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Mir A, Song Y, Lee H, Khanahmad H, Khorram E, Nasiri J, Tabatabaiefar MA. Whole exome sequencing revealed variants in four genes underlying X-linked intellectual disability in four Iranian families: novel deleterious variants and clinical features with the review of literature. BMC Med Genomics 2023; 16:239. [PMID: 37821930 PMCID: PMC10566173 DOI: 10.1186/s12920-023-01680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023] Open
Abstract
AIM AND OBJECTIVE Intellectual disability (ID) is a heterogeneous condition affecting brain development, function, and/or structure. The X-linked mode of inheritance of ID (X-linked intellectual disability; XLID) has a prevalence of 1 out of 600 to 1000 males. In the last decades, exome sequencing technology has revolutionized the process of disease-causing gene discovery in XLIDs. Nevertheless, so many of them still remain with unknown etiology. This study investigated four families with severe XLID to identify deleterious variants for possible diagnostics and prevention aims. METHODS Nine male patients belonging to four pedigrees were included in this study. The patients were studied genetically for Fragile X syndrome, followed by whole exome sequencing and analysis of intellectual disability-related genes variants. Sanger sequencing, co-segregation analysis, structural modeling, and in silico analysis were done to verify the causative variants. In addition, we collected data from previous studies to compare and situate our work with existing knowledge. RESULTS In three of four families, novel deleterious variants have been identified in three different genes, including ZDHHC9 (p. Leu189Pro), ATP2B3 (p. Asp847Glu), and GLRA2 (p. Arg350Cys) and also with new clinical features and in another one family, a reported pathogenic variant in the L1CAM (p. Glu309Lys) gene has been identified related to new clinical findings. CONCLUSION The current study's findings expand the existing knowledge of variants of the genes implicated in XLID and broaden the spectrum of phenotypes associated with the related conditions. The data have implications for genetic diagnosis and counseling.
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Affiliation(s)
- Atefeh Mir
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Yongjun Song
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Khorram
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Jafar Nasiri
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran.
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
- Deputy of Research and Technology, GenTArget Corp (GTAC), Isfahan University of Medical Sciences, Isfahan, Iran.
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2
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Poggio E, Vallese F, Hartel AJW, Morgenstern TJ, Kanner SA, Rauh O, Giamogante F, Barazzuol L, Shepard KL, Colecraft HM, Clarke OB, Brini M, Calì T. Perturbation of the host cell Ca 2+ homeostasis and ER-mitochondria contact sites by the SARS-CoV-2 structural proteins E and M. Cell Death Dis 2023; 14:297. [PMID: 37120609 PMCID: PMC10148623 DOI: 10.1038/s41419-023-05817-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
Coronavirus disease (COVID-19) is a contagious respiratory disease caused by the SARS-CoV-2 virus. The clinical phenotypes are variable, ranging from spontaneous recovery to serious illness and death. On March 2020, a global COVID-19 pandemic was declared by the World Health Organization (WHO). As of February 2023, almost 670 million cases and 6,8 million deaths have been confirmed worldwide. Coronaviruses, including SARS-CoV-2, contain a single-stranded RNA genome enclosed in a viral capsid consisting of four structural proteins: the nucleocapsid (N) protein, in the ribonucleoprotein core, the spike (S) protein, the envelope (E) protein, and the membrane (M) protein, embedded in the surface envelope. In particular, the E protein is a poorly characterized viroporin with high identity amongst all the β-coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43) and a low mutation rate. Here, we focused our attention on the study of SARS-CoV-2 E and M proteins, and we found a general perturbation of the host cell calcium (Ca2+) homeostasis and a selective rearrangement of the interorganelle contact sites. In vitro and in vivo biochemical analyses revealed that the binding of specific nanobodies to soluble regions of SARS-CoV-2 E protein reversed the observed phenotypes, suggesting that the E protein might be an important therapeutic candidate not only for vaccine development, but also for the clinical management of COVID designing drug regimens that, so far, are very limited.
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Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padova, Padova, Italy
| | - Francesca Vallese
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Travis J Morgenstern
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
| | - Scott A Kanner
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Rauh
- Membrane Biophysics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Biggs Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Marisa Brini
- Department of Biology, University of Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy.
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
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3
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The ataxia-linked E1081Q mutation affects the sub-plasma membrane Ca 2+-microdomains by tuning PMCA3 activity. Cell Death Dis 2022; 13:855. [PMID: 36207321 PMCID: PMC9546857 DOI: 10.1038/s41419-022-05300-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 01/23/2023]
Abstract
Calcium concentration must be finely tuned in all eukaryotic cells to ensure the correct performance of its signalling function. Neuronal activity is exquisitely dependent on the control of Ca2+ homeostasis: its alterations ultimately play a pivotal role in the origin and progression of many neurodegenerative processes. A complex toolkit of Ca2+ pumps and exchangers maintains the fluctuation of cytosolic Ca2+ concentration within the appropriate threshold. Two ubiquitous (isoforms 1 and 4) and two neuronally enriched (isoforms 2 and 3) of the plasma membrane Ca2+ATPase (PMCA pump) selectively regulate cytosolic Ca2+ transients by shaping the sub-plasma membrane (PM) microdomains. In humans, genetic mutations in ATP2B1, ATP2B2 and ATP2B3 gene have been linked with hearing loss, cerebellar ataxia and global neurodevelopmental delay: all of them were found to impair pump activity. Here we report three additional mutations in ATP2B3 gene corresponding to E1081Q, R1133Q and R696H amino acids substitution, respectively. Among them, the novel missense mutation (E1081Q) immediately upstream the C-terminal calmodulin-binding domain (CaM-BD) of the PMCA3 protein was present in two patients originating from two distinct families. Our biochemical and molecular studies on PMCA3 E1081Q mutant have revealed a splicing variant-dependent effect of the mutation in shaping the sub-PM [Ca2+]. The E1081Q substitution in the full-length b variant abolished the capacity of the pump to reduce [Ca2+] in the sub-PM microdomain (in line with the previously described ataxia-related PMCA mutations negatively affecting Ca2+ pumping activity), while, surprisingly, its introduction in the truncated a variant selectively increased Ca2+ extrusion activity in the sub-PM Ca2+ microdomains. These results highlight the importance to set a precise threshold of [Ca2+] by fine-tuning the sub-PM microdomains and the different contribution of the PMCA splice variants in this regulation.
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González-Domínguez C, Villarroel C, Rodríguez-Morales M, Manrique-Hernández S, González-Jaimes A, Olvera-Rodriguez F, Beutelspacher K, Molina-Garay C, Carrillo-Sánchez K, Flores-Lagunes L, Jiménez-Olivares M, Muñoz-Rivas A, Cruz-Muñoz M, Mora-Montes H, Salinas-Marín R, Alaez-Verson C, Martínez-Duncker I. Non-functional alternative splicing caused by a Latino pathogenic variant in a case of PMM2-CDG. Mol Genet Metab Rep 2021; 28:100781. [PMID: 34277356 PMCID: PMC8264207 DOI: 10.1016/j.ymgmr.2021.100781] [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: 04/30/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 12/13/2022] Open
Abstract
We report on a Mexican mestizo with a multisystemic syndrome including neurological involvement and a type I serum transferrin isoelectric focusing (Tf IEF) pattern. Diagnosis of PMM2-CDG was obtained by clinical exome sequencing (CES) that revealed compound heterozygous variants in PMM2, the encoding gene for the phosphomannomutase 2 (PMM2). This enzyme catalyzes the conversion of mannose-6-P to mannose-1-P required for the synthesis of GDP-Man and Dol-P-Man, donor substrates for glycosylation reactions. The identified variants were c.422G>A (R141H) and c.178G>T, the former being the most frequent PMM2 pathogenic mutation and the latter a previously uncharacterized variant restricted to the Latino population with conflicting interpretations of pathogenicity and that we here report causes leaky non-functional alternative splicing (p.V60Cfs*3).
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Affiliation(s)
- C.A. González-Domínguez
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - C.E. Villarroel
- Departamento de Genética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
| | - M. Rodríguez-Morales
- Departamento de Genética, Instituto Nacional de Pediatría, Ciudad de México 04530, Mexico
| | - S. Manrique-Hernández
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - A. González-Jaimes
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - F. Olvera-Rodriguez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - K. Beutelspacher
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - C. Molina-Garay
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - K. Carrillo-Sánchez
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - L.L. Flores-Lagunes
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - M. Jiménez-Olivares
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - A. Muñoz-Rivas
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - M.E. Cruz-Muñoz
- Laboratorio de Inmunología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - H.M. Mora-Montes
- Departamento de Biología, División de Ciencias Naturales y Exactas, Campus Guanajuato, Universidad de Guanajuato, Guanajuato 36050, Mexico
| | - R. Salinas-Marín
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
| | - C. Alaez-Verson
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Secretaría de Salud, Ciudad de México 14610, Mexico
| | - I. Martínez-Duncker
- Laboratorio de Glicobiología Humana y Diagnóstico Molecular, Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Mexico
- Corresponding author.
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5
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Crosstalk among Calcium ATPases: PMCA, SERCA and SPCA in Mental Diseases. Int J Mol Sci 2021; 22:ijms22062785. [PMID: 33801794 PMCID: PMC8000800 DOI: 10.3390/ijms22062785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Calcium in mammalian neurons is essential for developmental processes, neurotransmitter release, apoptosis, and signal transduction. Incorrectly processed Ca2+ signal is well-known to trigger a cascade of events leading to altered response to variety of stimuli and persistent accumulation of pathological changes at the molecular level. To counterbalance potentially detrimental consequences of Ca2+, neurons are equipped with sophisticated mechanisms that function to keep its concentration in a tightly regulated range. Calcium pumps belonging to the P-type family of ATPases: plasma membrane Ca2+-ATPase (PMCA), sarco/endoplasmic Ca2+-ATPase (SERCA) and secretory pathway Ca2+-ATPase (SPCA) are considered efficient line of defense against abnormal Ca2+ rises. However, their role is not limited only to Ca2+ transport, as they present tissue-specific functionality and unique sensitive to the regulation by the main calcium signal decoding protein—calmodulin (CaM). Based on the available literature, in this review we analyze the contribution of these three types of Ca2+-ATPases to neuropathology, with a special emphasis on mental diseases.
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6
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Gandini MA, Souza IA, Ferron L, Innes AM, Zamponi GW. The de novo CACNA1A pathogenic variant Y1384C associated with hemiplegic migraine, early onset cerebellar atrophy and developmental delay leads to a loss of Cav2.1 channel function. Mol Brain 2021; 14:27. [PMID: 33557884 PMCID: PMC7871581 DOI: 10.1186/s13041-021-00745-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
CACNA1A pathogenic variants have been linked to several neurological disorders including familial hemiplegic migraine and cerebellar conditions. More recently, de novo variants have been associated with severe early onset developmental encephalopathies. CACNA1A is highly expressed in the central nervous system and encodes the pore-forming CaVα1 subunit of P/Q-type (Cav2.1) calcium channels. We have previously identified a patient with a de novo missense mutation in CACNA1A (p.Y1384C), characterized by hemiplegic migraine, cerebellar atrophy and developmental delay. The mutation is located at the transmembrane S5 segment of the third domain. Functional analysis in two predominant splice variants of the neuronal Cav2.1 channel showed a significant loss of function in current density and changes in gating properties. Moreover, Y1384 variants exhibit differential splice variant-specific effects on recovery from inactivation. Finally, structural analysis revealed structural damage caused by the tyrosine substitution and changes in electrostatic potentials.
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Affiliation(s)
- Maria A Gandini
- Department of Physiology and Pharmacology, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ivana A Souza
- Department of Physiology and Pharmacology, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Laurent Ferron
- Department of Physiology and Pharmacology, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Gerald W Zamponi
- Department of Physiology and Pharmacology, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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7
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Rare CACNA1A mutations leading to congenital ataxia. Pflugers Arch 2020; 472:791-809. [DOI: 10.1007/s00424-020-02396-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/03/2023]
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Chen J, Sitsel A, Benoy V, Sepúlveda MR, Vangheluwe P. Primary Active Ca 2+ Transport Systems in Health and Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035113. [PMID: 31501194 DOI: 10.1101/cshperspect.a035113] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcium ions (Ca2+) are prominent cell signaling effectors that regulate a wide variety of cellular processes. Among the different players in Ca2+ homeostasis, primary active Ca2+ transporters are responsible for keeping low basal Ca2+ levels in the cytosol while establishing steep Ca2+ gradients across intracellular membranes or the plasma membrane. This review summarizes our current knowledge on the three types of primary active Ca2+-ATPases: the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) pumps, the secretory pathway Ca2+- ATPase (SPCA) isoforms, and the plasma membrane Ca2+-ATPase (PMCA) Ca2+-transporters. We first discuss the Ca2+ transport mechanism of SERCA1a, which serves as a reference to describe the Ca2+ transport of other Ca2+ pumps. We further highlight the common and unique features of each isoform and review their structure-function relationship, expression pattern, regulatory mechanisms, and specific physiological roles. Finally, we discuss the increasing genetic and in vivo evidence that links the dysfunction of specific Ca2+-ATPase isoforms to a broad range of human pathologies, and highlight emerging therapeutic strategies that target Ca2+ pumps.
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Affiliation(s)
- Jialin Chen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Aljona Sitsel
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Veronick Benoy
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - M Rosario Sepúlveda
- Department of Cell Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
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9
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Wang X, Shen X, Fang F, Ding CH, Zhang H, Cao ZH, An DY. Phenotype-Driven Virtual Panel Is an Effective Method to Analyze WES Data of Neurological Disease. Front Pharmacol 2019; 9:1529. [PMID: 30687093 PMCID: PMC6333749 DOI: 10.3389/fphar.2018.01529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 12/13/2018] [Indexed: 01/25/2023] Open
Abstract
Objective: Whole Exome Sequencing (WES) is an effective diagnostic method for complicated and multi-system involved rare diseases. However, annotation and analysis of the WES result, especially for single case analysis still remain a challenge. Here, we introduce a method called phenotype-driven designing "virtual panel" to simplify the procedure and assess the diagnostic rate of this method. Methods: WES was performed in samples of 30 patients, core phenotypes of probands were then extracted and inputted into an in-house software, "Mingjian" to calculate and generate associated gene list of a virtual panel. Mingjian is a self-updating genetic disease computer supportive diagnostic system that based on the databases of HPO, OMIM, HGMD. The virtual panel that generated by Mingjian system was then used to filter and annotate candidate mutations. Sanger sequencing and co-segregation analysis among the family were then used to confirm the filtered mutants. Result: We first used phenotype-driven designing "virtual panel" to analyze the WES data of a patient whose core phenotypes are ataxia, seizures, esotropia, puberty and gonadal disorders, and global developmental delay. Two mutations, c.430T > C and c.640G > C in PMM2 were identified by this method. This result was also confirmed by Sanger sequencing among the family. The same analysing method was then used in the annotation of WES data of other 29 neurological rare disease patients. The diagnostic rate was 65.52%, which is significantly higher than the diagnostic rate before. Conclusion: Phenotype-driven designing virtual panel could achieve low-cost individualized analysis. This method may decrease the time-cost of annotation, increase the diagnostic efficiency and the diagnostic rate.
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Affiliation(s)
- Xu Wang
- Department of Neurology, Beijing Children’s Hospital, National Centre for Children’s Health, Capital Medical University, Beijing, China
| | | | - Fang Fang
- Department of Neurology, Beijing Children’s Hospital, National Centre for Children’s Health, Capital Medical University, Beijing, China
| | - Chang-Hong Ding
- Department of Neurology, Beijing Children’s Hospital, National Centre for Children’s Health, Capital Medical University, Beijing, China
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10
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Vicario M, Zanni G, Vallese F, Santorelli F, Grinzato A, Cieri D, Berto P, Frizzarin M, Lopreiato R, Zonta F, Ferro S, Sandre M, Marin O, Ruzzene M, Bertini E, Zanotti G, Brini M, Calì T, Carafoli E. A V1143F mutation in the neuronal-enriched isoform 2 of the PMCA pump is linked with ataxia. Neurobiol Dis 2018; 115:157-166. [PMID: 29655659 DOI: 10.1016/j.nbd.2018.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/21/2018] [Accepted: 04/09/2018] [Indexed: 12/13/2022] Open
Abstract
The fine regulation of intracellular calcium is fundamental for all eukaryotic cells. In neurons, Ca2+ oscillations govern the synaptic development, the release of neurotransmitters and the expression of several genes. Alterations of Ca2+ homeostasis were found to play a pivotal role in neurodegenerative progression. The maintenance of proper Ca2+ signaling in neurons demands the continuous activity of Ca2+ pumps and exchangers to guarantee physiological cytosolic concentration of the cation. The plasma membrane Ca2+ATPases (PMCA pumps) play a key role in the regulation of Ca2+ handling in selected sub-plasma membrane microdomains. Among the four basic PMCA pump isoforms existing in mammals, isoforms 2 and 3 are particularly enriched in the nervous system. In humans, genetic mutations in the PMCA2 gene in association with cadherin 23 mutations have been linked to hearing loss phenotypes, while those occurring in the PMCA3 gene were associated with X-linked congenital cerebellar ataxias. Here we describe a novel missense mutation (V1143F) in the calmodulin binding domain (CaM-BD) of the PMCA2 protein. The mutant pump was present in a patient showing congenital cerebellar ataxia but no overt signs of deafness, in line with the absence of mutations in the cadherin 23 gene. Biochemical and molecular dynamics studies on the mutated PMCA2 have revealed that the V1143F substitution alters the binding of calmodulin to the CaM-BD leading to impaired Ca2+ ejection.
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Affiliation(s)
- Mattia Vicario
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Ginevra Zanni
- Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Vallese
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | | | - Alessandro Grinzato
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Domenico Cieri
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Paola Berto
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Martina Frizzarin
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Francesco Zonta
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China; Department of Biomedical Sciences, Institute of Cell Biology and Neurobiology, Italian National Research Council, 00015 Monterotondo, Rome, Italy
| | - Stefania Ferro
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Michele Sandre
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Maria Ruzzene
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Enrico Bertini
- Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giuseppe Zanotti
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Marisa Brini
- Department of Biology, University of Padova, Italy.
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; Padua Neuroscience Center (PNC), University of Padua, 35122 Padova, Italy.
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The PMCA pumps in genetically determined neuronal pathologies. Neurosci Lett 2018; 663:2-11. [DOI: 10.1016/j.neulet.2017.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 12/22/2022]
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