1
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Zhang J, Luo C, Long H. Sirtuin 5 regulates acute myeloid leukemia cell viability and apoptosis by succinylation modification of glycine decarboxylase. Open Life Sci 2024; 19:20220832. [PMID: 38585637 PMCID: PMC10997144 DOI: 10.1515/biol-2022-0832] [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: 09/20/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 04/09/2024] Open
Abstract
Acute myeloid leukemia (AML) is a blood system malignancy where sirtuin 5 (SIRT5) is abnormally expressed in AML cell lines. This study aimed to investigate the SIRT5 effects on the viability and apoptosis of AML cell lines. The mRNA and protein expression levels of succinylation regulatory enzyme in clinical samples and AML cell lines were detected by real-time quantitative polymerase chain reaction and western blotting while cell viability was measured using cell counting kit-8 assay. The apoptosis rate was assessed with flow cytometry. The interaction between SIRT5 and glycine decarboxylase (GLDC) was determined by co-immunoprecipitation and immunofluorescence staining techniques. Results indicated higher mRNA and protein expression levels of SIRT5 in clinical AML samples of AML than in normal subjects. Similarly, cell viability was inhibited, and apoptosis was promoted by downregulating SIRT5, in addition to inhibition of SIRT5-mediated GLDC succinylation. Moreover, rescue experiment results showed that GLDC reversed the effects of SIRT5 knockdown on cell viability and apoptosis. These results, in combination with SIRT5 and GLDC interactions, suggested that SIRT5 was involved in mediating AML development through GLDC succinylation. SIRT5 inhibits GLDC succinylation to promote viability and inhibit apoptosis of AML cells, suggesting that SIRT5 encourages the development of AML.
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Affiliation(s)
- Jun Zhang
- Department of Hematology, The Second Affiliated Hospital of Guizhou Medical University, No. 3, Kangfu Road, Kaili, Guizhou, 556000, China
| | - Cheng Luo
- Department of Hematology, The Second Affiliated Hospital of Guizhou Medical University, No. 3, Kangfu Road, Kaili, Guizhou, 556000, China
| | - Haiying Long
- Department of Hematology, The Second Affiliated Hospital of Guizhou Medical University, No. 3, Kangfu Road, Kaili, Guizhou, 556000, China
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2
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Arribas-Carreira L, Castro M, García F, Navarrete R, Bravo-Alonso I, Zafra F, Ugarte M, Richard E, Pérez B, Rodríguez-Pombo P. Metabolic Rewiring and Altered Glial Differentiation in an iPSC-Derived Astrocyte Model Derived from a Nonketotic Hyperglycinemia Patient. Int J Mol Sci 2024; 25:2814. [PMID: 38474060 DOI: 10.3390/ijms25052814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The pathophysiology of nonketotic hyperglycinemia (NKH), a rare neuro-metabolic disorder associated with severe brain malformations and life-threatening neurological manifestations, remains incompletely understood. Therefore, a valid human neural model is essential. We aimed to investigate the impact of GLDC gene variants, which cause NKH, on cellular fitness during the differentiation process of human induced pluripotent stem cells (iPSCs) into iPSC-derived astrocytes and to identify sustainable mechanisms capable of overcoming GLDC deficiency. We developed the GLDC27-FiPS4F-1 line and performed metabolomic, mRNA abundance, and protein analyses. This study showed that although GLDC27-FiPS4F-1 maintained the parental genetic profile, it underwent a metabolic switch to an altered serine-glycine-one-carbon metabolism with a coordinated cell growth and cell cycle proliferation response. We then differentiated the iPSCs into neural progenitor cells (NPCs) and astrocyte-lineage cells. Our analysis showed that GLDC-deficient NPCs had shifted towards a more heterogeneous astrocyte lineage with increased expression of the radial glial markers GFAP and GLAST and the neuronal markers MAP2 and NeuN. In addition, we detected changes in other genes related to serine and glycine metabolism and transport, all consistent with the need to maintain glycine at physiological levels. These findings improve our understanding of the pathology of nonketotic hyperglycinemia and offer new perspectives for therapeutic options.
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Affiliation(s)
- Laura Arribas-Carreira
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
| | - Margarita Castro
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Fernando García
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Rosa Navarrete
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Irene Bravo-Alonso
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Francisco Zafra
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Magdalena Ugarte
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Instituto de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), 28049 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, 28029 Madrid, Spain
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Huynh MT, Landais E, Agathe JMDS, Panchout A, Caroline DVDBL, Bruel H. Novel homozygous GLDC variant causing late-onset glycine encephalopathy: A case report and updated review of the literature. Mol Genet Metab Rep 2023; 34:100959. [PMID: 36817643 PMCID: PMC9932748 DOI: 10.1016/j.ymgmr.2023.100959] [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: 12/30/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Glycine encephalopathy (MIM #605899) is an autosomal recessive inborn error of metabolism caused by pathogenic variants in three genes GLDC, AMT, GCSH encoding glycine cleavage enzyme system. We report an 8-year-old boy with late-onset glycine encephalopathy who harbors a novel homozygous GLDC likely pathogenic variant c.707G > A p.(Arg236Gln). Polyhydramnios was noted at fetal ultrasound. He displayed global developmental delay, craniofacial dysmorphism, convulsions. Our report expands the phenotypic and genetic spectrum of late-onset nonketotic hyperglycinemia.
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Affiliation(s)
- Minh-Tuan Huynh
- Medical Genetics Department, Vinmec Times City International Hospital-Times City, HaNoi, Viet Nam
- Centre Hospitalier du Havre, Unité de Génétique Clinique, 29 Avenue Pierre Mendès-France, 76290 Montivilliers, France
- Corresponding author at: Medical Genetics Department, Vinmec Times City International Hospital-Times City, 458 Minh Khai, Hai Ba Trung District, VietNam.
| | - Emilie Landais
- Laboratoire de Génétique, CHRU de Reims, 45 rue Cognacq-Jay, 51092 Reims, France
| | | | - Anne Panchout
- Centre Hospitalier du Havre, Service de Gynécologie, 29 Avenue Pierre Mendès-France, 76290 Montivilliers, France
| | | | - Henri Bruel
- Centre Hospitalier du Havre, Service de Néonatologie, 29 Avenue Pierre Mendès-France, 76290 Montivilliers, France
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4
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Nonketotic Hyperglycinemia: Insight into Current Therapies. J Clin Med 2022; 11:jcm11113027. [PMID: 35683414 PMCID: PMC9181064 DOI: 10.3390/jcm11113027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 12/10/2022] Open
Abstract
Nonketotic hyperglycinemia (NKH) is a rare inborn error of glycine metabolism that is characterized by the accumulation of glycine in all tissues, especially in the central nervous system (CNS). Based on clinical outcomes, NKH can be divided into two forms, i.e., severe and attenuated NKH. A poor prognosis, including no developmental progress and intractable epilepsy, is typical of severe NKH, whereas patients with the attenuated form present with varied symptoms and neurodevelopmental outcomes. So far, no causal treatment of NKH is known. Currently, the therapy is based on sodium benzoate and NMDA (The N-methyl-D-aspartate receptor) receptor site antagonists (dextromethorphan, ketamine). Different clinical outcomes of the therapy raise doubts about the effectiveness of the treatment. The purpose of this review is to summarize the therapeutic potential, challenges and effectiveness of different NKH therapies.
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Zhou BB, Hui L, Zhang QH, Chen X, Zhang C, Zheng L, Feng X, Wang YP, Ding ZJ, Chen RR, Ma PP, Liu FR, Hao SJ. The Mutation Analysis of the AMT Gene in a Chinese Family With Nonketotic Hyperglycinemia. Front Genet 2022; 13:854712. [PMID: 35646099 PMCID: PMC9133660 DOI: 10.3389/fgene.2022.854712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Nonketotic hyperglycinemia is a metabolic disease with autosomal recessive inheritance due to the glycine cleavage system (GCS) defect leading to the accumulation of glycine that causes severe and fatal neurological symptoms in the neonatal period. Methods: Genomic DNA was extracted from the peripheral blood of the female proband and her family members. The AMT variation was detected in the patient by whole-exome sequencing (WES), and the variant was validated by Sanger sequencing. Results: The WES showed that there were novel compound heterozygous frameshift variations c.977delA (p.Glu326Glyfs*12) and c.982_983insG (p.Ala328Glyfs*22) in exon eight of the AMT gene (NM_000481.4) in the proband. Genetic analysis showed that the former was inherited from the mother, and the latter was inherited from the father. Conclusion: We report the novel compound heterozygous variation of the AMT gene in a Chinese girl with NKH by WES, which has never been reported previously. Our case expanded the AMT gene mutation spectrum, further strengthened the understanding of NKH, and deepened the genetic and clinical heterogeneity of the disease. However, the study of treatment and prognosis is still our future challenge and focus.
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Affiliation(s)
- Bing-bo Zhou
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Ling Hui
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Qing-hua Zhang
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Xue Chen
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Chuan Zhang
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Lei Zheng
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Xuan Feng
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Yu-pei Wang
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Zhong-jun Ding
- The Center for Reproductive Medicine in Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - Rui-rong Chen
- The Center for Medicine Imaging in Gansu Provincial Maternity and Child-care Hospital, Lanzhou, China
| | - Pan-pan Ma
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Fu-rong Liu
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
| | - Sheng-ju Hao
- The Center for Medical Genetics in Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou, China
- *Correspondence: Sheng-ju Hao,
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6
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Bayrak H, Yıldız Y, Olgaç A, Kasapkara ÇS, Küçükcongar A, Zenciroğlu A, Yüksel D, Ceylaner S, Kılıç M. Genotypic and phenotypic features in Turkish patients with classic nonketotic hyperglycinemia. Metab Brain Dis 2021; 36:1213-1222. [PMID: 33791923 DOI: 10.1007/s11011-021-00718-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Nonketotic hyperglycinemia is an autosomal recessive inborn error of glycine metabolism, characterized by deficient activity of the glycine cleavage enzyme system. Classic nonketotic hyperglycinemia is caused by mutations or genomic changes in genes that encode the protein components of the glycine cleavage enzyme system. We aimed to investigate clinical, biochemical, radiological findings and molecular genetic data in ten Turkish patients with classic nonketotic hyperglycinemia. Ten Turkish patients who were diagnosed with classic nonketotic hyperglycinemia in a single center from 2013 to 2019 were included in this study. Their clinical, radiological, electrophysiological and laboratory data were collected retrospectively. Sixty percent of the patients were in neonatal group, while 40 % of the patients were infantile. There were no late-onset patients. 90 % of the patients had the severe form. All patients had developmental delay and seizures. Mortality ratio was 30 % in all groups and 50 % in the neonatal group, while no mortality was seen in infantile group. Median (range) values of cerebrospinal fluid (CSF) glycine levels, plasma glycine levels and CSF/plasma glycine ratios were 148 (15-320) µmol/L, 896 (87-1910) µmol/L, 0.17 (0.09-0.21) respectively. Diffuse hypomyelination and corpus callosum anomaly were the most common cranial MRI findings and multifocal epileptic activity and burst supression pattern were the most common electroencephalographic findings. Six patients had variants in GLDC gene and four in AMT gene; five novel variants including AMT gene deletion were detected. Prognosis was poor and treatment was not effective, especially in the severe form. Classic nonketotic hyperglycinemia causes high morbidity and mortality. Neonatal-onset disease was more common and severe than infantile-onset disease. The ratio of AMT gene variants might be higher in Turkey than other countries. AMT gene deletion also plays a role in the etiology of classic nonketotic hyperglycinemia.
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Affiliation(s)
- Harun Bayrak
- Department of Pediatrics, Sami Ulus Children Hospital, Ankara, Turkey
| | - Yılmaz Yıldız
- Metabolism Unit, Sami Ulus Children Hospital, Babur cad. No: 44, Altındağ, Ankara, 06080, Turkey
| | - Asburçe Olgaç
- Metabolism Unit, Sami Ulus Children Hospital, Babur cad. No: 44, Altındağ, Ankara, 06080, Turkey
| | - Çiğdem Seher Kasapkara
- Metabolism Unit, Sami Ulus Children Hospital, Babur cad. No: 44, Altındağ, Ankara, 06080, Turkey
| | | | | | - Deniz Yüksel
- Neurology Unit, Sami Ulus Children Hospital, Ankara, Turkey
| | - Serdar Ceylaner
- Intergen, Genetic and Rare Disease Diagnosis and Research Center, Genetic Laboratory, Ankara, Turkey
| | - Mustafa Kılıç
- Metabolism Unit, Sami Ulus Children Hospital, Babur cad. No: 44, Altındağ, Ankara, 06080, Turkey.
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7
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Farris J, Alam MS, Rajashekara AM, Haldar K. Genomic analyses of glycine decarboxylase neurogenic mutations yield a large-scale prediction model for prenatal disease. PLoS Genet 2021; 17:e1009307. [PMID: 33524012 PMCID: PMC7850488 DOI: 10.1371/journal.pgen.1009307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/10/2020] [Indexed: 11/18/2022] Open
Abstract
Hundreds of mutations in a single gene result in rare diseases, but why mutations induce severe or attenuated states remains poorly understood. Defect in glycine decarboxylase (GLDC) causes Non-ketotic Hyperglycinemia (NKH), a neurological disease associated with elevation of plasma glycine. We unified a human multiparametric NKH mutation scale that separates severe from attenuated neurological disease with new in silico tools for murine and human genome level-analyses, gathered in vivo evidence from mice engineered with top-ranking attenuated and a highly pathogenic mutation, and integrated the data in a model of pre- and post-natal disease outcomes, relevant for over a hundred major and minor neurogenic mutations. Our findings suggest that highly severe neurogenic mutations predict fatal, prenatal disease that can be remedied by metabolic supplementation of dams, without amelioration of persistent plasma glycine. The work also provides a systems approach to identify functional consequences of mutations across hundreds of genetic diseases. Our studies provide a new framework for a large scale understanding of mutation functions and the prediction that severity of a neurogenic mutation is a direct measure of pre-natal disease in neurometabolic NKH mouse models. This framework can be extended to analyses of hundreds of monogenetic rare disorders where the underlying genes are known but understanding of the vast majority of mutations and why and how they cause disease, has yet to be realized. Building models of human genetic disease, both computational and animal, is an essential part of understanding the disease, designing treatments, and testing therapies. Here, we have developed new in silico tools to build models for the rare neurological disorder non-ketotic hyperglycinemia (NKH), which is caused by mutations in glycine decarboxylase (GLDC), a protein that degrades glycine. We first applied a mutation scoring tool to GLDC in both the human and mouse genomes, and then used this data to develop a computational model for predicting which mutations would be well-modeled in mice, and how severe their disease would be. We then validated this computational model by genetically-engineering a mutation predicted to cause mild disease and another predicted to cause severe disease. Our predictions were correct and we used them to develop a model relevant for over a hundred major and minor neurogenic mutations that suggests that the more severe the mutation, the greater chance it will cause disease that starts before birth and is likely to be fatal unless rescued by modifying diet. This study also demonstrates the power of in silico analyses for guiding the development of genetic disease models and incorporating them into scalable models that can be applied to understand hundreds of mutations that cause disease.
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Affiliation(s)
- Joseph Farris
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
| | - Md Suhail Alam
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
| | - Arpitha Mysore Rajashekara
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
| | - Kasturi Haldar
- Boler-Parseghian Center for Rare and Neglected Disease, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United State of America
- * E-mail:
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8
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Large scale analyses of genotype-phenotype relationships of glycine decarboxylase mutations and neurological disease severity. PLoS Comput Biol 2020; 16:e1007871. [PMID: 32421718 PMCID: PMC7259800 DOI: 10.1371/journal.pcbi.1007871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 04/13/2020] [Indexed: 12/14/2022] Open
Abstract
Monogenetic diseases provide unique opportunity for studying complex, clinical states that underlie neurological severity. Loss of glycine decarboxylase (GLDC) can severely impact neurological development as seen in non-ketotic hyperglycinemia (NKH). NKH is a neuro-metabolic disorder lacking quantitative predictors of disease states. It is characterized by elevation of glycine, seizures and failure to thrive, but glycine reduction often fails to confer neurological benefit, suggesting need for alternate tools to distinguish severe from attenuated disease. A major challenge has been that there are 255 unique disease-causing missense mutations in GLDC, of which 206 remain entirely uncharacterized. Here we report a Multiparametric Mutation Score (MMS) developed by combining in silico predictions of stability, evolutionary conservation and protein interaction models and suitable to assess 251 of 255 mutations. In addition, we created a quantitative scale of clinical disease severity comprising of four major disease domains (seizure, cognitive failure, muscular and motor control and brain-malformation) to comprehensively score patient symptoms identified in 131 clinical reports published over the last 15 years. The resulting patient Clinical Outcomes Scores (COS) were used to optimize the MMS for biological and clinical relevance and yield a patient Weighted Multiparametric Mutation Score (WMMS) that separates severe from attenuated neurological disease (p = 1.2 e-5). Our study provides understanding for developing quantitative tools to predict clinical severity of neurological disease and a clinical scale that advances monitoring disease progression needed to evaluate new treatments for NKH. Neurodegenerative disorders frequently have diverse, severe symptoms and health outcomes that can be difficult to predict. The rare disease non-ketotic hyperglycinemia (NKH) additionally has a wide range of disease-causing mutations in glycine decarboxylase (GLDC), a protein that breaks down glycine. But measuring glycine is not sufficient to foretell disease outcome. A method to predict whether a mutation will cause severe or more mild forms of NKH would be very helpful to both understanding the disease as well as developing treatments for it. We used computation-based approaches to develop a mutation score that comprehensively predicts how mutations decrease GLDC function. After training against clinical data, the score was able to predict whether a mutation will cause severe or attenuated disease. This study utilizes the power of computational and multidisciplinary analyses to advance understanding and treatment of genetically caused neurodegenerative diseases.
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Genes and Variants Underlying Human Congenital Lactic Acidosis-From Genetics to Personalized Treatment. J Clin Med 2019; 8:jcm8111811. [PMID: 31683770 PMCID: PMC6912785 DOI: 10.3390/jcm8111811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
Congenital lactic acidosis (CLA) is a rare condition in most instances due to a range of inborn errors of metabolism that result in defective mitochondrial function. Even though the implementation of next generation sequencing has been rapid, the diagnosis rate for this highly heterogeneous allelic condition remains low. The present work reports our group’s experience of using a clinical/biochemical analysis system in conjunction with genetic findings that facilitates the taking of timely clinical decisions with minimum need for invasive procedures. The system’s workflow combines different metabolomics datasets and phenotypic information with the results of clinical exome sequencing and/or RNA analysis. The system’s use detected genetic variants in 64% of a cohort of 39 CLA-patients; these variants, 14 of which were novel, were found in 19 different nuclear and two mitochondrial genes. For patients with variants of unknown significance, the genetic analysis was combined with functional genetic and/or bioenergetics analyses in an attempt to detect pathogenicity. Our results warranted subsequent testing of antisense therapy to rescue the abnormal splicing in cultures of fibroblasts from a patient with a defective GFM1 gene. The discussed system facilitates the diagnosis of CLA by avoiding the need to use invasive techniques and increase our knowledge of the causes of this condition.
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10
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Arribas-Carreira L, Bravo-Alonso I, López-Márquez A, Alonso-Barroso E, Briso-Montiano Á, Arroyo I, Ugarte M, Pérez B, Pérez-Cerdá C, Rodríguez-Pombo P, Richard E. Generation and characterization of a human iPSC line (UAMi005-A) from a patient with nonketotic hyperglycinemia due to mutations in the GLDC gene. Stem Cell Res 2019; 39:101503. [PMID: 31349202 DOI: 10.1016/j.scr.2019.101503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/05/2019] [Accepted: 07/14/2019] [Indexed: 01/07/2023] Open
Abstract
A human induced pluripotent stem cell (iPSC) line was generated from fibroblasts of a patient with nonketotic hyperglycinemia bearing the biallelic changes c.1742C > G (p.Pro581Arg) and c.2368C > T (p.Arg790Trp) in the GLDC gene. Reprogramming factors OCT3/4, SOX2, KLF4 and c-MYC were delivered using a non-integrative method based on the Sendai virus. Once established, iPSCs have shown full pluripotency, differentiation capacity and genetic stability. This cellular model provides a good resource for disease modeling and drug discovery.
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Affiliation(s)
- Laura Arribas-Carreira
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Irene Bravo-Alonso
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Arístides López-Márquez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | - Esmeralda Alonso-Barroso
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Álvaro Briso-Montiano
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Ignacio Arroyo
- Servicio de Neonatología, Hospital San Pedro de Alcántara, Cáceres, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Belén Pérez
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Celia Pérez-Cerdá
- Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain.
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain; Centro de Diagnóstico de Enfermedades Moleculares (CEDEM), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; Instituto de Investigación Sanitaria Hospital La Paz (IdiPaz), ISCIII, Madrid, Spain.
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Chen J, Li X, Niu Y, Wu Z, Qiu G. Functional and In Silico Assessment of GDF3 Gene Variants in a Chinese Congenital Scoliosis Population. Med Sci Monit 2018; 24:2992-3001. [PMID: 29735971 PMCID: PMC5978024 DOI: 10.12659/msm.910232] [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] [Indexed: 11/17/2022] Open
Abstract
Background The present study aimed to evaluate the pathogenicity of 5 GDF3 gene variations using functional and in silico assessment approaches in a Chinese congenital scoliosis population. Material/Methods We selected 13 patients carrying 5 variants from a congenital scoliosis cohort. The PCR products of samples were verified by Sanger sequencing. The data and sequence alignment were analyzed using Chromas and ClustalW. SIFT and PolyPhen-2 were used to predict the functional effects of each missense and amino acid substitutions. SWISS-MODEL server and Swiss-PdbViewer were used to analyze conformational changes of GDF3 structure. DUET, UCSF Chimera, and Ligplot software were used to further explore the protein stability, side chains, and hydrophobic interaction changes, respectively. Luciferase reporter gene and Western blot assays were used to perform functional assessments for every variant from the molecular level. Results Of the 13 patients, the S212L variant reoccurred in 9 patients. The rest of the patients carried 1 missense mutation each. The variants of R84L and R84C were predicted as probably damaging loci. S212L, N215S, A251T were predicted as benign loci. In functional assays, R84L, S212L, and A251T display inhibitory effects on functional assays. N251S mutation showed a negative effect in protein expression assays but not in luciferase reporter gene assays. The variant of R84C displayed no negative effects on 2 functional assays. Conclusions Our results suggest that the 4 of the 5 variants in GDF3 gene contribute different pathogenicity in congenital scoliosis, which may provide molecular evidence for clinical genetic testing.
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Affiliation(s)
- Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (mainland)
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research on Skeletal Deformity, Beijing, China (mainland)
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research on Skeletal Deformity, Beijing, China (mainland)
| | - Zhihong Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (mainland)
| | - Guixing Qiu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (mainland)
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12
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Lin Y, Zheng Z, Sun W, Fu Q. A novel compound heterozygous variant identified in GLDC gene in a Chinese family with non-ketotic hyperglycinemia. BMC MEDICAL GENETICS 2018; 19:5. [PMID: 29304759 PMCID: PMC5755286 DOI: 10.1186/s12881-017-0517-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/22/2017] [Indexed: 12/23/2022]
Abstract
Background Non-ketotic hyperglycinemia (NKH) is a rare, devastating autosomal recessive disorder of glycine metabolism with a very poor prognosis. Currently, few studies have reported genetic profiling of Chinese NKH patients. This study aimed to identify the genetic mutations in a Chinese family with NKH. Methods A Chinese family of Han ethnicity, with three siblings with NKH was studied. Sanger sequencing and multiplex ligation-dependent probe amplification combined with SYBR green real-time quantitative PCR was used to identify potential mutations in the GLDC, AMT and GCSH genes. The potential pathogenicity of the identified missense mutation was analyzed using SIFT, PolyPhen-2, PROVEAN and MutationTaster software. Results All patients exhibited severe and progressive clinical symptoms, including lethargy, hypotonia and seizures, and had greatly elevated glycine levels in their plasma and CSF. Molecular genetic analysis identified compound heterozygous variants in the GLDC gene in these three siblings, including a novel missense variant c.2680A > G (p.Thr894Ala) in exon 23 and a heterozygous deletion of exon 3, which were inherited respectively from their parents. In silico analysis, using several different types of bioinformatic software, predicted that the novel variant c.2680A > G in the GLDC gene was pathogenic. Moreover, the deletion of exon 3 was identified for the first time in a Chinese population. Conclusions A novel missense variant and a previously reported deletion in GLDC gene were identified. The two variants of GLDC gene identified probably underlie the pathogenesis of non-ketotic hyperglycinemia in this family, and also enrich the mutational spectrum of GLDC gene. Electronic supplementary material The online version of this article (10.1186/s12881-017-0517-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiming Lin
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Zhenzhu Zheng
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China
| | - Wenjia Sun
- Genuine Diagnostics Company Limited, 859 Shixiang West Road, Hangzhou, Zhejiang Province, 310007, China.
| | - Qingliu Fu
- Neonatal Disease Screening Center of Quanzhou, Quanzhou Women's and Children's Hospital, 700 Fengze Street, Quanzhou, Fujian Province, 362000, China.
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