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Tayebi N, Lichtenberg J, Hertz E, Sidransky E. Is Gauchian genotyping of GBA1 variants reliable? Commun Biol 2025; 8:718. [PMID: 40346301 PMCID: PMC12064688 DOI: 10.1038/s42003-025-08059-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/08/2025] [Indexed: 05/11/2025] Open
Affiliation(s)
- Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Jens Lichtenberg
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen Hertz
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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2
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Tayebi N, Lichtenberg J, Hertz E, Sidransky E. Is Gauchian genotyping of GBA1 variants reliable? MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.26.23297627. [PMID: 37986861 PMCID: PMC10659459 DOI: 10.1101/2023.10.26.23297627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Biallelic mutations in GBA1 result in Gaucher disease (GD), the inherited deficiency of glucocerebrosidase. Variants in GBA1 are also a common genetic risk factor for Parkinson disease (PD). Currently, some PD centers screen for mutant GBA1 alleles to stratify patients who may ultimately benefit from GBA1-targeted therapeutics. However, accurately detecting variants, especially recombinant alleles resulting from a crossover between GBA1 and its pseudogene, is challenging, impacting studies of both GD and GBA1-associated parkinsonism. Recently, the software tool Gauchian was introduced to identify GBA1 variants from whole genome sequencing. We evaluated Gauchian in 90 Sanger-sequenced patients with GD and five GBA1 heterozygotes. While Gauchian genotyped most patients correctly, it missed some rare or de novo mutations due to its limited internal database and over-reliance on intergenic structural variants. This resulted in misreported homozygosity, incomplete genotypes, and undetected recombination events, limiting Gauchian's utility in variant screening and precluding its use in diagnostics.
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Affiliation(s)
- Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Jens Lichtenberg
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Ellen Hertz
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
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3
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Wu YC, Chen CI, Chen PY, Kuo CH, Hung YH, Peng KY, Wu VC, Tsai-Wu JJ, Hsu CL, TAIPAI group. GRAde: a long-read sequencing approach to efficiently identifying the CYP11B1/CYP11B2 chimeric form in patients with glucocorticoid-remediable aldosteronism. BMC Bioinformatics 2022; 22:613. [PMID: 35012455 PMCID: PMC8750845 DOI: 10.1186/s12859-022-04561-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glucocorticoid-remediable aldosteronism (GRA) is a form of heritable hypertension caused by a chimeric fusion resulting from unequal crossing over between 11β-hydroxylase (CYP11B1) and aldosterone synthase (CYP11B2), which are two genes with similar sequences. Different crossover patterns of the CYP11B1 and CYP11B2 chimeric genes may be associated with a variety of clinical presentations. It is therefore necessary to develop an efficient approach for identifying the differences between the hybrid genes of a patient with GRA. RESULTS We developed a long-read analysis pipeline named GRAde (GRA deciphering), which utilizes the nonidentical bases in the CYP11B1 and CYP11B2 genomic sequences to identify and visualize the chimeric form. We sequenced the polymerase chain reaction (PCR) products of the CYP11B1/CYP11B2 chimeric gene from 36 patients with GRA using the Nanopore MinION device and analyzed the sequences using GRAde. Crossover events were identified for 30 out of the 36 samples. The crossover sites appeared in the region exhibiting high sequence similarity between CYP11B1 and CYP11B2, and 53.3% of the cases were identified as having a gene conversion in intron 2. More importantly, there were six cases for whom the PCR products indicated a chimeric gene, but the GRAde results revealed no crossover pattern. The crossover regions were further verified by Sanger sequencing analysis. CONCLUSIONS PCR-based target enrichment followed by long-read sequencing is an efficient and precise approach to dissecting complex genomic regions, such as those involved in GRA mutations, which could be directly applied to clinical diagnosis. The scripts of GRAde are available at https://github.com/hsu-binfo/GRAde .
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Affiliation(s)
- Yu-Ching Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-I Chen
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Peng-Ying Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Hung Kuo
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hsuan Hung
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Kang-Yung Peng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Vin-Cent Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Jyy-Jih Tsai-Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - TAIPAI group
- TAIPAI, Taiwan Primary Aldosteronism Investigator Group and TSA, Taiwan Society of Aldosteronism, Taipei, Taiwan
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4
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Woo EG, Tayebi N, Sidransky E. Next-Generation Sequencing Analysis of GBA1: The Challenge of Detecting Complex Recombinant Alleles. Front Genet 2021; 12:684067. [PMID: 34234814 PMCID: PMC8255797 DOI: 10.3389/fgene.2021.684067] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/27/2021] [Indexed: 01/23/2023] Open
Affiliation(s)
- Elizabeth G Woo
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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5
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Ju AP, Jiang F, Li J, Tang XW, Li DZ. Detection of an α-Globin Fusion Gene Using Real-Time Polymerase Chain Reaction-Based Multicolor Melting Curve. Hemoglobin 2020; 44:427-431. [PMID: 33148073 DOI: 10.1080/03630269.2020.1838923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Genetic recombination between homologous sequences on the human globin gene clusters can lead to the creation of fusion genes. In this study, we report the detection of an α-globin fusion gene by using real-time polymerase chain reaction (qPCR)-based multicolor melting curve analysis (MMCA). The carriers of this fusion gene had a mild α-thalassemia phenotype with a normal hemoglobin (Hb) value and borderline hematological indices. Sequence analysis revealed that the mutant gene was the result of a fusion between the α2 and ψα1 genes. Our results indicate that the MMCA has the ability to detect the fusion gene, which is helpful for genetic counseling in thalassemia prevalent areas.
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Affiliation(s)
- Ai-Ping Ju
- Clinical Laboratory, Huadu District Maternal and Neonatal Healthcare Hospital of Guangzhou, Hu Zhong Hospital, Guangzhou, People's Republic of China
| | - Fan Jiang
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Jian Li
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Xue-Wei Tang
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University, Guangzhou, People's Republic of China
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6
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Wolf P, Alcalay RN, Liong C, Cullen E, Pauciulo MW, Nichols WC, Gan-Or Z, Chung WK, Faulkner T, Bentis C, Pomponio RJ, Ma X, Kate Zhang X, Keutzer JM, Oliva P. Tandem mass spectrometry assay of β-glucocerebrosidase activity in dried blood spots eliminates false positives detected in fluorescence assay. Mol Genet Metab 2018; 123:135-139. [PMID: 29100779 PMCID: PMC5808899 DOI: 10.1016/j.ymgme.2017.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/19/2017] [Accepted: 10/19/2017] [Indexed: 12/23/2022]
Abstract
Deficiency of β-Glucocerebrosidase (GBA) activity causes Gaucher Disease (GD). GD can be diagnosed by measuring GBA activity (Beutler and Kuhl, 1990). In this study, we assayed dried blood spots from a cohort (n=528) enriched for GBA mutation carriers (n=78) and GD patients (n=18) using both the tandem mass spectrometry (MS/MS) and fluorescence assays and their respective synthetic substrates. The MS/MS assay differentiated normal controls, which included GBA mutation carriers, from GD patients with no overlap. The fluorescence assay did not always differentiate normal controls including GBA mutation carriers from GD patients and false positives were observed. The MS/MS assay improved specificity compared to the fluorescence assay.
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Affiliation(s)
- Pavlina Wolf
- Sanofi, P. O. Box 9322, Framingham, MA 01701, USA
| | - Roy N Alcalay
- Columbia University Medical Center, Neurological Institute, 710 West, 168th street, New York, NY 10032, USA
| | - Christopher Liong
- Columbia University Medical Center, Neurological Institute, 710 West, 168th street, New York, NY 10032, USA
| | - Emmaline Cullen
- Sanofi, P. O. Box 9322, Framingham, MA 01701, USA; Great Ormond Street Hospital for Children, NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ziv Gan-Or
- Department of Neurology & Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | | | | | | | - Xiwen Ma
- Sanofi, P. O. Box 9322, Framingham, MA 01701, USA
| | - X Kate Zhang
- Sanofi, P. O. Box 9322, Framingham, MA 01701, USA
| | | | - Petra Oliva
- Sanofi, P. O. Box 9322, Framingham, MA 01701, USA.
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7
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Zampieri S, Cattarossi S, Bembi B, Dardis A. GBA Analysis in Next-Generation Era: Pitfalls, Challenges, and Possible Solutions. J Mol Diagn 2017; 19:733-741. [PMID: 28727984 DOI: 10.1016/j.jmoldx.2017.05.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 01/11/2023] Open
Abstract
Mutations in the gene encoding the lysosomal enzyme acid β-glucosidase (GBA) are responsible for Gaucher disease and represent the main genetic risk factor for developing Parkinson disease. In past years, next-generation sequencing (NGS) technology has been applied for the molecular analysis of the GBA gene, both as a single gene or as part of gene panels. However, the presence of complex gene-pseudogene rearrangements, resulting from the presence of a highly homologous pseudogene (GBAP1) located downstream of the GBA gene, makes NGS analysis of GBA challenging. Therefore, adequate strategies should be adopted to avoid misdetection of GBA recombinant mutations. Here, we validated a strategy for the identification of GBA mutations using parallel massive sequencing and provide an overview of the major drawbacks encountered during GBA analysis by NGS. We implemented a NGS workflow, using a set of 38 patients with Gaucher disease carrying different GBA alleles identified previously by Sanger sequencing. As expected, the presence of the pseudogene significantly affected data output. However, the combination of specific procedures for the library preparation and data analysis resulted in maximal repeatability and reproducibility, and a robust performance with 97% sensitivity and 100% specificity. In conclusion, the pipeline described here represents a useful approach to deal with GBA sequencing using NGS technology.
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Affiliation(s)
- Stefania Zampieri
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Silvia Cattarossi
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Bruno Bembi
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, Academic Hospital Santa Maria della Misericordia, Udine, Italy.
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8
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El-Beshlawy A, Tylki-Szymanska A, Vellodi A, Belmatoug N, Grabowski GA, Kolodny EH, Batista JL, Cox GF, Mistry PK. Long-term hematological, visceral, and growth outcomes in children with Gaucher disease type 3 treated with imiglucerase in the International Collaborative Gaucher Group Gaucher Registry. Mol Genet Metab 2017; 120:47-56. [PMID: 28040394 DOI: 10.1016/j.ymgme.2016.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 12/21/2022]
Abstract
In Gaucher disease (GD), deficiency of lysosomal acid β-glucosidase results in a broad phenotypic spectrum that is classified into three types based on the absence (type 1 [GD1]) or presence and severity of primary central nervous system involvement (type 2 [GD2], the fulminant neuronopathic form, and type 3 [GD3], the milder chronic neuronopathic form). Enzyme replacement therapy (ERT) with imiglucerase ameliorates and prevents hematological and visceral manifestations in GD1, but data in GD3 are limited to small, single-center series. The effects of imiglucerase ERT on hematological, visceral and growth outcomes (note: ERT is not expected to directly impact neurologic outcomes) were evaluated during the first 5years of treatment in 253 children and adolescents (<18years of age) with GD3 enrolled in the International Collaborative Gaucher Group (ICGG) Gaucher Registry. The vast majority of GBA mutations in this diverse global population consisted of only 2 mutations: L444P (77%) and D409H (7%). At baseline, GD3 patients exhibited early onset of severe hematological and visceral disease and growth failure. During the first year of imiglucerase treatment, hemoglobin levels and platelet counts increased and liver and spleen volumes decreased, leading to marked decreases in the number of patients with moderate or severe anemia, thrombocytopenia, and hepatosplenomegaly. These improvements were maintained through Year 5. There was also acceleration in linear growth as evidenced by increasing height Z-scores. Despite devastating disease at baseline, the probability of surviving for at least 5years after starting imiglucerase was 92%. In this large, multinational cohort of pediatric GD3 patients, imiglucerase ERT provided a life-saving and life-prolonging benefit for patients with GD3, suggesting that, with proper treatment, many such severely affected patients can lead productive lives and contribute to society.
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Affiliation(s)
| | | | - Ashok Vellodi
- Great Ormond Street Children's Hospital NHS Foundation Trust, London, UK
| | - Nadia Belmatoug
- Referral Center for Lysosomal Diseases, University Hospital Paris Nord-Val de Seine Assistance Publique-Hôpitaux de Paris, France
| | - Gregory A Grabowski
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | | | - Julie L Batista
- Biostatistics/Epidemiology, Sanofi Genzyme, Cambridge, MA, USA
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9
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Amico G, Grossi S, Vijzelaar R, Lanza F, Mazzotti R, Corsolini F, Ketema M, Filocamo M. MLPA-based approach for initial and simultaneous detection of GBA deletions and recombinant alleles in patients affected by Gaucher Disease. Mol Genet Metab 2016; 119:329-337. [PMID: 27802905 DOI: 10.1016/j.ymgme.2016.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/24/2016] [Accepted: 10/24/2016] [Indexed: 11/23/2022]
Abstract
The chromosomal region, in which the GBA gene is located, is structurally subject to misalignments, reciprocal and nonreciprocal homologous recombination events, leading to structural defects such as deletions, duplications and gene-pseudogene complex rearrangements causing Gaucher Disease (GD). Interestingly deletions and duplications, belonging to the heterogeneous group of structural defects collectively termed Copy Number Variations (CNVs), together with gene-pseudogene complex rearrangements represent the main cause of pitfalls in GD mutational analysis. In the present study, we set up and validate a Multiplex Ligation-dependent Probe Amplification (MLPA)-based approach to simultaneously investigate the potential occurrence of CNVs and complex rearrangements in 8 unrelated GD patients who had still not-well-characterized or uncharacterized alleles. The findings allowed us to complete the mutational analysis in 4 patients, identifying a rare deletion (g.-3100_+834del3934) and 2 novel recombinant alleles (g.4356_7031conJ03060.1:g.2544_4568; g.1942_7319conJ03060.1:g.1092_4856). These results demonstrate the diagnostic usefulness of MLPA in the detection of GBA deletions and recombinations. In addition, MLPA findings have also served as a basis for developing molecular approaches to precisely pinpoint the breakpoints and characterize the underlying mechanism of copy number variations.
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Affiliation(s)
- Giulia Amico
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Serena Grossi
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Raymon Vijzelaar
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands.
| | - Federica Lanza
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Raffaella Mazzotti
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Fabio Corsolini
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
| | - Mirjam Ketema
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands.
| | - Mirella Filocamo
- Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto G. Gaslini, Via Gaslini 5, 16147 Genova, Italy.
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10
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Dandana A, Ben Khelifa S, Chahed H, Miled A, Ferchichi S. Gaucher Disease: Clinical, Biological and Therapeutic Aspects. Pathobiology 2015; 83:13-23. [PMID: 26588331 DOI: 10.1159/000440865] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 09/02/2015] [Indexed: 11/19/2022] Open
Abstract
We present a brief review of Gaucher disease (GD), the most common lysosomal storage disease. GD is a rare autosomal recessive disorder characterized by the defective function of the catabolic enzyme β-glucocerebrosidase (GBA), leading to an accumulation of its substrate, glucocerebroside. Clinical signs and symptoms include neurological dysfunctions, bone infarcts and malformations, hepatosplenomegaly and hypersplenism leading to anemia, neutropenia and thrombocytopenia. Enzyme replacement therapy with recombinant GBA is the mainstay of treatment for GD, which became the first successfully managed lipid storage disease. Future treatments may include oral enzyme replacement and/or gene therapy interventions.
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Affiliation(s)
- Azza Dandana
- Laboratory of Biochemistry, Farhat Hached Hospital, Sousse, Tunisia
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11
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Wang X, Mitra N, Cruz P, Deng L, Varki N, Angata T, Green ED, Mullikin J, Hayakawa T, Varki A. Evolution of siglec-11 and siglec-16 genes in hominins. Mol Biol Evol 2012; 29:2073-86. [PMID: 22383531 DOI: 10.1093/molbev/mss077] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We previously reported a human-specific gene conversion of SIGLEC11 by an adjacent paralogous pseudogene (SIGLEC16P), generating a uniquely human form of the Siglec-11 protein, which is expressed in the human brain. Here, we show that Siglec-11 is expressed exclusively in microglia in all human brains studied-a finding of potential relevance to brain evolution, as microglia modulate neuronal survival, and Siglec-11 recruits SHP-1, a tyrosine phosphatase that modulates microglial biology. Following the recent finding of a functional SIGLEC16 allele in human populations, further analysis of the human SIGLEC11 and SIGLEC16/P sequences revealed an unusual series of gene conversion events between two loci. Two tandem and likely simultaneous gene conversions occurred from SIGLEC16P to SIGLEC11 with a potentially deleterious intervening short segment happening to be excluded. One of the conversion events also changed the 5' untranslated sequence, altering predicted transcription factor binding sites. Both of the gene conversions have been dated to ~1-1.2 Ma, after the emergence of the genus Homo, but prior to the emergence of the common ancestor of Denisovans and modern humans about 800,000 years ago, thus suggesting involvement in later stages of hominin brain evolution. In keeping with this, recombinant soluble Siglec-11 binds ligands in the human brain. We also address a second-round more recent gene conversion from SIGLEC11 to SIGLEC16, with the latter showing an allele frequency of ~0.1-0.3 in a worldwide population study. Initial pseudogenization of SIGLEC16 was estimated to occur at least 3 Ma, which thus preceded the gene conversion of SIGLEC11 by SIGLEC16P. As gene conversion usually disrupts the converted gene, the fact that ORFs of hSIGLEC11 and hSIGLEC16 have been maintained after an unusual series of very complex gene conversion events suggests that these events may have been subject to hominin-specific selection forces.
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Affiliation(s)
- Xiaoxia Wang
- Glycobiology Research and Training Center, University of California at San Diego, San Diego, CA, USA
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12
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Hruska KS, LaMarca ME, Scott CR, Sidransky E. Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene (GBA). Hum Mutat 2008; 29:567-83. [DOI: 10.1002/humu.20676] [Citation(s) in RCA: 463] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Erdos M, Hodanova K, Taskó S, Palicz A, Stolnaja L, Dvorakova L, Hrebicek M, Maródi L. Genetic and clinical features of patients with Gaucher disease in Hungary. Blood Cells Mol Dis 2007; 39:119-23. [PMID: 17395504 DOI: 10.1016/j.bcmd.2007.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2007] [Revised: 02/15/2007] [Accepted: 02/15/2007] [Indexed: 11/29/2022]
Abstract
The aim of this study was to identify mutations in the gene encoding for lysosomal beta-glucocerebrosidase (GBA; gene symbol, GBA) in Hungarian patients with Gaucher disease (GD), and to study genotype-phenotype relationships. Genotypes and allele variations in 27 patients with type I GD of 25 unrelated families were studied. Of the 54 mutant alleles, we detected 38 frequent (N370S, 22/54; RecNciI, 8/54; L444P, 8/54) and 9 rare (N188S, R257Q, R285C, G377S, R120W, T323I, 84GG, 1263-1317del and 1263-1317del/RecTL) mutations. In addition, we identified two novel mutations. The N370S/RecNciI genotype found in 8 patients and the N370S/L444P genotype found in 5 patients were the most frequent genotypes in this cohort. In 22 patients the mutations occurred in heterozygosity with the N370S sequence variant, and one patient was homozygous for the L444P mutation. These data suggest that N370S, RecNciI, and L444P are the most prevalent mutations in Hungarian patients with GD. This mutation profile is characteristic for a Caucasian (non-Jewish) population. The c.260G>A and c.999G>A missense mutations are described here for the first time in GD patients contributing to the panel of reported GBA mutations.
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Affiliation(s)
- Melinda Erdos
- Department of Infectious and Pediatric Immunology, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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14
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Beutler E, Gelbart T, Scott CR. Hematologically important mutations: Gaucher disease. Blood Cells Mol Dis 2005; 35:355-64. [PMID: 16185900 DOI: 10.1016/j.bcmd.2005.07.005] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2005] [Accepted: 07/12/2005] [Indexed: 11/22/2022]
Affiliation(s)
- Ernest Beutler
- The Scripps Research Institute, Department of Molecular and Experimental Medicine, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Filocamo M, Grossi S, Stroppiano M, Tortori-Donati P, Regis S, Allegri A, Di Rocco M. Homozygosity for a non-pseudogene complex glucocerebrosidase allele as cause of an atypical neuronopathic form of Gaucher disease. Am J Med Genet A 2005; 134A:95-6. [PMID: 15690354 DOI: 10.1002/ajmg.a.30316] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zhao H, Keddache M, Bailey L, Arnold G, Grabowski G. Gaucher's disease: identification of novel mutant alleles and genotype-phenotype relationships. Clin Genet 2003; 64:57-64. [PMID: 12791040 DOI: 10.1034/j.1399-0004.2003.00100.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A sequencing protocol for the acid beta-glucosidase (GCase) gene (GBA) was developed using a long-range PCR template. This protocol has an advantage of greater DNA yields over similar strategies. Seven Gaucher's disease patients had four novel and five other rare alleles. A non-pseudogene in-frame deletion (g.2600-2602delTAC) and a new complex mutation (null allele) were identified in Gaucher's disease type 1, i.e. the g.2600-2602delTAC deletion is associated with the non-neuronopathic variant. An F251L allele was found in a baby with the collodion skin phenotype. Three mutant alleles were identified in a single primary family with type 3. The patients' father at 45 years is healthy and is heteroallelic for the G202R and E326K alleles. Family studies indicated that E326K is in trans to G202R and L444P, and that isolated E326K is non-pathogenic in this family. A rare mutation R257Q was identified in a type 2 patient, providing an association with neuronopathic disease. A genotype L444P/L444P was noted in a 22-year-old non-neuronopathic patient. Complete gene sequencing showed a new complex allele consisting of L444P and g.7741T > C in the 3' UTR. Three additional complex alleles also involved the 3' UTR. Complete gene characterization in Gaucher's disease should allow greater insights into the correlation of specific alleles with phenotype.
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Affiliation(s)
- H Zhao
- Division of Human Genetics, Children's Hospital Research Foundation, Cincinnati, OH 45229-3039, USA
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Wu G, Yan S. Determination of amino acid pairs sensitive to variants in human beta-glucocerebrosidase by means of a random approach. Protein Eng Des Sel 2003; 16:195-9. [PMID: 12702799 DOI: 10.1093/proeng/gzg023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this data-based theoretical analysis, we use the random approach to analyse the amino acid pairs in human beta-glucocerebrosidase in order to determine which amino acid pairs are more sensitive to 109 variants from missense mutant human glucocerebrosidase. The rationale of this study is based on our hypothesis and findings that the harmful variants are more likely to occur at randomly unpredictable amino acid pairs and the non-harmful variants are more likely to occur at randomly predictable amino acid pairs. This is because we argue that the randomly predictable amino acid pairs should not be deliberately evolved, whereas the randomly unpredictable amino acid pairs should be deliberately evolved with connection of protein function. The results show, for example, that 93.58% of 109 variants occur at randomly unpredictable amino acid pairs, which account for 71.40% of amino acid pairs in glucocerebrosidase, and the chance of occurrence of the variant is about 4.4 times higher in randomly unpredictable amino acid pairs than in predictable pairs. Hence the randomly unpredictable amino acid pairs are more sensitive to variants in human glucocerebrosidase. The results also suggest that human glucocerebrosidase has a natural tendency to variants.
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Affiliation(s)
- Guang Wu
- Laboratoire de Toxicocinétique et Pharmacocinétique, Faculté de Pharmacie, Université de la Méditerranée Aix-Marseille II, Marseille, France.
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Tayebi N, Stubblefield BK, Park JK, Orvisky E, Walker JM, LaMarca ME, Sidransky E. Reciprocal and nonreciprocal recombination at the glucocerebrosidase gene region: implications for complexity in Gaucher disease. Am J Hum Genet 2003; 72:519-34. [PMID: 12587096 PMCID: PMC1180228 DOI: 10.1086/367850] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Accepted: 11/26/2002] [Indexed: 11/03/2022] Open
Abstract
Gaucher disease results from an autosomal recessive deficiency of the lysosomal enzyme glucocerebrosidase. The glucocerebrosidase gene is located in a gene-rich region of 1q21 that contains six genes and two pseudogenes within 75 kb. The presence of contiguous, highly homologous pseudogenes for both glucocerebrosidase and metaxin at the locus increases the likelihood of DNA rearrangements in this region. These recombinations can complicate genotyping in patients with Gaucher disease and contribute to the difficulty in interpreting genotype-phenotype correlations in this disorder. In the present study, DNA samples from 240 patients with Gaucher disease were examined using several complementary approaches to identify and characterize recombinant alleles, including direct sequencing, long-template polymerase chain reaction, polymorphic microsatellite repeats, and Southern blots. Among the 480 alleles studied, 59 recombinant alleles were identified, including 34 gene conversions, 18 fusions, and 7 downstream duplications. Twenty-two percent of the patients evaluated had at least one recombinant allele. Twenty-six recombinant alleles were found among 310 alleles from patients with type 1 disease, 18 among 74 alleles from patients with type 2 disease, and 15 among 96 alleles from patients with type 3 disease. Several patients carried two recombinations or mutations on the same allele. Generally, alleles resulting from nonreciprocal recombination (gene conversion) could be distinguished from those arising by reciprocal recombination (crossover and exchange), and the length of the converted sequence was determined. Homozygosity for a recombinant allele was associated with early lethality. Ten different sites of crossover and a shared pentamer motif sequence (CACCA) that could be a hotspot for recombination were identified. These findings contribute to a better understanding of genotype-phenotype relationships in Gaucher disease and may provide insights into the mechanisms of DNA rearrangement in other disorders.
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Affiliation(s)
- Nahid Tayebi
- Clinical Neuroscience Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
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Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002; 298:1912-34. [PMID: 12471243 DOI: 10.1126/science.1075762] [Citation(s) in RCA: 5932] [Impact Index Per Article: 257.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.
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Affiliation(s)
- G Manning
- SUGEN Inc., 230 East Grand Avenue, South San Francisco, CA 94080, USA.
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