have a role in growth, muscle strength, somatosensory development and brain function. The current study has clinical implications for human patients. Patients presenting slow growth and muscle weakness that could result from a mitochondrial impairment and mental retardation should be considered for sequence analysis of the CaM KMT gene. Calmodulin (CaM) is a highly abundant, ubiquitous, small protein, which plays a major role in the transmission of calcium signals to target proteins in eukaryotes. Hundreds of CaM targets are known, and their respective cellular functions include signaling, metabolism, cytoskeletal regulation, and ion channel regulation, to name but a few. CaM is frequently modified after translation, including frequently trimethylation at a single amino acid, however, the role of this methylation is not known. Human patients with a homozygous deletion of the gene that methylates CaM, CaM-KMT, are known, but they also have a deletion of additional genes. Thus, to study the role of CaM–KMT, we produced a mouse model in which CaM-KMT is the only deleted gene, with the deletion constructed as in the human patients. The model proved to reveal the function of methylation of CaM, since CaM was found to be non-methylated and the methylation of CaM found to be important in growth, muscle strength, somatosensory development and brain function. The current study also has clinical implications for human patients. Patients presenting slow growth and muscle weakness that could result from a mitochondrial impairment and mental retardation should be considered for sequence analysis of the CaM KMT gene.
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Affiliation(s)
- Sitvanit Haziza
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Roberta Magnani
- Department of Horticulture, University of Kentucky, Lexington, Kentucky, United States of America
| | - Dima Lan
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Omer Keinan
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ann Saada
- Department of Genetic and Metabolic Diseases, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Eli Hershkovitz
- Pediatric Endocrinology & Metabolism Unit, Soroka Medical Center, Beer Sheva, Israel
| | - Nurit Yanay
- Pediatric Neuromuscular Laboratory and Pediatric Neurology Unit Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Yoram Cohen
- Pesticides and Mycotoxins Division, Aminolab, Weizmann Science Park, Ness Ziona, Israel
| | - Yoram Nevo
- Pediatric Neuromuscular Laboratory and Pediatric Neurology Unit Hadassah, Hebrew University Medical Center, Jerusalem, Israel
- Institute of Neurology, Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Robert L. Houtz
- Department of Horticulture, University of Kentucky, Lexington, Kentucky, United States of America
| | - Val C. Sheffield
- Department of Pediatrics, Division of Medical Genetics and Hughes Medical Institute, University of Iowa, Iowa City, Iowa, United States of America
| | - Hava Golan
- Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ruti Parvari
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- National Institute of Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
- * E-mail:
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Aygun N. Correlations between long inverted repeat (LIR) features, deletion size and distance from breakpoint in human gross gene deletions. Sci Rep 2015; 5:8300. [PMID: 25657065 PMCID: PMC4319165 DOI: 10.1038/srep08300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/14/2015] [Indexed: 11/09/2022] Open
Abstract
Long inverted repeats (LIRs) have been shown to induce genomic deletions in yeast. In this study, LIRs were investigated within ±10 kb spanning each breakpoint from 109 human gross deletions, using Inverted Repeat Finder (IRF) software. LIR number was significantly higher at the breakpoint regions, than in control segments (P < 0.001). In addition, it was found that strong correlation between 5' and 3' LIR numbers, suggesting contribution to DNA sequence evolution (r = 0.85, P < 0.001). 138 LIR features at ±3 kb breakpoints in 89 (81%) of 109 gross deletions were evaluated. Significant correlations were found between distance from breakpoint and loop length (r = -0.18, P < 0.05) and stem length (r = -0.18, P < 0.05), suggesting DNA strands are potentially broken in locations closer to bigger LIRs. In addition, bigger loops cause larger deletions (r = 0.19, P < 0.05). Moreover, loop length (r = 0.29, P < 0.02) and identity between stem copies (r = 0.30, P < 0.05) of 3' LIRs were more important in larger deletions. Consequently, DNA breaks may form via LIR-induced cruciform structure during replication. DNA ends may be later repaired by non-homologous end-joining (NHEJ), with following deletion.
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Affiliation(s)
- Nevim Aygun
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylul University, Inciralti, Izmir, Turkey
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Régal L, Shen XM, Selcen D, Verhille C, Meulemans S, Creemers JWM, Engel AG. PREPL deficiency with or without cystinuria causes a novel myasthenic syndrome. Neurology 2014; 82:1254-60. [PMID: 24610330 PMCID: PMC4001208 DOI: 10.1212/wnl.0000000000000295] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/26/2013] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE To investigate the genetic and physiologic basis of the neuromuscular symptoms of hypotonia-cystinuria syndrome (HCS) and isolated PREPL deficiency, and their response to therapy. METHODS We performed molecular genetic, histochemical, immunoblot, and ultrastructural studies, investigated neuromuscular transmission in vitro in a patient with isolated PREPL deficiency, and evaluated the effect of pyridostigmine in this patient and in 3 patients with the HCS. RESULTS HCS is caused by recessive deletions involving the SLC3A1 and PREPL genes. The major clinical features of HCS are type A cystinuria, growth hormone deficiency, muscle weakness, ptosis, and feeding problems. The proband with isolated PREPL deficiency had myasthenic symptoms since birth and a positive edrophonium test but no cystinuria. She and 1 of 3 patients with HCS responded transiently to pyridostigmine during infancy. The proband harbors a paternally inherited nonsense mutation in PREPL and a maternally inherited deletion involving both PREPL and SLC3A1; therefore, the PREPL deficiency determines the phenotype. We detected no PREPL expression in the patient's muscle and endplates. Electrophysiology studies revealed decreased quantal content of the endplate potential and reduced amplitude of the miniature endplate potential without endplate acetylcholine receptor deficiency or altered endplate geometry. CONCLUSION Isolated PREPL deficiency is a novel monogenic disorder that causes a congenital myasthenic syndrome with pre- and postsynaptic features and growth hormone deficiency. The myasthenic symptoms in PREPL deficiency with or without cystinuria may respond to pyridostigmine in early life. We attribute the myasthenia to abrogated interaction of PREPL with adaptor protein 1.
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Affiliation(s)
- Luc Régal
- From the Center of Human Genetics (L.R., J.W.M.C., S.M.), Laboratory of Biochemical Neuroendocrinology, KU Leuven; Department of Pediatrics and Pediatric Metabolic Disorders (C.V.), University Hospital Leuven, Belgium; and Department of Neurology (X.-M.S., D.S., A.G.E.), Mayo Clinic, Rochester, MN
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Lone AM, Leidl M, McFedries AK, Horner JW, Creemers J, Saghatelian A. Deletion of PREPl causes growth impairment and hypotonia in mice. PLoS One 2014; 9:e89160. [PMID: 24586561 PMCID: PMC3938459 DOI: 10.1371/journal.pone.0089160] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/03/2014] [Indexed: 01/22/2023] Open
Abstract
Genetic studies of rare diseases can identify genes of unknown function that strongly impact human physiology. Prolyl endopeptidase-like (PREPL) is an uncharacterized member of the prolyl peptidase family that was discovered because of its deletion in humans with hypotonia-cystinuria syndrome (HCS). HCS is characterized by a number of physiological changes including diminished growth and neonatal hypotonia or low muscle tone. HCS patients have deletions in other genes as well, making it difficult to tease apart the specific role of PREPL. Here, we develop a PREPL null (PREPL(-/-)) mouse model to address the physiological role of this enzyme. Deletion of exon 11 from the Prepl gene, which encodes key catalytic amino acids, leads to a loss of PREPL protein as well as lower Prepl mRNA levels. PREPL(-/-) mice have a pronounced growth phenotype, being significantly shorter and lighter than their wild type (PREPL(+/+)) counterparts. A righting assay revealed that PREPL(-/-) pups took significantly longer than PREPL(+/+) pups to right themselves when placed on their backs. This deficit indicates that PREPL(-/-) mice suffer from neonatal hypotonia. According to these results, PREPL regulates growth and neonatal hypotonia in mice, which supports the idea that PREPL causes diminished growth and neonatal hypotonia in humans with HCS. These animals provide a valuable asset in deciphering the underlying biochemical, cellular and physiological pathways that link PREPL to HCS, and this may eventually lead to new insights in the treatment of this disease.
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Affiliation(s)
- Anna Mari Lone
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Mathias Leidl
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Amanda K. McFedries
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - James W. Horner
- Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Institute for Applied Cancer Science, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - John Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
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Abe Y, Sakamoto S, Morimoto E, Watanabe Y, Nagahara K, Mikawa T, Watanabe S, Itabashi K. Persistent Leukocyturia Was a Clue to Diagnosis of Cystinuria in a Female Patient. Glob Pediatr Health 2014; 1:2333794X14551275. [PMID: 27335907 PMCID: PMC4804682 DOI: 10.1177/2333794x14551275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Yoshifusa Abe
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Shinichi Sakamoto
- Department of Urology, Chiba University School of Medicine, Chiba, Japan
| | - Eiji Morimoto
- Clinical Laboratory, Showa University Hospital, Tokyo, Japan
| | - Yoshitaka Watanabe
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Keiko Nagahara
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Takeshi Mikawa
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | | | - Kazuo Itabashi
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
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Bartholdi D, Asadollahi R, Oneda B, Schmitt-Mechelke T, Tonella P, Baumer A, Rauch A. Further delineation of genotype-phenotype correlation in homozygous 2p21 deletion syndromes: first description of patients without cystinuria. Am J Med Genet A 2013; 161A:1853-9. [PMID: 23794250 DOI: 10.1002/ajmg.a.35994] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 03/28/2013] [Indexed: 02/04/2023]
Abstract
Homozygous contiguous gene deletion syndromes are rare. On 2p21, however, several overlapping homozygous gene deletion syndromes have been described, all presenting with cystinuria but otherwise distinct phenotypes. Hypotonia-cystinuria syndrome (HCS, OMIM606407) is characterized by infantile hypotonia, poor feeding, and growth hormone deficiency. Affected individuals carry homozygous deletions including the cystinuria gene SLC3A1 and the adjacent PREPL gene. Larger homozygous deletions in this region encompassing the PPM1B, SLC3A1, PREPL, and C2orf34 (CAMKMT) genes result in a more severe phenotype, the 2p21 deletion syndrome. A phenotype intermediate to HCS and the 2p21 deletion syndrome is termed atypical HCS and is caused by deletion of SLC3A1, PREPL, and C2orf34 (CAMKMT). Using high resolution SNP array molecular karyotyping we identified two siblings with a homozygous deletion of 83 kb partially encompassing the genes PREPL and C2orf34 (CAMKMT), but not the SLC3A1 gene. The affected siblings display a recognizable phenotype which is similar to atypical HCS with regard to growth failure and neuro-muscular features, but is characterized by lack of cystinuria. The patients also exhibit features which have not been reported to date such as cleft palate and genital abnormalities. In conclusion, we report the first patients with a homozygous 2p21 deletion syndrome without cystinuria and further delineate the complex genotype-phenotype correlations of homozygous microdeletion syndromes of this region.
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Affiliation(s)
- Deborah Bartholdi
- Institute of Medical Genetics, University of Zurich, Schwerzenbach, Switzerland.
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Morawski M, Nuytens K, Juhasz T, Zeitschel U, Seeger G, Waelkens E, Regal L, Schulz I, Arendt T, Szeltner Z, Creemers J, Rossner S. Cellular and ultra structural evidence for cytoskeletal localization of prolyl endopeptidase-like protein in neurons. Neuroscience 2013; 242:128-39. [PMID: 23485813 DOI: 10.1016/j.neuroscience.2013.02.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 12/11/2022]
Abstract
The biochemical properties and subcellular localization of prolyl endopeptidase (PREP) in brain are well characterized and its implications in the realization of cognitive processes and in the pathogenesis of neurodegenerative disorders are a matter of intensive investigation. In contrast, very little is known about its homolog, the PREP-like protein (PREPL). In order to obtain initial hints about the involvement of PREPL in physiological processes, a differential proteomic screen was performed with human skin fibroblasts from controls and patients with PREPL deficiency (hypotonia-cystinuria syndrome). The majority of affected proteins represented cytoskeletal proteins, including caldesmon, tropomyosin α3 chain, lamin A, β-actin, γ-actin, vimentin and zyxin. Therefore, the analysis of PREPL subcellular localization by confocal laser scanning and electron microscopy in mouse neurons was focused on the cytoskeleton. The co-localization of PREPL with cytoskeletal marker proteins such as β-actin and microtubulin-associated protein-2 was observed, in addition to the presence of PREPL within Golgi apparatus and growth cones. In the mouse brain, PREPL is neuronally expressed and highly abundant in neocortex, substantia nigra and locus coeruleus. This mirrors to some extent the distribution pattern of PREP and points toward redundant functions of both proteins. In the human neocortex, PREPL immunostaining was found in the cytoplasm and in neuropil, in particular of layer V pyramidal neurons. This staining was reduced in the neocortex of Alzheimer's disease (AD) patients. Moreover, in AD brains, PREPL immunoreactivity was observed in the nucleus and in varicose neuritic processes. Our data indicate physiological functions of PREPL associated with the cytoskeleton, which may be affected under conditions of cytoskeletal degeneration.
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Affiliation(s)
- M Morawski
- Paul Flechsig Institute for Brain Research, University of Leipzig, 04109 Leipzig, Jahnallee 59, Germany
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Radhakrishnan K, Baltes J, Creemers JWM, Schu P. TGN morphology and sorting regulated by prolyl-oligopeptidase–like protein PREPL and AP-1 μ1A. J Cell Sci 2013; 126:1155-63. [DOI: 10.1242/jcs.116079] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The AP-1 complex recycles between membranes and the cytoplasm and dissociates from membranes during clathrin-coated-vesicle uncoating, but also independent of vesicular transport. The μ1A N-terminal seventy amino acids are involved in regulating AP-1 recycling. In a yeast-2-hybrid library screen we identified the cytoplasmic prolyl-oligopeptidase-like protein PREPL as an interaction partner of this domain. PREPL overexpression leads to reduced AP-1 membrane binding, whereas reduced PREPL expression increases membrane binding and it impairs AP-1 recycling. Altered AP-1 membrane binding in PREPL-deficient cells mirrors the membrane binding of the mutant AP-1* complex, not able to bind PREPL. Colocalisation of PREPL with residual membrane bound AP-1 can be demonstrated. Patient cell lines deficient in PREPL have an expanded TGN, which could be rescued by PREPL expression. These data demonstrate PREPL as an AP-1 effector, which takes part in the regulation of AP-1 membrane binding. PREPL is highly expressed in brain, and at lower levels also in muscle and kidney, and its deficiency causes hypotonia and growth hormone hyposecretion supporting essential PREPL functions in AP-1-dependent secretory pathways
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Régal L, Aydin HI, Dieltjens AM, Van Esch H, Francois I, Okur I, Zeybek C, Meulemans S, Van Mol C, Van Bruwaene L, Then SH, Jaeken J, Creemers J. Two novel deletions in hypotonia-cystinuria syndrome. Mol Genet Metab 2012; 107:614-6. [PMID: 22796000 DOI: 10.1016/j.ymgme.2012.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 06/19/2012] [Indexed: 11/26/2022]
Abstract
Hypotonia-cystinuria syndrome (HCS) is an autosomal recessive disorder caused by combined deletions of SLC3A1 and PREPL. Clinical features include cystinuria, neonatal hypotonia with spontaneous improvement, poor feeding in neonates, hyperphagia in childhood, growth hormone deficiency, and variable cognitive problems. Only 14 families with 6 different deletions have been reported. Patients are often initially misdiagnosed, while correct diagnosis enables therapeutic interventions. We report two novel deletions, further characterizing the clinical and molecular genetics spectrum of HCS.
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Affiliation(s)
- Luc Régal
- Laboratory for Biochemical Neuroendocrinology, Center for Human Genetics, University of Leuven, KU Leuven, Belgium.
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Eggermann T, Spengler S, Venghaus A, Denecke B, Zerres K, Baudis M, Ensenauer R. 2p21 Deletions in hypotonia-cystinuria syndrome. Eur J Med Genet 2012; 55:561-3. [PMID: 22766003 DOI: 10.1016/j.ejmg.2012.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
Abstract
The significant role of the SLC3A1 gene in the aetiology of cystinuria is meanwhile well established and more than 130 point mutations have been reported. With the reports on genomic deletions including at least both SLC3A1 and the neighboured PREPL gene the spectrum of cystinuria mutations and of clinical symptoms could recently be enlarged: patients homozygous for these deletions suffer from a general neonatal hypotonia and growth retardation in addition to cystinuria. The hypotonia in these hypotonia-cystinuria (HCS) patients has been attributed to the total loss of the PREPL protein. Here we report on the clinical course and molecular findings in a HCS patient compound heterozygote for a new deletion in 2p21 and a previously reported deletion, both identified by molecular karyotyping. The diagnostic workup in this patient illustrates the need for a careful clinical examination in context with powerful molecular genetic tools in patients with unusual phenotypes. The identification of unique genomic alterations and their interpretation serves as a prerequisite for the individual counselling of patients and their families. In diagnostic strategies to identify the molecular basis of both cystinuria and hypotonia 2p21 deletions should be considered as the molecular basis of the phenotype.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, RWTH Aachen, Pauwelsstr. 30, D-52074 Aachen, Germany.
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Eggermann T, Venghaus A, Zerres K. Cystinuria: an inborn cause of urolithiasis. Orphanet J Rare Dis 2012; 7:19. [PMID: 22480232 PMCID: PMC3464901 DOI: 10.1186/1750-1172-7-19] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 04/05/2012] [Indexed: 12/04/2022] Open
Abstract
Cystinuria (OMIM 220100) is an inborn congenital disorder characterised by a defective cystine metabolism resulting in the formation of cystine stones. Among the heterogeneous group of kidney stone diseases, cystinuria is the only disorder which is exclusively caused by gene mutations. So far, two genes responsible for cystinuria have been identified: SLC3A1 (chromosome 2p21) encodes the heavy subunit rBAT of a renal b0,+ transporter while SLC7A9 (chromosome 19q12) encodes its interacting light subunit b0,+AT. Mutations in SLC3A1 are generally associated with an autosomal-recessive mode of inheritance whereas SLC7A9 variants result in a broad clinical variability even within the same family. The detection rate for mutations in these genes is larger than 85%, but it is influenced by the ethnic origin of a patient and the pathophysiological significance of the mutations. In addition to isolated cystinuria, patients suffering from the hypotonia-cystinuria syndrome have been reported carrying deletions including at least the SLC3A1 and the PREPL genes in 2p21. By extensive molecular screening studies in large cohort of patients a broad spectrum of mutations could be identified, several of these variants were functionally analysed and thereby allowed insights in the pathology of the disease as well as in the renal trafficking of cystine and the dibasic amino acids. In our review we will summarize the current knowledge on the physiological and the genetic basis of cystinuria as an inborn cause of kidney stones, and the application of this knowledge in genetic testing strategies.
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Affiliation(s)
- Thomas Eggermann
- Institute of Human Genetics, University Hospital, RWTH Aachen, Pauwelsstr, 30, Aachen, D-52074, Germany.
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Jaeken J, Creemers J, Régal L. Evaluation of the pediatric patient with hypotonia: don't forget the hypotonia-cystinuria syndrome! Dev Med Child Neurol 2012; 54:288. [PMID: 22211458 DOI: 10.1111/j.1469-8749.2011.04195.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lone AM, Bachovchin DA, Westwood D, Speers AE, Spicer TP, Fernandez-Vega V, Chase P, Hodder PS, Rosen H, Cravatt BF, Saghatelian A. A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors. J Am Chem Soc 2011; 133:11665-74. [PMID: 21692504 PMCID: PMC3145007 DOI: 10.1021/ja2036095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidases play vital roles in physiology through the biosynthesis, degradation, and regulation of peptides. Prolyl endopeptidase-like (PREPL) is a newly described member of the prolyl peptidase family, with significant homology to mammalian prolyl endopeptidase and the bacterial peptidase oligopeptidase B. The biochemistry and biology of PREPL are of fundamental interest due to this enzyme's homology to the biomedically important prolyl peptidases and its localization in the central nervous system. Furthermore, genetic studies of patients suffering from hypotonia-cystinuria syndrome (HCS) have revealed a deletion of a portion of the genome that includes the PREPL gene. HCS symptoms thought to be caused by lack of PREPL include neuromuscular and mild cognitive deficits. A number of complementary approaches, ranging from biochemistry to genetics, will be required to understand the biochemical, cellular, physiological, and pathological mechanisms regulated by PREPL. We are particularly interested in investigating physiological substrates and pathways controlled by PREPL. Here, we use a fluorescence polarization activity-based protein profiling (fluopol-ABPP) assay to discover selective small-molecule inhibitors of PREPL. Fluopol-ABPP is a substrate-free approach that is ideally suited for studying serine hydrolases for which no substrates are known, such as PREPL. After screening over 300,000 compounds using fluopol-ABPP, we employed a number of secondary assays to confirm assay hits and characterize a group of 3-oxo-1-phenyl-2,3,5,6,7,8-hexahydroisoquinoline-4-carbonitrile and 1-alkyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile PREPL inhibitors that are able to block PREPL activity in cells. Moreover, when administered to mice, 1-isobutyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile distributes to the brain, indicating that it may be useful for in vivo studies. The application of fluopol-ABPP has led to the first reported PREPL inhibitors, and these inhibitors will be of great value in studying the biochemistry of PREPL and in eventually understanding the link between PREPL and HCS.
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Affiliation(s)
- Anna Mari Lone
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Daniel A. Bachovchin
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - David Westwood
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Anna E. Speers
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Timothy P. Spicer
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Virneliz Fernandez-Vega
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Peter Chase
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Peter S. Hodder
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458
| | - Hugh Rosen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
- The Scripps Research Institute Molecular Screening Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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Long JZ, Cravatt BF. The metabolic serine hydrolases and their functions in mammalian physiology and disease. Chem Rev 2011; 111:6022-63. [PMID: 21696217 DOI: 10.1021/cr200075y] [Citation(s) in RCA: 299] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jonathan Z Long
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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Abstract
Amino acids are essential building blocks of all mammalian cells. In addition to their role in protein synthesis, amino acids play an important role as energy fuels, precursors for a variety of metabolites and as signalling molecules. Disorders associated with the malfunction of amino acid transporters reflect the variety of roles that they fulfil in human physiology. Mutations of brain amino acid transporters affect neuronal excitability. Mutations of renal and intestinal amino acid transporters affect whole-body homoeostasis, resulting in malabsorption and renal problems. Amino acid transporters that are integral parts of metabolic pathways reduce the function of these pathways. Finally, amino acid uptake is essential for cell growth, thereby explaining their role in tumour progression. The present review summarizes the involvement of amino acid transporters in these roles as illustrated by diseases resulting from transporter malfunction.
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Abstract
Prolyl endopeptidase (Prep) is a member of the prolyl peptidase family and is of interest because of its unique biochemistry and connections to cognitive function. Using an unbiased mass spectrometry (MS)-based peptidomics platform, we identified Prep-regulated peptides in the central nervous system (CNS) of mice by measuring changes in the peptidome as a function of Prep activity. This approach was validated by the identification of known Prep substrates, such as the neuropeptide substance P and thymosin-beta4, the precursor to the bioactive peptide Ac-SDKP. In addition to these known substrates, we also discovered that Prep regulates many additional peptides, including additional bioactive peptides and proline rich peptides (PRPs). Biochemical experiments confirmed that some of these Prep-regulated peptides are indeed substrates of the enzyme. Moreover, these experiments also supported the known preference of Prep for shorter peptides while revealing a previously unknown cleavage site specificity of Prep when processing certain multi-proline-containing peptides, including PRPs. The discovery of Prep-regulated peptides implicates Prep in new biological pathways and provides insights into the biochemistry of this enzyme.
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