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Manjunath LE, Singh A, Devi Kumar S, Vasu K, Kar D, Sellamuthu K, Eswarappa SM. Transcript-specific induction of stop codon readthrough using a CRISPR-dCas13 system. EMBO Rep 2024; 25:2118-2143. [PMID: 38499809 PMCID: PMC11015002 DOI: 10.1038/s44319-024-00115-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using a CRISPR-dCas13 system. Using specific guide RNAs, we target dCas13 to the region downstream of canonical stop codons of mammalian AGO1 and VEGFA mRNAs, known to exhibit natural SCR. Readthrough assays reveal enhanced SCR of these mRNAs (both exogenous and endogenous) caused by the dCas13-gRNA complexes. This effect is associated with ribosomal pausing, which has been reported for several SCR events. Our data show that CRISPR-dCas13 can also induce SCR across premature termination codons (PTCs) in the mRNAs of green fluorescent protein and TP53. We demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA and hereditary spherocytosis-causing PTC in SPTA1 mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Karthi Sellamuthu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- University of Texas Medical Branch, Galveston, TX, USA
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
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Häuser F, Rossmann H, Adenaeuer A, Shrestha A, Marandiuc D, Paret C, Faber J, Lackner KJ, Lämmle B, Beck O. Hereditary Spherocytosis: Can Next-Generation Sequencing of the Five Most Frequently Affected Genes Replace Time-Consuming Functional Investigations? Int J Mol Sci 2023; 24:17021. [PMID: 38069343 PMCID: PMC10707146 DOI: 10.3390/ijms242317021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Congenital defects of the erythrocyte membrane are common in northern Europe and all over the world. The resulting diseases, for example, hereditary spherocytosis (HS), are often underdiagnosed, partly due to their sometimes mild and asymptomatic courses. In addition to a broad clinical spectrum, this is also due to the occasionally complex diagnostics that are not available to every patient. To test whether next-generation sequencing (NGS) could replace time-consuming spherocytosis-specific functional tests, 22 consecutive patients with suspected red cell membranopathy underwent functional blood tests. We were able to identify the causative genetic defect in all patients with suspected HS who underwent genetic testing (n = 17). The sensitivity of the NGS approach, which tests five genes (ANK1 (gene product: ankyrin1), EPB42 (erythrocyte membrane protein band4.2), SLC4A1 (band3), SPTA1 (α-spectrin), and SPTB (β-spectrin)), was 100% (95% confidence interval: 81.5-100.0%). The major advantage of genetic testing in the paediatric setting is the small amount of blood required (<200 µL), and compared to functional assays, sample stability is not an issue. The combination of medical history, basic laboratory parameters, and an NGS panel with five genes is sufficient for diagnosis in most cases. Only in rare cases, a more comprehensive functional screening is required.
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Affiliation(s)
- Friederike Häuser
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Anke Adenaeuer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Annette Shrestha
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Dana Marandiuc
- Transfusion Center, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Claudia Paret
- Department of Pediatric Hematology, Oncology & Hemostaseology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Jörg Faber
- Department of Pediatric Hematology, Oncology & Hemostaseology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Karl J. Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Bernhard Lämmle
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
- Haemostasis Research Unit, University College London, London WC1E6BT, UK
| | - Olaf Beck
- Department of Pediatric Hematology, Oncology & Hemostaseology, Center for Pediatric and Adolescent Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
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Wang Y, Huang L, Zhu Y, An X, Li J, Zhen J, Yu J. De novo variations of ANK1 gene caused hereditary spherocytosis in two Chinese children by affecting pre-mRNA splicing. BMC Pediatr 2023; 23:23. [PMID: 36647015 PMCID: PMC9841706 DOI: 10.1186/s12887-022-03795-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 12/09/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND AIMS Hereditary spherocytosis (HS) is one of the most common hereditary haemolytic disorders. Here, two unrelated families with the probands displaying typical manifestations of HS were enrolled. Our study aimed to characterize the effect of two novel variants in HS patients on gene splicing to help minimize the rate of misdiagnosis of HS and enhance clinicians' understanding of the disease. PARTICIPANTS AND METHODS A retrospective review was conducted. Peripheral blood samples were collected from all the family members, and genomic DNA was extracted for genetic diagnostics. First, high-throughput sequencing technology was used for the preliminary screening of candidate causative variants. Thereafter, the variants were verified via Sanger sequencing. Furthermore, a pathogenicity analysis of the detected variants was performed including in silico prediction and in vitro experiments. We constructed matched wild-type and mutant-type minigene plasmid of ANK1 based on HEK293T cells to address the effects of variants on mRNA splicing. RESULTS The c.1305 + 2 T > A (family1) and c.1305 + 2del (family2) variants were detected in the ANK1 gene. These two de novo mutations described by us which have not been reported prior to this study. Moreover, the validation results of splicing reporter systems revealed that the intronic mutations resulted in abnormal pre-mRNA splicing. Specifically, the minigene plasmid expressing the c.1305 + 2 T > A variant transcribed the two aberrant transcripts: r.1305_1306ins1305 + 1_1305 + 229 and r.1305_1306ins1305 + 1_1305 + 552. The minigene plasmid expressing c.1305 + 2del transcribed the two aberrant transcripts: r.1305_1306ins1305 + 1_1305 + 228 and r.1305_1306ins1305 + 1_1305 + 551. CONCLUSION The two de novo variants identified in the ANK1 gene were the genetic etiology of the probands with HS in our study. Our findings further enrich the HS genotype database and provide a basis for genetic counselling and molecular diagnosis.
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Affiliation(s)
- Yang Wang
- grid.488412.3Department of Hematology and Oncology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, 136 Zhong shan er lu, Yu zhong district, Chongqing, 400014 China ,grid.488412.3Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Lan Huang
- grid.488412.3Department of Hematology and Oncology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, 136 Zhong shan er lu, Yu zhong district, Chongqing, 400014 China ,grid.488412.3Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Yao Zhu
- grid.488412.3Department of Hematology and Oncology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, 136 Zhong shan er lu, Yu zhong district, Chongqing, 400014 China ,grid.488412.3Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Xizhou An
- grid.488412.3Department of Hematology and Oncology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, 136 Zhong shan er lu, Yu zhong district, Chongqing, 400014 China
| | - Jiacheng Li
- grid.488412.3Department of Hematology and Oncology, Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children’s Hospital of Chongqing Medical University, 136 Zhong shan er lu, Yu zhong district, Chongqing, 400014 China ,grid.488412.3Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Jiangwei Zhen
- grid.440186.fDepartment of Endocrinology, Shenzhen Samii International Medical Center, Shenzhen, 518000 China
| | - Jie Yu
- Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, 136 Zhong shan er lu, Yu zhong district, Chongqing, 400014, China. .,Chongqing Key Laboratory of Pediatrics, Chongqing, China.
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Vercellati C, Marcello AP, Fattizzo B, Zaninoni A, Seresini A, Barcellini W, Bianchi P, Fermo E. Effect of primary lesions in cytoskeleton proteins on red cell membrane stability in patients with hereditary spherocytosis. Front Physiol 2022; 13:949044. [PMID: 36035481 PMCID: PMC9413078 DOI: 10.3389/fphys.2022.949044] [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: 05/20/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
We investigated by targeted next generation sequencing the genetic bases of hereditary spherocytosis in 25 patients and compared the molecular results with the biochemical lesion of RBC membrane obtained by SDS-PAGE analysis. The HS diagnosis was based on available guidelines for diagnosis of congenital hemolytic anemia, and patients were selected because of atypical clinical presentation or intra-family variability, or because presented discrepancies between laboratory investigation and biochemical findings. In all patients but 5 we identified pathogenic variants in SPTA1, SPTB, ANK1, SLC4A1, EPB42 genes able to justify the clinical phenotype. Interestingly, a correspondence between the biochemical lesion and the molecular defect was identified in only 11/25 cases, mostly with band 3 deficiency due to SLC4A1 mutations. Most of the mutations in SPTB and ANK1 gene didn’t hesitate in abnormalities of RBC membrane protein; conversely, in two cases the molecular lesion didn’t correspond to the biochemical defect, suggesting that a mutation in a specific cytoskeleton protein may result in a more complex RBC membrane damage or suffering. Finally, in two cases the HS diagnosis was maintained despite absence of both protein defect and molecular lesion, basing on clinical and family history, and on presence of clear laboratory markers of HS. The study revealed complex relationships between the primary molecular lesion and the final effect in the RBC membrane cytoskeleton, and further underlines the concept that there is not a unique approach to the diagnosis of HS.
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Affiliation(s)
- Cristina Vercellati
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
| | - Anna Paola Marcello
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
| | - Bruno Fattizzo
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
| | - Anna Zaninoni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
| | - Agostino Seresini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Laboratorio Centrale, UOS Laboratorio Genetica Medica, Milan, Italy
| | - Wilma Barcellini
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
| | - Paola Bianchi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
- *Correspondence: Paola Bianchi,
| | - Elisa Fermo
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano—UOC Ematologia, UOS Fisiopatologia Delle Anemie, Milan, Italy
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Jin D, Shen L, Huang Y. Intraoperative Cell-Saver Caused More Autologous Salvage Hemolysis in a Hereditary Spherocytosis Patient Than in a Normal Erythrocyte Patient. Front Physiol 2022; 13:926398. [PMID: 35846021 PMCID: PMC9280079 DOI: 10.3389/fphys.2022.926398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
Hereditary spherocytosis is a common red blood cell disease caused by an inherited red blood cell membrane defect, leading to a spherical shape and propensity for hemolysis. There is a lack of reports on intraoperative autologous blood transfusion for hereditary spherocytosis patients. We hereby report our recent experience with using the Cell Saver® system for intraoperative red blood cell salvage on a hereditary spherocytosis patient. There was a drastic increase in salvaged blood free-hemoglobin compared with the preoperative sample (82.6 mg/dl vs. 6.2 mg/dl) which indicated severe hemolysis. Although our patient recovered smoothly with a normal liver and renal function test and reported no adverse reaction during follow-up, it is noteworthy that severe hemolysis could happen during the cell salvage process for patients with hemolytic anemia, as there are similar reports on sickle cell anemia, beta-thalassemia intermedia, and paroxysmal nocturnal hemoglobinuria. Therefore, more clinical attention and thorough research should be drawn into this perspective, namely, hemolysis during the red blood cell salvage process for patients with hemolytic anemia.
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Affiliation(s)
- Di Jin
- Department of Anesthesiology, Peking Union Medical College Hospital, Beijing, China
| | - Le Shen
- Department of Anesthesiology, Peking Union Medical College Hospital, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases (Peking Union Medical College Hospital), Beijing, China
- *Correspondence: Le Shen,
| | - Yuguang Huang
- Department of Anesthesiology, Peking Union Medical College Hospital, Beijing, China
- State Key Laboratory of Complex Severe and Rare Diseases (Peking Union Medical College Hospital), Beijing, China
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