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Yang F, Xu S, Huang C, Shao Z, Hu Y, Yang Yang, Lai Y, Ke Q, Liang D, Wu Y. Therapeutic genome editing of an aberrant splice site in β-thalassemia by CRISPR/Cas9 with multiple sgRNAs. Genes Dis 2024; 11:15-18. [PMID: 37588192 PMCID: PMC10425742 DOI: 10.1016/j.gendis.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/07/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Fei Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- BRL Medicine Inc., Shanghai 201108, China
| | - Shuqian Xu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Chao Huang
- BRL Medicine Inc., Shanghai 201108, China
| | | | - Yuefen Hu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Yang Yang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530000, China
| | - Yongrong Lai
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530000, China
| | - Qing Ke
- Department of Neurology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China
| | - Dan Liang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui 230032, China
| | - Yuxuan Wu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- BRL Medicine Inc., Shanghai 201108, China
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Walker AJ, Graham C, Greenwood M, Woodall M, Maeshima R, O’Hara-Wright M, Sanz DJ, Guerrini I, Aldossary AM, O’Callaghan C, Baines DL, Harrison PT, Hart SL. Molecular and functional correction of a deep intronic splicing mutation in CFTR by CRISPR-Cas9 gene editing. Mol Ther Methods Clin Dev 2023; 31:101140. [PMID: 38027060 PMCID: PMC10661860 DOI: 10.1016/j.omtm.2023.101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/17/2023] [Indexed: 12/01/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CFTR gene. The 10th most common mutation, c.3178-2477C>T (3849+10kb C>T), involves a cryptic, intronic splice site. This mutation was corrected in CF primary cells homozygous for this mutation by delivering pairs of guide RNAs (gRNAs) with Cas9 protein in ribonucleoprotein (RNP) complexes that introduce double-strand breaks to flanking sites to excise the 3849+10kb C>T mutation, followed by DNA repair by the non-homologous end-joining pathway, which functions in all cells of the airway epithelium. RNP complexes were delivered to CF basal epithelial cell by a non-viral, receptor-targeted nanocomplex comprising a formulation of targeting peptides and lipids. Canonical CFTR mRNA splicing was, thus, restored leading to the restoration of CFTR protein expression with concomitant restoration of electrophysiological function in airway epithelial air-liquid interface cultures. Off-target editing was not detected by Sanger sequencing of in silico-selected genomic sites with the highest sequence similarities to the gRNAs, although more sensitive unbiased whole genome sequencing methods would be required for possible translational developments. This approach could potentially be used to correct aberrant splicing signals in several other CF mutations and other genetic disorders where deep-intronic mutations are pathogenic.
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Affiliation(s)
- Amy J. Walker
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Carina Graham
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Miriam Greenwood
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Maximillian Woodall
- Institute for Infection and Immunity, St. George’s, University of London, London, UK
| | - Ruhina Maeshima
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Michelle O’Hara-Wright
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - David J. Sanz
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Ileana Guerrini
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Ahmad M. Aldossary
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Christopher O’Callaghan
- Infection, Immunity & Inflammation Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Deborah L. Baines
- Institute for Infection and Immunity, St. George’s, University of London, London, UK
| | - Patrick T. Harrison
- Department of Physiology, BioSciences Institute, University College Cork, Cork, Ireland
| | - Stephen L. Hart
- Genetics and Genomic Medicine Department, UCL Great Ormond Street Institute of Child Health, London, UK
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Paschoudi K, Yannaki E, Psatha N. Precision Editing as a Therapeutic Approach for β-Hemoglobinopathies. Int J Mol Sci 2023; 24:ijms24119527. [PMID: 37298481 DOI: 10.3390/ijms24119527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Beta-hemoglobinopathies are the most common genetic disorders worldwide, caused by a wide spectrum of mutations in the β-globin locus, and associated with morbidity and early mortality in case of patient non-adherence to supportive treatment. Allogeneic transplantation of hematopoietic stem cells (allo-HSCT) used to be the only curative option, although the indispensable need for an HLA-matched donor markedly restricted its universal application. The evolution of gene therapy approaches made possible the ex vivo delivery of a therapeutic β- or γ- globin gene into patient-derived hematopoietic stem cells followed by the transplantation of corrected cells into myeloablated patients, having led to high rates of transfusion independence (thalassemia) or complete resolution of painful crises (sickle cell disease-SCD). Hereditary persistence of fetal hemoglobin (HPFH), a syndrome characterized by increased γ-globin levels, when co-inherited with β-thalassemia or SCD, converts hemoglobinopathies to a benign condition with mild clinical phenotype. The rapid development of precise genome editing tools (ZFN, TALENs, CRISPR/Cas9) over the last decade has allowed the targeted introduction of mutations, resulting in disease-modifying outcomes. In this context, genome editing tools have successfully been used for the introduction of HPFH-like mutations both in HBG1/HBG2 promoters or/and in the erythroid enhancer of BCL11A to increase HbF expression as an alternative curative approach for β-hemoglobinopathies. The current investigation of new HbF modulators, such as ZBTB7A, KLF-1, SOX6, and ZNF410, further expands the range of possible genome editing targets. Importantly, genome editing approaches have recently reached clinical translation in trials investigating HbF reactivation in both SCD and thalassemic patients. Showing promising outcomes, these approaches are yet to be confirmed in long-term follow-up studies.
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Affiliation(s)
- Kiriaki Paschoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece
- Department of Hematology, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nikoletta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) renaissance was catalysed by the discovery that RNA-guided prokaryotic CRISPR-associated (Cas) proteins can create targeted double-strand breaks in mammalian genomes. This finding led to the development of CRISPR systems that harness natural DNA repair mechanisms to repair deficient genes more easily and precisely than ever before. CRISPR has been used to knock out harmful mutant genes and to fix errors in coding sequences to rescue disease phenotypes in preclinical studies and in several clinical trials. However, most genetic disorders result from combinations of mutations, deletions and duplications in the coding and non-coding regions of the genome and therefore require sophisticated genome engineering strategies beyond simple gene knockout. To overcome this limitation, the toolbox of natural and engineered CRISPR-Cas systems has been dramatically expanded to include diverse tools that function in human cells for precise genome editing and epigenome engineering. The application of CRISPR technology to edit the non-coding genome, modulate gene regulation, make precise genetic changes and target infectious diseases has the potential to lead to curative therapies for many previously untreatable diseases.
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Affiliation(s)
- Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Paul B Finn
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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Abstract
I have been fortunate and privileged to have participated in amazing breakthroughs in human genetics since the 1960s. I was lucky to have trained in medical school at Dartmouth and Johns Hopkins, in pediatrics at the University of Minnesota and Johns Hopkins, and in genetics and molecular biology with Dr. Barton Childs at Johns Hopkins and Dr. Harvey Itano at the National Institutes of Health. Later, the collaborative spirit at Johns Hopkins and the University of Pennsylvania were important to my career. Here, I describe the thrill of scientific discovery in two diverse areas of human genetics: DNA haplotypes and their role in solving the molecular basis of beta thalassemia and the role of retrotransposons (jumping genes) in human biology. I hope that this article may inspire others who love human genetics as much as I do.
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Affiliation(s)
- Haig H Kazazian
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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7
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Gadgil A, Raczyńska KD. U7 snRNA: A tool for gene therapy. J Gene Med 2021; 23:e3321. [PMID: 33590603 PMCID: PMC8243935 DOI: 10.1002/jgm.3321] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 01/22/2021] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
Most U-rich small nuclear ribonucleoproteins (snRNPs) are complexes that mediate the splicing of pre-mRNAs. U7 snRNP is an exception in that it is not involved in splicing but is a key factor in the unique 3' end processing of replication-dependent histone mRNAs. However, by introducing controlled changes in the U7 snRNA histone binding sequence and in the Sm motif, it can be used as an effective tool for gene therapy. The modified U7 snRNP (U7 Sm OPT) is thus not involved in the processing of replication-dependent histone pre-mRNA but targets splicing by inducing efficient skipping or inclusion of selected exons. U7 Sm OPT is of therapeutic importance in diseases that are an outcome of splicing defects, such as myotonic dystrophy, Duchenne muscular dystrophy, amyotrophic lateral sclerosis, β-thalassemia, HIV-1 infection and spinal muscular atrophy. The benefits of using U7 Sm OPT for gene therapy are its compact size, ability to accumulate in the nucleus without causing any toxic effects in the cells, and no immunoreactivity. The risk of transgene misregulation by using U7 Sm OPT is also low because it is involved in correcting the expression of an endogenous gene controlled by its own regulatory elements. Altogether, using U7 Sm OPT as a tool in gene therapy can ensure lifelong treatment, whereas an oligonucleotide or other drug/compound would require repeated administration. It would thus be strategic to harness these unique properties of U7 snRNP and deploy it as a tool in gene therapy.
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Affiliation(s)
- Ankur Gadgil
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznanPoland
| | - Katarzyna Dorota Raczyńska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznanPoland
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Brusson M, Miccio A. Genome editing approaches to β-hemoglobinopathies. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:153-183. [PMID: 34175041 DOI: 10.1016/bs.pmbts.2021.01.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
β-hemoglobinopathies are the most common monogenic disorders worldwide and are caused by mutations in the β-globin locus altering the production of adult hemoglobin (HbA). Transplantation of autologous hematopoietic stem cells (HSCs) corrected by lentiviral vector-mediated addition of a functional β-like globin raised new hopes to treat sickle cell disease and β-thalassemia patients; however, the low expression of the therapeutic gene per vector copy is often not sufficient to fully correct the patients with a severe clinical phenotype. Recent advances in the genome editing field brought new possibilities to cure β-hemoglobinopathies by allowing the direct modification of specific endogenous loci. Double-strand breaks (DSBs)-inducing nucleases (i.e., ZFNs, TALENs and CRISPR-Cas9) or DSB-free tools (i.e., base and prime editing) have been used to directly correct the disease-causing mutations, restoring HbA expression, or to reactivate the expression of the fetal hemoglobin (HbF), which is known to alleviate clinical symptoms of β-hemoglobinopathy patients. Here, we describe the different genome editing tools, their application to develop therapeutic approaches to β-hemoglobinopathies and ongoing clinical trials using genome editing strategies.
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Affiliation(s)
- Mégane Brusson
- Université de Paris, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France.
| | - Annarita Miccio
- Université de Paris, Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR 1163, Paris, France.
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9
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Profile of Haig H. Kazazian Jr. Proc Natl Acad Sci U S A 2020; 117:32185-32188. [DOI: 10.1073/pnas.2023398117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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d'Arqom A, Nualkaew T, Jearawiriyapaisarn N, Kole R, Svasti S. Engineered U7 Small Nuclear RNA Restores Correct β-Globin Pre-mRNA Splicing in Mouse β IVS2-654-Thalassemic Erythroid Progenitor Cells. Hum Gene Ther 2020; 32:473-480. [PMID: 32977730 DOI: 10.1089/hum.2020.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Restoration of correct splicing of βIVS2-654-globin pre-mRNA was previously accomplished in erythroid cells from β-thalassemia/HbE patients by an engineered U7 small nuclear RNA (snRNA) that carried a sequence targeted to the cryptic branch point and an exonic splicing enhancer, U7.BP+623 snRNA. In this study, this approach was tested in thalassemic mice carrying the βIVS2-654 mutation. While correction of βIVS2-654 pre-mRNA splicing was achieved in erythroid progenitors transduced with a lentiviral vector carrying the U7.BP+623 snRNA, a high level of truncated U7.BP+623 snRNA was also observed. The discrepancy of processing of the modified U7 snRNA in human and mouse constructs hamper the evaluation of pathologic improvement in mouse model.
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Affiliation(s)
- Annette d'Arqom
- Graduate Program in Molecular Medicine.,Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Department of Pharmacology, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Tiwaporn Nualkaew
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Natee Jearawiriyapaisarn
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Ryszard Kole
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand.,Department of Biochemistry; Faculty of Science, Mahidol University, Bangkok, Thailand
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Aziz MA, Khan WA, Banu B, Das SA, Sadiya S, Begum S. Prenatal Diagnosis and Screening of Thalassemia Mutations in Bangladesh: Presence of Rare Mutations. Hemoglobin 2020; 44:397-401. [PMID: 33092414 DOI: 10.1080/03630269.2020.1830797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Thalassemia is the most common congenital monogenic disorder in Bangladesh. Prenatal diagnosis (PND) and pregnation termination of an affected child is one of the best options to reduce the burden of thalassemic children. This article reports the results of DNA analyses of chorionic villus sampling (CVS) and amniocentesis of fetuses of mothers who came to the thalassemia center of Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh. DNA analysis was done by real-time polymerase chain reaction (qPCR) and Sanger sequencing. Maternal contamination was ruled out by variable number of tandem repeats (VNTRs). A total of 232 samples were analyzed. Hb E (HBB: c.79G>A)/β-thalassemia (Hb E/β-thal) was the most common type of thalassemia seen in 32 samples (13.79%) followed by β-thal major (β-TM) in 10 cases (4.31%). Molecular characterization of the most predominant mutation was IVS-I-5 (G>A) (HBB: c.92+5G>C). The analysis also revealed five rare mutations: IVS-II-654 (C>T) (HBB: c.316-197C>T), IVS-II-1 (G>A) (HBB: c.315+5G>A), codon 44 (-C) (HBB: c.135delC), -86 (C>A) (HBB: c.-136C>A) and codons 14/15 (+G) (HBB: c.45_46insG), which have not been reported previously in Bangladesh. This study provides important information for PND and will help in the development of similar diagnostic programs for other DNA centers in Bangladesh.
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Affiliation(s)
- Md Abdul Aziz
- Department of Biochemistry and Molecular Biology, Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh
| | - Waqar A Khan
- Department of Biochemistry and Molecular Biology, Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh
| | - Bilquis Banu
- Department of Clinical Pathology, Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh
| | - Sudipta A Das
- Department of Biochemistry and Molecular Biology, Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh
| | - Salma Sadiya
- Department of Biochemistry and Molecular Biology, Dhaka Shishu (Children) Hospital, Dhaka, Bangladesh
| | - Sayeda Begum
- Department of Gynaecology and Obstetrics, Bangladesh Medical College and Hospital, Dhaka, Bangladesh
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Patsali P, Mussolino C, Ladas P, Floga A, Kolnagou A, Christou S, Sitarou M, Antoniou MN, Cathomen T, Lederer CW, Kleanthous M. The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements. J Clin Med 2019; 8:jcm8111959. [PMID: 31766235 PMCID: PMC6912506 DOI: 10.3390/jcm8111959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/22/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022] Open
Abstract
The common IVSI-110 (G>A) β-thalassemia mutation is a paradigm for intronic disease-causing mutations and their functional repair by non-homologous end joining-mediated disruption. Such mutation-specific repair by disruption of aberrant regulatory elements (DARE) is highly efficient, but to date, no systematic analysis has been performed to evaluate disease-causing mutations as therapeutic targets. Here, DARE was performed in highly characterized erythroid IVSI-110(G>A) transgenic cells and the disruption events were compared with published observations in primary CD34+ cells. DARE achieved the functional correction of β-globin expression equally through the removal of causative mutations and through the removal of context sequences, with disruption events and the restriction of indel events close to the cut site closely resembling those seen in primary cells. Correlation of DNA-, RNA-, and protein-level findings then allowed the extrapolation of findings to other mutations by in silico analyses for potential repair based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9, Cas12a, and transcription activator-like effector nuclease (TALEN) platforms. The high efficiency of DARE and unexpected freedom of target design render the approach potentially suitable for 14 known thalassemia mutations besides IVSI-110(G>A) and put it forward for several prominent mutations causing other inherited diseases. The application of DARE, therefore, has a wide scope for sustainable personalized advanced therapy medicinal product development for thalassemia and beyond.
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Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center–University of Freiburg, 79106 Freiburg, Germany; (C.M.); (T.C.)
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Petros Ladas
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Argyro Floga
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
| | - Annita Kolnagou
- Thalassemia Clinic Paphos, Paphos General Hospital, 8100 Paphos, Cyprus;
| | - Soteroula Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, 1474 Nicosia, Cyprus;
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, 6301 Larnaca, Cyprus;
| | - Michael N. Antoniou
- Department of Medical and Molecular Genetics, King’s College London, London SE1 9RT, UK;
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center–University of Freiburg, 79106 Freiburg, Germany; (C.M.); (T.C.)
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Carsten Werner Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
- Correspondence: ; Tel.: +357-22-392-764
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, 2371 Nicosia, Cyprus; (P.P.); (A.F.); (M.K.)
- Cyprus School of Molecular Medicine, 2371 Nicosia, Cyprus
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13
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Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, Luo HY, Brendel C, Pinello L, Chui DHK, Wolfe SA, Bauer DE. Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia. Blood 2019; 133:2255-2262. [PMID: 30704988 PMCID: PMC6533605 DOI: 10.1182/blood-2019-01-895094] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
The thalassemias are compelling targets for therapeutic genome editing in part because monoallelic correction of a subset of hematopoietic stem cells (HSCs) would be sufficient for enduring disease amelioration. A primary challenge is the development of efficient repair strategies that are effective in HSCs. Here, we demonstrate that allelic disruption of aberrant splice sites, one of the major classes of thalassemia mutations, is a robust approach to restore gene function. We target the IVS1-110G>A mutation using Cas9 ribonucleoprotein (RNP) and the IVS2-654C>T mutation by Cas12a/Cpf1 RNP in primary CD34+ hematopoietic stem and progenitor cells (HSPCs) from β-thalassemia patients. Each of these nuclease complexes achieves high efficiency and penetrance of therapeutic edits. Erythroid progeny of edited patient HSPCs show reversal of aberrant splicing and restoration of β-globin expression. This strategy could enable correction of a substantial fraction of transfusion-dependent β-thalassemia genotypes with currently available gene-editing technology.
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Affiliation(s)
- Shuqian Xu
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Haematology, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Molecular Pathology Unit
- Center for Cancer Research, and
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA
| | - Anne H Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Shanghai Key Laboratory of Regulatory Biology
- Institute of Biomedical Sciences, and
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hong-Yuan Luo
- Department of Medicine and
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA
- Hemoglobin Diagnostic Reference Laboratory, Boston Medical Center, Boston, MA
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA; and
| | - Luca Pinello
- Broad Institute, Cambridge, MA
- Molecular Pathology Unit
- Center for Cancer Research, and
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA
| | - David H K Chui
- Department of Medicine and
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA
- Hemoglobin Diagnostic Reference Laboratory, Boston Medical Center, Boston, MA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
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14
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Nualkaew T, Jearawiriyapaisarn N, Hongeng S, Fucharoen S, Kole R, Svasti S. Restoration of correct β IVS2-654-globin mRNA splicing and HbA production by engineered U7 snRNA in β-thalassaemia/HbE erythroid cells. Sci Rep 2019; 9:7672. [PMID: 31113996 PMCID: PMC6529457 DOI: 10.1038/s41598-019-43964-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 05/02/2019] [Indexed: 01/03/2023] Open
Abstract
A cytosine to thymine mutation at nucleotide 654 of human β-globin intron 2 (βIVS2-654) is one of the most common mutations causing β-thalassaemia in Chinese and Southeast Asians. This mutation results in aberrant β-globin pre-mRNA splicing and prevents synthesis of β-globin protein. Splicing correction using synthetic splice-switching oligonucleotides (SSOs) has been shown to restore expression of the β-globin protein, but to maintain therapeutically relevant levels of β-globin it would require lifelong administration. Here, we demonstrate long-term splicing correction using U7 snRNA lentiviral vectors engineered to target several pre-mRNA splicing elements on the βIVS2-654-globin pre-mRNA such as cryptic 3' splice site, aberrant 5' splice site, cryptic branch point and an exonic splicing enhancer. A double-target engineered U7 snRNAs targeted to the cryptic branch point and an exonic splicing enhancer, U7.BP + 623, was the most effective in a model cell line, HeLa IVS2-654. Moreover, the therapeutic potential of the vector was demonstrated in erythroid progenitor cells derived from βIVS2-654-thalassaemia/HbE patients, which showed restoration of correctly spliced β-globin mRNA and led to haemoglobin A synthesis, and consequently improved thalassaemic erythroid cell pathology. These results demonstrate proof of concept of using the engineered U7 snRNA lentiviral vector for treatment of β-thalassaemia.
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Affiliation(s)
- Tiwaporn Nualkaew
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Natee Jearawiriyapaisarn
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Suradej Hongeng
- Departments of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | | | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand. .,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
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15
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Fang Y, Cheng Y, Lu D, Gong X, Yang G, Gong Z, Zhu Y, Sang X, Fan S, Zhang J, Zeng F. Treatment of β 654 -thalassaemia by TALENs in a mouse model. Cell Prolif 2018; 51:e12491. [PMID: 30070404 DOI: 10.1111/cpr.12491] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/11/2018] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES This study explored whether TALENs-mediated non-homologous end joining (NHEJ) targeting the mutation site can correct the aberrant β-globin RNA splicing, and ameliorate the β-thalassaemia phenotype in β654 mice. MATERIAL AND METHODS TALENs vectors targeted to the human β-globin gene (HBB) IVS2-654C >T mutation in a mouse model were constructed and selected to generate double heterozygous TALENs+ /β654 mice. The gene editing and off-target effects were analysed by sequencing analysis. β-globin expression was identified by RT-PCR and Western blot analysis. Various clinical indices including haematologic parameters and tissue pathology were examined to determine the therapeutic effect in these TALENs+ /β654 mice. RESULTS Sequencing analysis revealed that the HBB IVS2-654C >T point mutation was deleted in over 50% of the TALENs+ /β654 mice tested, and off-target effects were not detected. RT-PCR and Western blot analysis confirmed the expression of normal β-globin in TALENs+ /β654 mice. The haematologic parameters were significantly improved as compared with their affected littermates. The proportion of nucleated cells in bone marrow was considerably decreased, splenomegaly with extramedullary haematopoiesis was reduced, and significant decreases in iron deposition were seen in spleen and liver of the TALENs+ /β654 mice. CONCLUSION These results suggest effective treatment of the anaemia phenotype in TALENs+ /β654 mice following deletion of the mutation site by TALENs, demonstrating a simple and straightforward strategy for gene therapy of β654 -thalassaemia in the future.
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Affiliation(s)
- Yudan Fang
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yan Cheng
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.,Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dan Lu
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Xiuli Gong
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Guanheng Yang
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Zhijuan Gong
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yiwen Zhu
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Xiao Sang
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shuyue Fan
- Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingzhi Zhang
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Fanyi Zeng
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University, Shanghai, China.,Department of Histo-Embryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.,Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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16
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Traivaree C, Monsereenusorn C, Rujkijyanont P, Prasertsin W, Boonyawat B. Genotype-phenotype correlation among beta-thalassemia and beta-thalassemia/HbE disease in Thai children: predictable clinical spectrum using genotypic analysis. J Blood Med 2018; 9:35-41. [PMID: 29695942 PMCID: PMC5905821 DOI: 10.2147/jbm.s159295] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Introduction Beta-thalassemia is a group of inherited hemolytic anemias and one of the most common genetic disorders in Thailand. The clinical spectrum of beta-thalassemia disease ranges from mild to severe clinical symptoms including mild beta-thalassemia intermedia (TI) and severe beta-thalassemia major (TM). Objective This study aimed to determine the correlation between beta-globin gene (HBB) mutations and their phenotypic manifestations by evaluating patients' clinical characteristics, transfusion requirements, growth and hematologic parameters, and hemoglobin typing among pediatric patients treated at Phramongkutklao Hospital. Materials and methods Seventy beta-thalassemia patients, including 63 with beta-thalassemia/hemoglobin E (HbE) and 7 with either homozygous or compound heterozygous beta-thalassemia, were enrolled in this study. Their clinical presentation, growth parameters and laboratory findings were reviewed and analyzed. The mean follow-up time was 10.52±5.62 years. Mutation analysis in each individual was performed using multiplex amplification refractory mutation system (M-ARMS), direct DNA sequencing of beta-globin gene and gap PCR for 3.4 kb deletion detection. Results All 7 homozygous and compound heterozygous beta-thalassemia patients were classified in TM. Among 63 patients with beta-thalassemia/HbE, 58 were classified in TM and 4 were classified in TI. Mean age at diagnosis was 0.8±0.49 years for homozygous or compound heterozygous beta-thalassemia and 3.43±3.5 years for beta-thalassemia/HbE. The most common HBB mutation was HBB:c.126_129delCTTT [codon 41/42 (-TCTT)] found in 34 alleles (48.6%). The height for age was also lower in homozygous beta-thalassemia patients (<3rd percentile) compared to compound heterozygous beta-thalassemia patients (25-50th percentile). Conclusion This study revealed a genotype-phenotype correlation of the most prevalent beta-thalassemia in Thai children using diagnostic capacity in genotypic analysis of HBB mutation. Our findings can provide a better prediction of clinical manifestation and severity by early identification of the type of the HBB mutations.
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Affiliation(s)
- Chanchai Traivaree
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Chalinee Monsereenusorn
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Piya Rujkijyanont
- Division of Hematology/Oncology, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
| | - Warakorn Prasertsin
- Department of Pediatrics, Queen Savang Vadhana Memorial Hospital, Chonburi, Thailand
| | - Boonchai Boonyawat
- Division of Genetics, Department of Pediatrics, Phramongkutklao Hospital and College of Medicine, Bangkok, Thailand
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17
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Islam MT, Sarkar SK, Sultana N, Begum MN, Bhuyan GS, Talukder S, Muraduzzaman AKM, Alauddin M, Islam MS, Biswas PP, Biswas A, Qadri SK, Shirin T, Banu B, Sadya S, Hussain M, Sarwardi G, Khan WA, Mannan MA, Shekhar HU, Chowdhury EK, Sajib AA, Akhteruzzaman S, Qadri SS, Qadri F, Mannoor K. High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh. BMC Genet 2018; 19:1. [PMID: 29295702 PMCID: PMC5751541 DOI: 10.1186/s12863-017-0594-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/22/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c.1 - c.92), intron-1 (c.92 + 1 - c.92 + 130) and a portion of exon-2 (c.93 - c.217) of the HBB gene which harbors more than 95% of mutant alleles responsible for beta-thalassemia in Bangladesh. RESULTS Our HRM approach could successfully differentiate ten beta-globin gene mutations, namely c.79G > A, c.92 + 5G > C, c.126_129delCTTT, c.27_28insG, c.46delT, c.47G > A, c.92G > C, c.92 + 130G > C, c.126delC and c.135delC in heterozygous states from the wild type alleles, implying the significance of the approach for carrier screening as the first three of these mutations account for ~85% of total mutant alleles in Bangladesh. Moreover, different combinations of compound heterozygous mutations were found to generate melt curves that were distinct from the wild type alleles and from one another. Based on the findings, sixteen reference samples were run in parallel to 41 unknown specimens to perform direct genotyping of the beta-thalassemia specimens using HRM. The HRM-based genotyping of the unknown specimens showed 100% consistency with the sequencing result. CONCLUSIONS Targeting the mutational hot-spot, the HRM approach could be successfully applied for screening of beta-thalassemia carriers in Bangladesh as well as in other countries of South Asia and Southeast Asia. The approach could be a useful supplement of hematological and electrophortic indices in order to avoid false positive and false negative results.
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Affiliation(s)
- Md Tarikul Islam
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Suprovath Kumar Sarkar
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Nusrat Sultana
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Mst Noorjahan Begum
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Golam Sarower Bhuyan
- Infectious Diseases Laboratory, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Shezote Talukder
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - A K M Muraduzzaman
- Department of Virology, Institute of Epidemiology, Disease Control and Research, Mohakhali, Dhaka, Bangladesh
| | - Md Alauddin
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Mohammad Sazzadul Islam
- Infectious Diseases Laboratory, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Pritha Promita Biswas
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Aparna Biswas
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Syeda Kashfi Qadri
- Department of Paediatric Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, Singapore
| | - Tahmina Shirin
- Department of Virology, Institute of Epidemiology, Disease Control and Research, Mohakhali, Dhaka, Bangladesh
| | - Bilquis Banu
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Salma Sadya
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Manzoor Hussain
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Golam Sarwardi
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Waqar Ahmed Khan
- Department of Biochemistry and Molecular Biology, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammad Abdul Mannan
- Department of Neonatology, Bangabandhu Sheikh Mujib Medical University, Shahbag, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Emran Kabir Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Syed Saleheen Qadri
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh
| | - Firdausi Qadri
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh.,Department of Enteric and Respiratory Infectious Diseases, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kaiissar Mannoor
- Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh.
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18
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Jiang F, Chen GL, Zhou JY, Li DZ. First Report of the Rare IVS-II-705 (T>G) β-Thalassemia Mutation in a Chinese Family. Hemoglobin 2017; 41:286-287. [PMID: 29251008 DOI: 10.1080/03630269.2017.1408647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We have found an example of the mutation at the intronic region of the second intervening sequence of the β-globin gene, IVS-II-705 (T>G) (HBB: c.316-146T>G), in a Chinese family. The two subjects heterozygous for this mutation presented with typical β-thalassemia (β-thal) trait.
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Affiliation(s)
- Fan Jiang
- a Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Gui-Lan Chen
- a Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Jian-Ying Zhou
- a Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Dong-Zhi Li
- a Guangzhou Women and Children Medical Center affiliated to Guangzhou Medical University , Guangzhou , Guangdong Province , People's Republic of China
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19
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Kazazian HH. Fifty years in human genetics--a career retrospective. FASEB J 2017; 31:3712-3718. [PMID: 28860307 DOI: 10.1096/fj.201700502rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 06/27/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Haig H Kazazian
- Institute for Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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20
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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21
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Phanthong P, Borwornpinyo S, Kitiyanant N, Jearawiriyapaisarn N, Nuntakarn L, Saetan J, Nualkaew T, Sa-Ngiamsuntorn K, Anurathapan U, Dinnyes A, Kitiyanant Y, Hongeng S. Enhancement of β-Globin Gene Expression in Thalassemic IVS2-654 Induced Pluripotent Stem Cell-Derived Erythroid Cells by Modified U7 snRNA. Stem Cells Transl Med 2017; 6:1059-1069. [PMID: 28213976 PMCID: PMC5442829 DOI: 10.1002/sctm.16-0121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 11/27/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022] Open
Abstract
The therapeutic use of patient‐specific induced pluripotent stem cells (iPSCs) is emerging as a potential treatment of β‐thalassemia. Ideally, patient‐specific iPSCs would be genetically corrected by various approaches to treat β‐thalassemia including lentiviral gene transfer, lentivirus‐delivered shRNA, and gene editing. These corrected iPSCs would be subsequently differentiated into hematopoietic stem cells and transplanted back into the same patient. In this article, we present a proof of principle study for disease modeling and screening using iPSCs to test the potential use of the modified U7 small nuclear (sn) RNA to correct a splice defect in IVS2‐654 β‐thalassemia. In this case, the aberration results from a mutation in the human β‐globin intron 2 causing an aberrant splicing of β‐globin pre‐mRNA and preventing synthesis of functional β‐globin protein. The iPSCs (derived from mesenchymal stromal cells from a patient with IVS2‐654 β‐thalassemia/hemoglobin (Hb) E) were transduced with a lentivirus carrying a modified U7 snRNA targeting an IVS2‐654 β‐globin pre‐mRNA in order to restore the correct splicing. Erythroblasts differentiated from the transduced iPSCs expressed high level of correctly spliced β‐globin mRNA suggesting that the modified U7 snRNA was expressed and mediated splicing correction of IVS2‐654 β‐globin pre‐mRNA in these cells. Moreover, a less active apoptosis cascade process was observed in the corrected cells at transcription level. This study demonstrated the potential use of a genetically modified U7 snRNA with patient‐specific iPSCs for the partial restoration of the aberrant splicing process of β‐thalassemia. Stem Cells Translational Medicine2017;6:1059–1069
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Affiliation(s)
| | - Suparerk Borwornpinyo
- Biotechnology.,Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | | | | | - Jirawat Saetan
- Anatomy Department, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | | | | | - Usanarat Anurathapan
- Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Andras Dinnyes
- Biotalentum Ltd, Godollo, Hungary.,Molecular Animal Biotechnology Laboratory, Szent Istvan University, Godollo, Hungary
| | - Yindee Kitiyanant
- Departments of Anatomy.,Stem Cell Research Group.,Reproductive Biology Research Group, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Suradej Hongeng
- Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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22
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β-globin gene cluster haplotypes in ethnic minority populations of southwest China. Sci Rep 2017; 7:42909. [PMID: 28205625 PMCID: PMC5311981 DOI: 10.1038/srep42909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/17/2017] [Indexed: 12/12/2022] Open
Abstract
The genetic diversity and relationships among ethnic minority populations of southwest China were investigated using seven polymorphic restriction enzyme sites in the β-globin gene cluster. The haplotypes of 1392 chromosomes from ten ethnic populations living in southwest China were determined. Linkage equilibrium and recombination hotspot were found between the 5′ sites and 3′ sites of the β-globin gene cluster. 5′ haplotypes 2 (+−−−), 6 (−++−+), 9 (−++++) and 3′ haplotype FW3 (−+) were the predominant haplotypes. Notably, haplotype 9 frequency was significantly high in the southwest populations, indicating their difference with other Chinese. The interpopulation differentiation of southwest Chinese minority populations is less than those in populations of northern China and other continents. Phylogenetic analysis shows that populations sharing same ethnic origin or language clustered to each other, indicating current β-globin cluster diversity in the Chinese populations reflects their ethnic origin and linguistic affiliations to a great extent. This study characterizes β-globin gene cluster haplotypes in southwest Chinese minorities for the first time, and reveals the genetic variability and affinity of these populations using β-globin cluster haplotype frequencies. The results suggest that ethnic origin plays an important role in shaping variations of the β-globin gene cluster in the southwestern ethnic populations of China.
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Vinciguerra M, Passarello C, Leto F, Crivello A, Fustaneo M, Cassarà F, Cannata M, Maggio A, Giambona A. Coinheritance of a Rare Nucleotide Substitution on theβ-Globin Gene and Other Known Mutations in the Globin Clusters: Management in Genetic Counseling. Hemoglobin 2016; 40:231-5. [DOI: 10.1080/03630269.2016.1188400] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Thongchote K, Svasti S, Teerapornpuntakit J, Suntornsaratoon P, Krishnamra N, Charoenphandhu N. Bone microstructural defects and osteopenia in hemizygous βIVSII-654 knockin thalassemic mice: sex-dependent changes in bone density and osteoclast function. Am J Physiol Endocrinol Metab 2015; 309:E936-48. [PMID: 26487004 DOI: 10.1152/ajpendo.00329.2015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/06/2015] [Indexed: 11/22/2022]
Abstract
β-Thalassemia, a hereditary anemic disorder, is often associated with skeletal complications that can be found in both males and females. The present study aimed to investigate the age- and sex-dependent changes in bone mineral density (BMD) and trabecular microstructure in β(IVSII-654) knockin thalassemic mice. Dual-energy X-ray absorptiometry and computer-assisted bone histomorphometry were employed to investigate temporal changes in BMD and histomorphometric parameters in male and female mice of a β(IVSII-654) knockin mouse model of human β-thalassemia, in which impaired splicing of β-globin transcript was caused by hemizygous C→T mutation at nucleotide 654 of intron 2. Young, growing β(IVSII-654) mice (1 mo old) manifested shorter bone length and lower BMD than their wild-type littermates, indicating possible growth retardation and osteopenia, the latter of which persisted until 8 mo of age (adult mice). Interestingly, two-way analysis of variance suggested an interaction between sex and β(IVSII-654) genotype, i.e., more severe osteopenia in adult female mice. Bone histomorphometry further suggested that low trabecular bone volume in male β(IVSII-654) mice, particularly during a growing period (1-2 mo), was primarily due to suppression of bone formation, whereas both a low bone formation rate and a marked increase in osteoclast surface were observed in female β(IVSII-654) mice. In conclusion, osteopenia and trabecular microstructural defects were present in both male and female β(IVSII-654) knockin thalassemic mice, but the severity, disease progression, and cellular mechanism differed between the sexes.
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Affiliation(s)
- Kanogwun Thongchote
- Center of Calcium and Bone Research, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand; Exercise Science Graduate Program, Faculty of Science, Mahidol University, Bangkok, Thailand; and
| | - Saovaros Svasti
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Thailand
| | - Jarinthorn Teerapornpuntakit
- Center of Calcium and Bone Research, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Panan Suntornsaratoon
- Center of Calcium and Bone Research, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nateetip Krishnamra
- Center of Calcium and Bone Research, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Narattaphol Charoenphandhu
- Center of Calcium and Bone Research, Faculty of Science, Mahidol University, Bangkok, Thailand; Department of Physiology, Faculty of Science, Mahidol University, Bangkok, Thailand;
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Chatterjee T, Chakravarty A, Chakravarty S, Chowdhury MA, Sultana R. Mutation Spectrum ofβ-Thalassemia and Other Hemoglobinopathies in Chittagong, Southeast Bangladesh. Hemoglobin 2015; 39:389-92. [DOI: 10.3109/03630269.2015.1078810] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Both TALENs and CRISPR/Cas9 directly target the HBB IVS2-654 (C > T) mutation in β-thalassemia-derived iPSCs. Sci Rep 2015; 5:12065. [PMID: 26156589 PMCID: PMC4496796 DOI: 10.1038/srep12065] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/16/2015] [Indexed: 12/19/2022] Open
Abstract
β-Thalassemia is one of the most common genetic blood diseases and is caused by either point mutations or deletions in the β-globin (HBB) gene. The generation of patient-specific induced pluripotent stem cells (iPSCs) and subsequent correction of the disease-causing mutations may be a potential therapeutic strategy for this disease. Due to the low efficiency of typical homologous recombination, endonucleases, including TALENs and CRISPR/Cas9, have been widely used to enhance the gene correction efficiency in patient-derived iPSCs. Here, we designed TALENs and CRISPR/Cas9 to directly target the intron2 mutation site IVS2-654 in the globin gene. We observed different frequencies of double-strand breaks (DSBs) at IVS2-654 loci using TALENs and CRISPR/Cas9, and TALENs mediated a higher homologous gene targeting efficiency compared to CRISPR/Cas9 when combined with the piggyBac transposon donor. In addition, more obvious off-target events were observed for CRISPR/Cas9 compared to TALENs. Finally, TALENs-corrected iPSC clones were selected for erythroblast differentiation using the OP9 co-culture system and detected relatively higher transcription of HBB than the uncorrected cells. This comparison of using TALENs or CRISPR/Cas9 to correct specific HBB mutations in patient-derived iPSCs will guide future applications of TALENs- or CRISPR/Cas9-based gene therapies in monogenic diseases.
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Lee HW, Han SM, Yang Y, Lin TH, Tzeng HE, Chang KH, Hwang WL, Teng CLJ. Thalassemia Phenotypes and Genotypes in Taiwan: A Retrospective Study Based on Thalassemia Screening of Young Men for Military Conscription. Hemoglobin 2015; 39:173-7. [PMID: 26088101 DOI: 10.3109/03630269.2015.1036165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Prenatal thalassemia studies from Taiwan show that one-third of fetuses with genetic abnormalities have β-thalassemia major (β-TM). However, the phenotypes and genotypes of adult thalassemia warrant further investigation. From September 2006 to April 2014, 741 male candidates drafted for military service with mean corpuscular volume (MCV) <80 fL and serum ferritin >20 µg/L were analyzed. The results showed that the detection rates of α- and β-thalassemia (α- an β-thal) were 50.20% (372/741) and 49.12% (364/741), respectively. Only five patients (0.67%) were diagnosed with both α- and β-thal. The - -(SEA)/αα mutation was found in 76.88% (286/372) of α-thal patients. Heterozygous mutations in IVS-II-654 (C > T) and codons 41/42 (-TCTT) accounted for 55.77% (203/364) of β-thal cases. The leukocyte counts for α- and β-thal were 6241.74 ± 1552.99 and 6622.87 ± 1814.41 × 10(9)/L, respectively (p = 0.007). The α-thal patients had lower red blood cell (RBC) mass (5.85 ± 0.44 × 10(12)/L vs. 6.09 ± 0.45 × 10(12)/L; p < 0.001) and higher hemoglobin (Hb) (12.82 ± 0.72 vs. 12.35 ± 0.71 g/dL; p < 0.001) than β-thal patients. Mean serum ferritin values were 169.67 and 241.36 µg/L, respectively, in α- and β-thal patients (p < 0.001), indicating more profound ineffective erythropoiesis in β-thal. Only four of the 741 patients underwent further hematological follow-up. Our study suggests that iron overload might be a potential problem in β-thal patients; therefore, regular follow-up is highly recommended.
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Affiliation(s)
- Hsiao-Wei Lee
- Division of Hematology/Medical Oncology, Department of Medicine, Taichung Veterans General Hospital , Taichung City , Taiwan
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Vinciguerra M, Passarello C, Leto F, Cassarà F, Cannata M, Maggio A, Giambona A. Identification of three new nucleotide substitutions in the β-globin gene: laboratoristic approach and impact on genetic counselling for beta-thalassaemia. Eur J Haematol 2014; 92:444-9. [PMID: 24401016 DOI: 10.1111/ejh.12267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2013] [Indexed: 11/28/2022]
Abstract
PURPOSE Over the past two decades, a wide range of available methods for DNA analysis have allowed us to identify defects in globin genes associated with haemoglobin disorders and to correlate specific mutations with phenotypic expression. The purpose of this study was to evaluate the nature of three new nucleotide changes, mutation or single nucleotide polymorphism, found in the beta-globin gene, to conduct an appropriate genetic counselling. PATIENTS AND METHODS We report the molecular study performed in three probands and their families, sampling during the screening programme conducted at the Laboratory for Molecular Prenatal Diagnosis of Hemoglobinopathies at Villa Sofia-Cervello Hospital in Palermo, Italy. RESULTS This work allowed us to report three new nucleotide substitutions of the β-globin gene: a substitution of the nucleotide 16 in the CAP site area (HBB: c.-35 A>G), a substitution of the nucleotide 478 in the second intron (HBB: c.316-373) in association with β-haemoglobin variant Hb G Copenhagen (HBB:c.142G>A) and a substitution of the nucleotide 1656 within the 3' UTR (HBB: c.*+182 G>A) in association with the 1393-bp deletion (NG_000007.3:g.70060_71452del1393). CONCLUSION The present work emphasizes the importance of reporting the observed nucleotide changes to the Haemoglobin Variant Database, especially in the case of new or rare undefined mutations, to facilitate the determination of their phenotypic expression and the possible interactions with known molecular defects and to formulate an appropriate genetic counselling for couples at risk.
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Affiliation(s)
- Margherita Vinciguerra
- Department of Haematology for Rare Diseases of Blood and Blood-forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Haemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
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Abstract
The β-thalassemias are characterized by a quantitative deficiency of β-globin chains underlaid by a striking heterogeneity of molecular defects. Although most of the molecular lesions involve the structural β gene directly, some down-regulate the gene through distal cis effects, and rare trans-acting mutations have also been identified. Most β-thalassemias are inherited in a Mendelian recessive fashion but there is a subgroup of β-thalassemia alleles that behave as dominant negatives. Unraveling the molecular basis of β-thalassemia has provided a paradigm for understanding of much of human genetics.
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Affiliation(s)
- Swee Lay Thein
- Department of Haematological Medicine, King's College London School of Medicine/King's College Hospital NHS Foundation Trust, London SE5 9NU, United Kingdom.
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Flanagan S, Xie W, Caswell R, Damhuis A, Vianey-Saban C, Akcay T, Darendeliler F, Bas F, Guven A, Siklar Z, Ocal G, Berberoglu M, Murphy N, O’Sullivan M, Green A, Clayton P, Banerjee I, Clayton P, Hussain K, Weedon M, Ellard S. Next-generation sequencing reveals deep intronic cryptic ABCC8 and HADH splicing founder mutations causing hyperinsulinism by pseudoexon activation. Am J Hum Genet 2013; 92:131-6. [PMID: 23273570 PMCID: PMC3542457 DOI: 10.1016/j.ajhg.2012.11.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 10/30/2012] [Accepted: 11/20/2012] [Indexed: 02/01/2023] Open
Abstract
Next-generation sequencing (NGS) enables analysis of the human genome on a scale previously unachievable by Sanger sequencing. Exome sequencing of the coding regions and conserved splice sites has been very successful in the identification of disease-causing mutations, and targeting of these regions has extended clinical diagnostic testing from analysis of fewer than ten genes per phenotype to more than 100. Noncoding mutations have been less extensively studied despite evidence from mRNA analysis for the existence of deep intronic mutations in >20 genes. We investigated individuals with hyperinsulinaemic hypoglycaemia and biochemical or genetic evidence to suggest noncoding mutations by using NGS to analyze the entire genomic regions of ABCC8 (117 kb) and HADH (94 kb) from overlapping ~10 kb PCR amplicons. Two deep intronic mutations, c.1333-1013A>G in ABCC8 and c.636+471G>T HADH, were identified. Both are predicted to create a cryptic splice donor site and an out-of-frame pseudoexon. Sequence analysis of mRNA from affected individuals' fibroblasts or lymphoblastoid cells confirmed mutant transcripts with pseudoexon inclusion and premature termination codons. Testing of additional individuals showed that these are founder mutations in the Irish and Turkish populations, accounting for 14% of focal hyperinsulinism cases and 32% of subjects with HADH mutations in our cohort. The identification of deep intronic mutations has previously focused on the detection of aberrant mRNA transcripts in a subset of disorders for which RNA is readily obtained from the target tissue or ectopically expressed at sufficient levels. Our approach of using NGS to analyze the entire genomic DNA sequence is applicable to any disease.
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Affiliation(s)
- Sarah E. Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Weijia Xie
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Richard Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Annet Damhuis
- Department of Molecular Genetics, Royal Devon and Exeter National Health Service Foundation Trust, Exeter EX2 5AD, UK
| | - Christine Vianey-Saban
- Service Maladies Héréditaires du Métabolisme et Dépistage Néonatal, Centre de Biologie et de Pathologie Est, Centre Hospitalier Universitaire, Lyon 69677, France
| | - Teoman Akcay
- Department of Pediatric Endocrinology, Sisli Etfal Educational and Research Hospital, Sisli, Istanbul 34377, Turkey
| | - Feyza Darendeliler
- Pediatric Endocrinology Unit, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34394, Turkey
| | - Firdevs Bas
- Pediatric Endocrinology Unit, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34394, Turkey
| | - Ayla Guven
- Department of Pediatric Endocrinology, Göztepe Educational and Research Hospital, Kadiköy, Istanbul 34730, Turkey
| | - Zeynep Siklar
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara 06100, Turkey
| | - Gonul Ocal
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara 06100, Turkey
| | - Merih Berberoglu
- Department of Pediatric Endocrinology, Ankara University School of Medicine, Ankara 06100, Turkey
| | - Nuala Murphy
- Department of Endocrinology, Children’s University Hospital, Temple Street, Dublin 12, Ireland
| | - Maureen O’Sullivan
- Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
- University of Dublin, Trinity College, Dublin 12, Ireland
| | - Andrew Green
- National Centre for Medical Genetics, Our Lady’s Children’s Hospital, Crumlin, Dublin 12, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin 12, Ireland
| | - Peter E. Clayton
- Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9WL, UK
| | - Indraneel Banerjee
- Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9WL, UK
- Department of Paediatric Endocrinology, Royal Manchester Children’s Hospital, Manchester M13 9WL, UK
| | - Peter T. Clayton
- Clinical and Molecular Genetics Unit, University College London Institute of Child Health, in partnership with the Great Ormond Street Hospital for Children National Health Service Trust, London WC1N 1EH, UK
| | - Khalid Hussain
- London Centre for Paediatric Endocrinology and Metabolism, in partnership with the Great Ormond Street Hospital for Children National Health Service Trust, London WC1N 1EH, UK
- Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
- Department of Molecular Genetics, Royal Devon and Exeter National Health Service Foundation Trust, Exeter EX2 5AD, UK
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Affiliation(s)
- Y-Q Li
- Clinical Laboratory, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - D-Z Li
- Prenatal Diagnostic Center, Guangzhou Maternal & Neonatal Hospital, Guangzhou Women & Children Medical Center, Guangzhou Medical College, Guangzhou, Guangdong, China
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32
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Wei X, Ju X, Yi X, Zhu Q, Qu N, Liu T, Chen Y, Jiang H, Yang G, Zhen R, Lan Z, Qi M, Wang J, Yang Y, Chu Y, Li X, Guang Y, Huang J. Identification of sequence variants in genetic disease-causing genes using targeted next-generation sequencing. PLoS One 2011; 6:e29500. [PMID: 22216297 PMCID: PMC3244462 DOI: 10.1371/journal.pone.0029500] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 11/29/2011] [Indexed: 01/17/2023] Open
Abstract
Background Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest. Methodology/Principal Findings To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR. Conclusions/Significance Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed.
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Affiliation(s)
- Xiaoming Wei
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xiangchun Ju
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xin Yi
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Qian Zhu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Ning Qu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Tengfei Liu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yang Chen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Hui Jiang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Guanghui Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Ruan Zhen
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | | | - Ming Qi
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jinming Wang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yi Yang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yuxing Chu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Xiaoyan Li
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Yanfang Guang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Jian Huang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Shanghai-Ministry Key Laboratory of Disease and Health Genomics, National Engineering Center for Biochip at Shanghai, Shanghai, China
- * E-mail:
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Kulkarni GD, Kulkarni SS, Kadakol GS, Kulkarni BB, Kyamangoudar PH, Lakkakula BVKS, Thangaraj K, Shepur TA, Kulkarni ML, Gai PB. Molecular basis of β-thalassemia in Karnataka, India. Genet Test Mol Biomarkers 2011; 16:138-41. [PMID: 21978377 DOI: 10.1089/gtmb.2011.0035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In β-thalassemia, point mutations in the β-globin gene are largely responsible for either decreased or no β-globin synthesis. The β-globin gene has three exons and two introns. The molecular characterization of β-thalassemia is absolutely necessary for carrier screening, for genetic counseling, and to offer prenatal diagnosis. The objective of the present study was to identify the rare mutations in β-globin gene of β-thalassemia patients. We have sequenced the entire β-globin gene in 36 clinically identified thalassemia patients from the Karnataka region using polymerase chain reaction and sequencing. Our analysis revealed 11 β-thalassemia variants. The most common being IVSII-16 G>C, IVSI-5G>C, IVSII-74 T>G, codon 3 (T>C), and Poly A site (T>C). In addition, we have also documented a novel deletion at codon 6 (-CT) (HBB:c.16delCT). These data are useful in future molecular screening of the population for implementing a thalassemia prevention and control program. Further it is found that family studies and comprehensive hematological analyses would provide useful insights for accurate molecular diagnosis of thalassemia phenotype and offers an interesting subject for further investigations in the Indian populations.
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Affiliation(s)
- Gururaj D Kulkarni
- Research Center for DNA Diagnostics, Department of Applied Genetics, Karnatak University, Dharwad, Karnataka, India
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Impaired bone formation and osteopenia in heterozygous β(IVSII-654) knockin thalassemic mice. Histochem Cell Biol 2011; 136:47-56. [PMID: 21656224 DOI: 10.1007/s00418-011-0823-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2011] [Indexed: 10/18/2022]
Abstract
β-thalassemia caused by the C→T mutation at nucleotide 654 of the intron 2 (β(IVSII-654)) results in aberrant splicing of β-globin RNA, leading to an almost absence of β-globin synthesis. Although trabecular and cortical bone loss was previously reported in β-thalassemic mice with deletion of β-globin gene, the microscopic changes in trabecular structure in β(IVSII-654) thalassemic mice remained elusive. Here, we investigated the macroscopic and microscopic bone changes in 12-week-old β(IVSII-654) knockin thalassemic mice by dual-energy X-ray absorptiometry (DXA) and histomorphometric analysis, respectively. DXA revealed a decrease in bone mineral density in the lumbar vertebrae and tibial metaphysis, but not in the femoral diaphysis, suggesting that β(IVSII-654) thalassemia predominantly led to osteopenia at the trabecular site, but not the cortical site. Further histomorphometric analysis of the tibial secondary spongiosa showed that trabecular bone volume was significantly decreased with the expansion of marrow cavity. Decreases in osteoblast surface, osteoid surface, mineral apposition rate, mineralizing surface, and mineralized volume were also observed. Moreover, trabecular bone resorption was markedly enhanced as indicated by increases in the osteoclast surface and eroded surface. It could be concluded that β(IVSII-654) thalassemia impaired bone formation and enhanced bone resorption, thereby leading to osteopenia especially at the trabecular sites, such as the tibial metaphysis.
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Hammond SM, Wood MJA. Genetic therapies for RNA mis-splicing diseases. Trends Genet 2011; 27:196-205. [PMID: 21497936 DOI: 10.1016/j.tig.2011.02.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 02/08/2011] [Accepted: 02/11/2011] [Indexed: 02/07/2023]
Abstract
RNA mis-splicing diseases account for up to 15% of all inherited diseases, ranging from neurological to myogenic and metabolic disorders. With greatly increased genomic sequencing being performed for individual patients, the number of known mutations affecting splicing has risen to 50-60% of all disease-causing mutations. During the past 10years, genetic therapy directed toward correction of RNA mis-splicing in disease has progressed from theoretical work in cultured cells to promising clinical trials. In this review, we discuss the use of antisense oligonucleotides to modify splicing as well as the principles and latest work in bifunctional RNA, trans-splicing and modification of U1 and U7 snRNA to target splice sites. The success of clinical trials for modifying splicing to treat Duchenne muscular dystrophy opens the door for the use of splicing modification for most of the mis-splicing diseases.
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Affiliation(s)
- Suzan M Hammond
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK, OX1 3QX
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Xie SY, Li W, Ren ZR, Huang SZ, Zeng F, Zeng YT. Correction of β654-thalassaemia mice using direct intravenous injection of siRNA and antisense RNA vectors. Int J Hematol 2011; 93:301-310. [PMID: 21369857 DOI: 10.1007/s12185-010-0727-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Revised: 10/27/2010] [Accepted: 11/10/2010] [Indexed: 01/17/2023]
Abstract
Although the therapeutic efficacy of β(654)-thalassaemia treatment using a combination of RNAi and antisense RNA to balance the synthesis of α- and β-globin chains has been demonstrated previously, and the safety of lentiviral delivery remains unclear. Herein, we used the same β(654)-thalassaemia mouse model to develop a therapy involving direct delivery of siRNA and antisense RNA plasmids via intravenous injection to simultaneously knock down α-globin transcript levels and restore correct β-globin splicing. The amount of α-globin mRNAs in siRNA-treated MEL cells decreased significantly, and the properly spliced β-globin mRNA was restored in HeLaβ(654) cells transfected with pcDNA-antisense plasmid. Furthermore, treatment of β(654)-thalassaemic mice with siRNA and antisense RNA plasmids resulted in significant reduction of poikilocytosis and reticulocyte counts in blood samples, decreased nucleated cell populations in bone marrow, and reduced intrasinusoidal extramedullary haematopoiesis loci and iron accumulation in liver. RT-PCR analysis revealed that treatment resulted in down-regulation of α-globin mRNA synthesis by ~50% along with an increase in the presence of normally spliced β-globin transcripts, indicating that the phenotypic changes observed in β(654)-thalassaemic mice following treatment resulted from restoration of the balance of α/β-globin biosynthesis.
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Affiliation(s)
- Shu-Yang Xie
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 24/1400 West Beijing Road, Shanghai, 200040, People's Republic of China
| | - Wei Li
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 24/1400 West Beijing Road, Shanghai, 200040, People's Republic of China
| | - Zhao-Rui Ren
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 24/1400 West Beijing Road, Shanghai, 200040, People's Republic of China
- Key Lab of Medical Embryo Molecular Biology, Ministry of Health, China, Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, People's Republic of China
| | - Shu-Zhen Huang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 24/1400 West Beijing Road, Shanghai, 200040, People's Republic of China
- Key Lab of Medical Embryo Molecular Biology, Ministry of Health, China, Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, People's Republic of China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 24/1400 West Beijing Road, Shanghai, 200040, People's Republic of China.
- Key Lab of Medical Embryo Molecular Biology, Ministry of Health, China, Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, People's Republic of China.
- Institute of Medical Science, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China.
| | - Yi-Tao Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, 24/1400 West Beijing Road, Shanghai, 200040, People's Republic of China.
- Key Lab of Medical Embryo Molecular Biology, Ministry of Health, China, Shanghai Lab of Embryo and Reproduction Engineering, Shanghai, People's Republic of China.
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Dhir A, Buratti E. Alternative splicing: role of pseudoexons in human disease and potential therapeutic strategies. FEBS J 2010; 277:841-55. [PMID: 20082636 DOI: 10.1111/j.1742-4658.2009.07520.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
What makes a nucleotide sequence an exon (or an intron) is a question that still lacks a satisfactory answer. Indeed, most eukaryotic genes are full of sequences that look like perfect exons, but which are nonetheless ignored by the splicing machinery (hence the name 'pseudoexons'). The existence of these pseudoexons has been known since the earliest days of splicing research, but until recently the tendency has been to view them as an interesting, but rather rare, curiosity. In recent years, however, the importance of pseudoexons in regulating splicing processes has been steadily revalued. Even more importantly, clinically oriented screening studies that search for splicing mutations are beginning to uncover a situation where aberrant pseudoexon inclusion as a cause of human disease is more frequent than previously thought. Here we aim to provide a review of the mechanisms that lead to pseudoexon activation in human genes and how the various cis- and trans-acting cellular factors regulate their inclusion. Moreover, we list the potential therapeutic approaches that are being tested with the aim of inhibiting their inclusion in the final mRNA molecules.
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Affiliation(s)
- Ashish Dhir
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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39
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40
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Landin B, Berglund S, Lindoff B. Hb Trollhättan [β20(B2)Val& RR; Glu] - a new haemoglobin variant with increased oxygen affinity causing erythrocytosis. Eur J Haematol 2009. [DOI: 10.1111/j.1600-0609.1994.tb00174.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Affiliation(s)
- Haig H Kazazian
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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42
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RNA repair restores hemoglobin expression in IVS2-654 thalassemic mice. Proc Natl Acad Sci U S A 2009; 106:1205-10. [PMID: 19164558 DOI: 10.1073/pnas.0812436106] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Repair of beta-globin pre-mRNA rendered defective by a thalassemia-causing splicing mutation, IVS2-654, in intron 2 of the human beta-globin gene was accomplished in vivo in a mouse model of IVS2-654 thalassemia. This was effected by a systemically delivered splice-switching oligonucleotide (SSO), a morpholino oligomer conjugated to an arginine-rich peptide. The SSO blocked the aberrant splice site in the targeted pre-mRNA and forced the splicing machinery to reselect existing correct splice sites. Repaired beta-globin mRNA restored significant amounts of hemoglobin in the peripheral blood of the IVS2-654 mouse, improving the number and quality of erythroid cells.
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Shimizu K, Nagaoka E, Okada Y, Takeuchi Y, Harihara S, Omoto K, Imanishi T, Kim W, Shin DJ, Hao L, Jin F. Characteristics of the β-Globin Gene Cluster Haplotypes of Three Han Chinese Populations at Beijing, Xi’an, and Kunming as Compared with Those of Other Asian Populations. Biochem Genet 2008; 46:566-82. [DOI: 10.1007/s10528-008-9171-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2007] [Accepted: 03/28/2008] [Indexed: 10/21/2022]
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44
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Chen XW, Mo QH, Li Q, Zeng R, Xu XM. A novel mutation of −73(A→T) in the CCAAT box of the β-globin gene identified in a patient with the mild β-thalassemia intermedia. Ann Hematol 2007; 86:653-7. [PMID: 17516066 DOI: 10.1007/s00277-007-0312-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Accepted: 05/03/2007] [Indexed: 11/28/2022]
Abstract
The beta-thalassemia is one of the most common autosomal recessive disorders in Southern China. The point mutation of beta-globin gene is the commonest molecular pathogenic mechanism. In Chinese population, over 30 mutations have now been identified. In this paper, we describe a novel beta(++)-thalassemia mutation of -73(A-->T) within the conserved CCAAT box at position -76 to -72 from the cap site of the beta-globin gene. The proband, an 8-year-old Chinese boy, was a compound heterozygote of this promoter mutation and a common beta(0)-thalassemia mutation of codon 41/42(-TCTT). He had a mild thalassemia intermedia phenotype and was transfusion independent with a hemoglobin (Hb) level of 9.4 g/dl, mean corpuscular volume (MCV) of 55.2 fl, and mean corpuscular hemoglobin (MCH) of 17.5 pg. His mother and two maternal uncles were carriers of -73(A-->T) mutation in beta-globin gene with hematological phenotype of silent beta-thalassemia. Real-time quantitative reverse transcript polymerase chain reaction (RT-PCR) analysis showed a slightly reduced beta-globin messenger RNA (mRNA) level (19.35%) in three heterozygotes compared with that in normal subjects. In restriction fragment length polymorphism (RFLP) haplotype analysis, the results indicated that this promoter mutation might be linked to the absence of BamHI-3'beta restriction site.
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Affiliation(s)
- Xiao-Wei Chen
- Department of Medical Genetics of School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangdong Province, People's Republic of China
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45
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Potter MJ, Wong E, Szabo SM, McTaggart KE. Clinical findings in a carrier of a new mutation in the choroideremia gene. Ophthalmology 2004; 111:1905-9. [PMID: 15465555 DOI: 10.1016/j.ophtha.2004.04.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2003] [Accepted: 04/21/2004] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To describe the clinical and molecular findings of a female carrier of a new mutation in the choroideremia (CHM) gene. DESIGN Single interventional case report. METHODS A 27-year-old woman was seen with mild difficulties with dark adaptation and a history of a retinal degeneration in her father and choroideremia in 3 male paternal first cousins. Visual acuity measurements, peripheral and color vision tests, electroretinography (ERG), Goldmann visual fields, fluorescein angiogram, computed tomography scan, and DNA analysis were performed. MAIN OUTCOME MEASURES (1) Visual fields, (2) fluorescein angiography, and (3) DNA analysis. RESULTS Visual acuity decreased from 20/30 to 10/200 in the right eye abruptly over 2 months, then remained stable over 2 years of follow-up and remained 20/25 in the left eye. Goldmann visual fields showed development of a central scotoma in the right eye concurrent with the rapid decline. A small amount of subretinal hemorrhage was visible on dilated fundus examination at that time, but definite leakage was not evident on fluorescein angiography; afterwards, a choroidal neovascular membrane (CNV) was suspected. The ERG was normal. DNA analysis revealed that the patient was heterozygous for a previously undescribed substitution mutation at the 3'-splice site of intron 6 of the CHM gene (850-1 G to C), confirmed by mRNA analysis with reverse transcriptase polymerase chain reaction. CONCLUSIONS Severe visual acuity loss rarely occurs in female carriers of choroideremia mutations. The diagnosis should be considered in patients with a suitable family history and fundus findings. Physicians should consider the possibility of CNV development in such patients, which may be a response to abnormal retinal pigment epithelium. Recognition of this new mutation may help identify patients who could benefit from current and future treatments to protect against vision loss.
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Affiliation(s)
- Michael J Potter
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, Canada
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46
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Vacek MM, Ma H, Gemignani F, Lacerra G, Kafri T, Kole R. High-level expression of hemoglobin A in human thalassemic erythroid progenitor cells following lentiviral vector delivery of an antisense snRNA. Blood 2003; 101:104-11. [PMID: 12393543 DOI: 10.1182/blood-2002-06-1869] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations at nucleotides 654, 705, or 745 in intron 2 of the human beta-globin gene activate aberrant 3' and 5' splice sites within the intron and prevent correct splicing of beta-globin pre-mRNA, resulting in inhibition of beta-globin synthesis and in consequence beta-thalassemia. Transfection of HeLa cells expressing the 3 thalassemic mutants with modified U7 snRNA (U7.623), containing a sequence antisense to a region between the aberrant splice sites, reduced the incorrect splicing of pre-mRNA and led to increased levels of the correctly spliced beta-globin mRNA and protein. A lentiviral vector carrying the U7.623 gene was effective in restoration of correct splicing in the model cell lines for at least 6 months. Importantly, the therapeutic value of this system was demonstrated in hematopoietic stem cells and erythroid progenitor cells from a patient with IVS2-745/IVS2-1 thalassemia. Twelve days after transduction of the patient cells with the U7.623 lentiviral vector, the levels of correctly spliced beta-globin mRNA and hemoglobin A were approximately 25-fold over background. These results should be regarded as a proof of principle for lentiviral vector-based gene therapy for beta-thalassemia.
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Affiliation(s)
- Marla M Vacek
- Curriculum in Genetics and Molecular Biology, University of North Carolina Gene Therapy Center, Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, 27599, USA
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47
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Gemignani F, Sazani P, Morcos P, Kole R. Temperature-dependent splicing of beta-globin pre-mRNA. Nucleic Acids Res 2002; 30:4592-8. [PMID: 12409448 PMCID: PMC135830 DOI: 10.1093/nar/gkf607] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A T-->G mutation at nucleotide 705 of human beta-globin intron 2 creates an aberrant 5' splice site and activates a cryptic 3' splice site upstream. In consequence, the pre-mRNA is spliced via aberrant splice sites, despite the presence of the still functional correct sites. Surprisingly, when IVS2-705 HeLa or K562 cells were cultured at temperatures below 30 degrees C, aberrant splicing was inhibited and correct splicing was restored. Similar temperature effects were seen for another beta-globin pre-mRNA, IVS2-745, and in a construct in which a beta-globin intron was inserted into a coding sequence of EGFP. Temperature-induced alternative splicing was affected by the nature of the internal aberrant splice sites flanking the correct sites and by exonic sequences. The results indicate that in the context of thalassemic splicing mutations and possibly in other alternatively spliced pre-mRNAs, temperature is one of the parameters that affect splice site selection.
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Affiliation(s)
- Federica Gemignani
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, CB 7295, University of North Carolina, Chapel Hill, NC 27599-7295, USA
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48
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Suwanmanee T, Sierakowska H, Lacerra G, Svasti S, Kirby S, Walsh CE, Fucharoen S, Kole R. Restoration of human beta-globin gene expression in murine and human IVS2-654 thalassemic erythroid cells by free uptake of antisense oligonucleotides. Mol Pharmacol 2002; 62:545-53. [PMID: 12181431 DOI: 10.1124/mol.62.3.545] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Correct human beta-globin mRNA has been restored in erythroid cells from transgenic mice carrying the human gene with beta-globin IVS2-654 splice mutation and from thalassemia patients with the IVS2-654/beta(E) genotype. This was accomplished in a dose- and time-dependent manner by free uptake of morpholino oligonucleotide antisense to the aberrant splice site at position 652 of intron 2 in beta-globin pre-mRNA. Under optimal conditions of oligonucleotide uptake, the maximal levels of correct human beta-globin mRNA and hemoglobin A in patients' erythroid cells were 77 and 54%, respectively. These levels of correction were equal to, if not higher than, those obtained by syringe loading of the oligonucleotide into the cells. Comparison of splicing correction results with the cellular uptake of fluorescein-labeled oligonucleotide indicated that the levels of mRNA and hemoglobin A correlate well with the nuclear localization of the oligonucleotide and the degree of erythroid differentiation of cultured cells. Similar but not as pronounced results were obtained after the oligonucleotide treatment of bone marrow cells from IVS2-654 mouse. The effectiveness of the free antisense morpholino oligonucleotide in restoration of correct splicing of IVS2-654 pre-mRNA in cultured erythropoietic cells from transgenic mice and thalassemic patients suggests the applicability of this or similar compounds in in vivo experiments and possibly in treatment of thalassemia.
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Affiliation(s)
- Thipparat Suwanmanee
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7295, USA
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49
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Sadiq MF, Eigel A, Horst J. Spectrum of beta-thalassemia in Jordan: identification of two novel mutations. Am J Hematol 2001; 68:16-22. [PMID: 11559932 DOI: 10.1002/ajh.1143] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Two hundred and forty-four beta-thalassemia alleles were identified from 135 unrelated occasionally and periodically transfusion dependent beta- and S/beta-thalassemia patients from all regions of Jordan. Allele identification was achieved by PCR amplification of beta-globin genes, dot-blotting the amplified DNA, hybridization with allele specific synthetic probes, and direct sequencing of amplified genomic DNA. A total of 19 different mutations were detected, eight of them constituted about 86% of the Jordanian thalassemic chromosomes. These mutations were IVS1-110 (G>A) (25%), IVS2-1 (G>A) (15%), IVS2-745 (C>G) (14.2%), IVS1-1 (G>A) (10%), IVS1-6 (T>C) (8.3%), codon 37 (G>A) (6.3%), codon 39 (C>T) (4.6%), and codon 5 (-C) (3.8%). The remaining eleven mutations were rare, presented with frequencies ranging between 0.4% and 1.6%. These included two novel mutations and four others detected in Jordan for the first time. The novel mutations were the frame shift (-C) at codon 49 and the substitution (A>C) at position -29 in the TATA box. Four alleles (1.6%) remained unidentified; having no abnormalities in their beta-globin gene sequences and therefore, constituted additional defects causing beta-thalassemia in the Jordanian population. These unknown alleles are expected to be candidates for upstream or downstream mutations affecting the expression of beta-globin gene. The results provided the essential foundation for planning a national preventive program for thalassemia in Jordan and will help improving the medical services for the patients and their families by helping their clinicians and genetic counselors in evaluating their variants and designing their treatment regimens.
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Affiliation(s)
- M F Sadiq
- Department of Biological Sciences, Yarmouk University, Irbid, Jordan.
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50
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Laosombat V, Wongchanchailert M, Sattayasevana B, Wiriyasateinkul A, Fucharoen S. Clinical and hematological features of beta(+)-thalassemia (IVS-1 nt 5, G-C mutation) in Thai patients. Eur J Haematol 2001; 67:100-4. [PMID: 11722597 DOI: 10.1034/j.1600-0609.2001.t01-1-00431.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Seventy-eight patients with IVS-1 nt 5, G-C, which is the common mutation of beta+-thalassemia found in the southern part of Thailand, were studied to determine whether it is possible to predict phenotypic severity from genetic factors. The clinical phenotype of homozygotes for IVS-1 nt 5, G-C and compound heterozygotes for IVS-1 nt 5, G-C and beta(0) - or beta(+)-thalassemia were variable and could not be accurately predicted. The associations between concomittant alpha-thalassemia or Hb CS or the presence of XmnI-Ggamma polymorphism and a mild clinical phenotype are not apparent, indicating the involvement of other ameliorating determinants or genetic modifications.
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Affiliation(s)
- V Laosombat
- Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkla, Thailand.
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