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Xi B, Liu S, Zhu Y, Zhang D, Zhang Y, Liu A. Case report: Genetic analysis of a novel intronic inversion variant in the SPTB gene associated with hereditary spherocytosis. Front Genet 2023; 14:1309040. [PMID: 38111681 PMCID: PMC10726134 DOI: 10.3389/fgene.2023.1309040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
Background: Hereditary spherocytosis (HS) is a congenital haemolytic anaemia attributed to dysregulation or abnormal quantities of erythrocyte membrane proteins. Currently, the most common erythrocytic gene, spectrin β (SPTB), variants are located in exons and give rise to mRNA defects. However, the genetic characteristics and pathogenic mechanisms of SPTB intronic variants are not completely understood. This study aimed to analyse a rare intronic inversion variant in the SPTB gene associated with HS, and explore the impact of the variant on SPTB mRNA splicing. Method: The clinical manifestations of the patient were summarised and analysed for spherocytosis phenotype diagnosis. The pathogenic variant was identified in the proband using targeted next-generation and Sanger sequencing. RNA sequencing was performed to analyse whether SPTB gene splicing and expression were affected. Results: Targeted next-generation sequencing identified a novel disease-associated intronic inversion variant of the SPTB gene in the proband. The inversion variant was located between intron 19 and 20, and contained the entire exon 20 and partial sequences of adjacent introns. Sanger sequencing confirmed that the intronic inversion variant only appeared in the genome of the proband, not in his parents. RNA sequencing revealed that the variant could result in the skipping of exon 20 and reduced expression of SPTB mRNA. Conclusion: This study identifies a rare intronic inversion variant in the SPTB gene associated with hereditary spherocytosis. The pathogenic variant can lead to exon 20 skipping and decreased SPTB gene expression. This finding has not been previously reported in any literature. This study can expand the intronic variant spectrum of the SPTB gene, deepen our understanding of HS pathogenesis, and contribute to the genetic diagnosis and clinical management of patients.
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Affiliation(s)
- Bixin Xi
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siying Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongbing Zhu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dedong Zhang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhang
- Department of Gynaecology, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aiguo Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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A novel SPTB mutation causes hereditary spherocytosis via loss-of-function of β-spectrin. Ann Hematol 2022; 101:731-738. [PMID: 35099593 DOI: 10.1007/s00277-022-04773-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 01/20/2022] [Indexed: 11/01/2022]
Abstract
Hereditary spherocytosis (HS) is the most frequently observed chronic non-immune hemolytic disorder caused by altered red cell membrane function. SPTB gene mutation is one of the most common causes of HS, but pathogenicity analyses and pathogenesis research on these mutations have not been widely conducted. In this study, a novel heterozygous mutation of the SPTB gene (c.1509_1518del; p.K503Nfs*67) was identified in a Chinese family with HS by whole-exome sequencing (WES) and was then confirmed by Sanger sequencing. Next, the pathogenicity and pathogenesis of this mutation were studied using peripheral blood. We found that this mutation disrupted the synthesis and localization of β-spectrin and weakened the interaction between β-spectrin and ankyrin, which may be caused by the nonsense-mediated mRNA degradation pathway. These changes lead to the transformation of discoid erythrocytes into spherocytes, resulting in hemolytic anemia. Therefore, we classified this novel mutation as a pathogenic mutation leading to loss-of-function of β-spectrin. It would be insightful to perform the same mutation test and to provide genetic counseling to other relatives of the proband. Our study increases the current understanding of the molecular mechanisms related to mutations in SPTB.
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Ma S, Tang L, Wu C, Tang H, Pu X, Niu J. Study on Management of Blood Transfusion Therapy in Patients with Hereditary Spherocytosis. Appl Bionics Biomech 2022; 2022:6228965. [PMID: 35126660 PMCID: PMC8816590 DOI: 10.1155/2022/6228965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 12/17/2022] Open
Abstract
Hereditary spherocytosis (HS) is a chronic hemolytic disorder caused by inherited defects in the red blood cell membrane. This study discusses the treatment strategy for the decline in hemoglobin level in three HS probands with moderately severe or severe hemolysis and summarizes the appropriate laboratory tests that help improve clinical management of blood transfusion in HS patients. Three probands who were diagnosed with HS in our hospital and their family members were included in this study. Clinical data of the three families were reviewed to summarize their hematopoietic characteristics. DNA from all family members of the 3 HS probands was amplified by polymerase chain reaction (PCR) and sequenced by the Sanger method to assess genetic relation for HS. Based on the sequencing results, the type of mutated membrane protein in each proband was analyzed using the eosin-5'-maleimide (EMA) binding test and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The hemoglobin level was reduced in all 3 probands after different levels of infection. The fluorescence of EMA-labeled red blood cell (RBC) was decreased. DNA sequencing showed that His54Pro, Leu1858Val, and 6531-12C>T compound heterozygous mutations were present in the SPTA1 gene of patient I-1, Arg344Gln and c.609+86G>A heterozygous mutations were present in the SLC4A1 gene of patient II-1, and Leu2032Pro homozygous mutation was present in the SPTB gene of patient III-1. SDS-PAGE results demonstrated that the concentration of band 3 was reduced in II-1, whereas the levels of the corresponding mutant proteins in the other probands were unchanged. The family members of the respective patients presented mutations in major genes causing HS. The Leu2032Pro mutation identified in patient III-1 is a new missense mutation of the SPTB gene in the Chinese population that has never been reported in literature previously. The presence or absence of acute or chronic infections is a critical deciding factor for the treatment and clinical management of HS patient via blood transfusion. For patients with infections, hemoglobin concentration can be restored once the infection is controlled, thus obviating the need for proper infection control before blood transfusion.
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Affiliation(s)
- Shiyue Ma
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin City 541001, Guangxi Zhuang Autonomous Region, China
| | - Lingjian Tang
- Department of Rehabilitation Medicine, Affiliated Hospital of Guilin Medical University, Guilin City 541001, Guangxi Zhuang Autonomous Region, China
| | - Chaoli Wu
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin City 541001, Guangxi Zhuang Autonomous Region, China
| | - Hui Tang
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin City 541001, Guangxi Zhuang Autonomous Region, China
| | - Xue Pu
- Department of Laboratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin City 541001, Guangxi Zhuang Autonomous Region, China
| | - Jinhong Niu
- Department of Medical Administration, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin City 541002, Guangxi Zhuang Autonomous Region, China
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Aggarwal A, Jamwal M, Sharma P, Sachdeva MUS, Bansal D, Malhotra P, Das R. Deciphering molecular heterogeneity of Indian families with hereditary spherocytosis using targeted next-generation sequencing: First South Asian study. Br J Haematol 2019; 188:784-795. [PMID: 31602632 DOI: 10.1111/bjh.16244] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/25/2019] [Accepted: 08/14/2019] [Indexed: 12/17/2022]
Abstract
Defects in various erythrocyte membrane proteins genes (ankyrin, band-3, β- and α-spectrin and protein 4·2) can cause hereditary spherocytosis (HS). This molecular heterogeneity of HS, together with co-inherited genetic modifiers, results in marked phenotypic variability among patients. We studied the molecular spectrum and genotype-phenotype correlations in 73 families (with 113 patients) with HS. Deleterious variants including nonsense (42%), deletions (18%), splice site (20%), missense (10%) and duplication/insertion (10%) were found in 47 patients. The variants detected included sporadic and dominantly-inherited defects in ANK1 (53·2%), SPTB (36·2%) and SLC4A1 (4·2%). Compound heterozygous variants in SPTA1 (6·4%) showed autosomal recessive inheritance. Alpha-spectrin variants were associated with severe anaemia and splenectomy alleviated symptoms. Co-inherited glucose-6-phosphate dehydrogenase (G6PD) deficiency was found in 15%. G6PD variants (n = 5) led to greater transfusion requirements (1-8 times) in males with HS. Homozygosity (41%) for the promoter variant of UGT1A1 (Gilbert syndrome) led to a significantly higher mean bilirubin level (126·54 µmol/l) with a higher frequency of cholelithiasis (30%) (P < 0·001). This first-ever south Asian study on the molecular spectrum of HS found ANK1 and SPTB genes variants to be the commonest with inheritance being sporadic/dominant. Next-generation sequencing provided a relatively sensitive and rapid tool for molecular diagnosis with a diagnostic yield of 64·4%.
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Affiliation(s)
- Anu Aggarwal
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manu Jamwal
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prashant Sharma
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepak Bansal
- Haematology-Oncology Unit, Department of Paediatrics, Advanced Paediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Internal Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Reena Das
- Department of Haematology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Park J, Jeong DC, Yoo J, Jang W, Chae H, Kim J, Kwon A, Choi H, Lee JW, Chung NG, Kim M, Kim Y. Mutational characteristics of ANK1 and SPTB genes in hereditary spherocytosis. Clin Genet 2016; 90:69-78. [PMID: 26830532 DOI: 10.1111/cge.12749] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 01/04/2016] [Accepted: 01/25/2016] [Indexed: 12/18/2022]
Abstract
The aim of this study was to describe the mutational characteristics in Korean hereditary spherocytosis (HS) patients. Relevant literatures including genetically confirmed cases with well-documented clinical summaries and relevant information were also reviewed to investigate the mutational gene- or domain-specific laboratory and clinical association. Twenty-five HS patients carried one heterozygous mutation of ANK1 (n = 13) or SPTB (n = 12) but not in SPTA1, SLC4A1, or EPB42. Deleterious mutations including frameshift, nonsense, and splice site mutations were identified in 91% (21/23), and non-hotspot mutations were dispersed across multiple exons. Genotype-phenotype correlation was clarified after combined analysis of the cases and the literature review; anemia was most severe in HS patients with mutations on the ANK1 spectrin-binding domain (p < 0.05), and SPTB mutations in HS patients spared the tetramerization domain in which mutations of hereditary elliptocytosis and pyropoikilocytosis are located. Splenectomy (17/75) was more frequent in ANK1 mutant HS (32%) than in HS with SPTB mutation (10%) (p = 0.028). Aplastic crisis occurred in 32.0% of the patients (8/25; 3 ANK1 and 5 SPTB), and parvovirus B19 was detected in 88%. The study clarifies ANK1 or SPTB mutational characteristics in HS Korean patients. The genetic association of laboratory and clinical aspects suggests comprehensive considerations for genetic-based management of HS.
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Affiliation(s)
- J Park
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - D-C Jeong
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,The Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - J Yoo
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - W Jang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Division of Laboratory Medicine, Samkwang Medical Laboratories, Seoul, Republic of Korea
| | - H Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - J Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - A Kwon
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - H Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - J W Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - N-G Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - M Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Y Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Salas PC, Rosales JML, Milla CP, Montiel JL, Siles JL. A novel mutation in the β-spectrin gene causes the activation of a cryptic 5'-splice site and the creation of a de novo 3'-splice site. Hum Genome Var 2015; 2:15029. [PMID: 27081538 PMCID: PMC4785562 DOI: 10.1038/hgv.2015.29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 11/16/2022] Open
Abstract
The analysis of genes involved in hereditary spherocytosis, by next-generation sequencing in two patients with clinical diagnosis of the disease, showed the presence of the c.1795+1G>A mutation in the SPTB gene. cDNA amplification then revealed the occurrence of a consequent aberrant mRNA isoform produced from the activation of a cryptic 5′-splice site and the creation of a newly 3′-splice site. The mechanisms by which these two splice sites are used as a result of the same mutation should be analyzed in depth in further studies.
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Abstract
Our knowledge about human genes and the consequences of mutations leading to human genetic diseases has drastically improved over the last few years. It has been recognized that many mutations are indeed pathogenic because they impact the mRNA rather than the protein itself. With our better understanding of the very complex mechanism of splicing, various bioinformatics tools have been developed. They are now frequently used not only to search for sequence motifs corresponding to splicing signals (splice sites, branch points, ESE, and ESS) but also to predict the impact of mutations on these signals. We now need to address the impact of mutations that affect the splicing process, as their consequences could vary from the activation of cryptic signals to the skipping of one or multiple exons. Despite the major developments of the bioinformatics field coupled to experimental data generated on splicing, it is today still not possible to efficiently predict the consequences of mutations impacting splicing signals, especially to predict if they will lead to exon skipping or to cryptic splice site activation.
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Symoens S, Malfait F, Vlummens P, Hermanns-Lê T, Syx D, De Paepe A. A novel splice variant in the N-propeptide of COL5A1 causes an EDS phenotype with severe kyphoscoliosis and eye involvement. PLoS One 2011; 6:e20121. [PMID: 21611149 PMCID: PMC3096658 DOI: 10.1371/journal.pone.0020121] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 04/12/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The Ehlers-Danlos Syndrome (EDS) is a heritable connective tissue disorder characterized by hyperextensible skin, joint hypermobility and soft tissue fragility. The classic subtype of EDS is caused by mutations in one of the type V collagen genes (COL5A1 and COL5A2). Most mutations affect the type V collagen helical domain and lead to a diminished or structurally abnormal type V collagen protein. Remarkably, only two mutations were reported to affect the extended, highly conserved N-propeptide domain, which plays an important role in the regulation of the heterotypic collagen fibril diameter. We identified a novel COL5A1 N-propeptide mutation, resulting in an unusual but severe classic EDS phenotype and a remarkable splicing outcome. METHODOLOGY/PRINCIPAL FINDINGS We identified a novel COL5A1 N-propeptide acceptor-splice site mutation (IVS6-2A>G, NM_000093.3_c.925-2A>G) in a patient with cutaneous features of EDS, severe progressive scoliosis and eye involvement. Two mutant transcripts were identified, one with an exon 7 skip and one in which exon 7 and the upstream exon 6 are deleted. Both transcripts are expressed and secreted into the extracellular matrix, where they can participate in and perturb collagen fibrillogenesis, as illustrated by the presence of dermal collagen cauliflowers. Determination of the order of intron removal and computational analysis showed that simultaneous skipping of exons 6 and 7 is due to the combined effect of delayed splicing of intron 7, altered pre-mRNA secondary structure, low splice site strength and possibly disturbed binding of splicing factors. CONCLUSIONS/SIGNIFICANCE We report a novel COL5A1 N-propeptide acceptor-splice site mutation in intron 6, which not only affects splicing of the adjacent exon 7, but also causes a splicing error of the upstream exon 6. Our findings add further insights into the COL5A1 splicing order and show for the first time that a single COL5A1 acceptor-splice site mutation can perturb splicing of the upstream exon.
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Affiliation(s)
- Sofie Symoens
- Center for Medical Genetics, University Hospital Ghent, Ghent, Belgium.
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