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Xiong T, Xu Z, Wan Q, Chen F, Ye Y, Wang H, Wu C. Identification of a novel ANK1 gene variant c.1504-9G>A and its mechanism of intron retention in hereditary spherocytosis. Front Genet 2024; 15:1390924. [PMID: 38655052 PMCID: PMC11035775 DOI: 10.3389/fgene.2024.1390924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Objective: The objective of this study was to pinpoint pathogenic genes and assess the mutagenic pathogenicity in two pediatric patients with hereditary spherocytosis. Methods: We utilized whole-exome sequencing (WES) for individual analysis (case 1) and family-based trio analysis (case 2). The significance of the intronic mutation was validated through a Minigene splicing assay and supported by subsequent in vitro experiments. Results: Both probands received a diagnosis of hereditary spherocytosis. WES identified a novel ANK1 c.1504-9G>A mutation in both patients, causing the retention of seven nucleotides at the 5' end of intron 13, as substantiated by the Minigene assay. This variant results in a premature stop codon and the production of a truncated protein. In vitro studies indicated a reduced expression of the ANK1 gene. Conclusion: The novel ANK1 c.1504-9G>A variant is established as the causative factor for hereditary spherocytosis, with the c.1504-9G site functioning as a splicing receptor.
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Affiliation(s)
- Ting Xiong
- Department of Endocrine Genetics and Metabolism, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Zhongjin Xu
- Department of Hematology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Qian Wan
- Department of Hematology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Feng Chen
- Department of Hematology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Yao Ye
- Department of Hematology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Hong Wang
- Department of Hematology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Chongjun Wu
- Department of Hematology, Jiangxi Provincial Children’s Hospital, Nanchang, China
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Yang J, Ni L, Li A, Li M, Ruan S, Xiang D, Zhu Z, Ye L. A novel homozygous splice-site mutation of JK gene leads to Jk(a-b-) phenotype. Transfus Med 2024; 34:39-45. [PMID: 37950522 DOI: 10.1111/tme.13016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
OBJECTIVES This study aimed to investigate the molecular mechanism of the Jk(a-b-) phenotype in a Chinese transfusion patient. BACKGROUND Many different mutation types relating to Jk(a-b-) phenotype have been reported. However, the splice-site mutation is relatively rare and the related functional verification is lacking. MATERIALS AND METHODS In this study, the blood sample was collected from a transfusion patient with the Jk(a-b-) phenotype. Serotyping was performed using routine serological methods. The exons sequences and coding regions of the JK gene were amplified using polymerase chain reaction and directly sequenced. To perform a minigene splicing assay, the intronic mutation sequences were cloned into a pSPL3 splice reporting vector. The splicing reporter minigene assay was performed in HEK 293T cells. RESULTS The Jk(a-b-) phenotype of the blood sample was identified through serological testing. Sequencing results revealed that the sample had a novel homozygous splice-site mutation JK*02N (NM_015865.7: c.663+3A>C). Further analysis, including cDNA sequencing and minigene splicing assay, confirmed that the novel splice-site mutation resulted in exon skipping. Interestingly, different numbers of exons being skipped were obtained by the two methods. CONCLUSION This study revealed a novel homozygous splicing-site mutation associated with the Jk(a-b-) phenotype in Chinese population. Our results emphasise the importance of the in vitro functional method minigene splicing assay, while also acknowledging its potential limitations when compared to cDNA sequencing.
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Affiliation(s)
- Jiaxuan Yang
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Lina Ni
- Department of Blood Transfusion, Weihai Central Hospital, Weihai, China
| | - Aijing Li
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Minghao Li
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Shulin Ruan
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Dong Xiang
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Ziyan Zhu
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Luyi Ye
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
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Smith C, Burugula BB, Dunn I, Aradhya S, Kitzman JO, Yee JL. High-Throughput Splicing Assays Identify Known and Novel WT1 Exon 9 Variants in Nephrotic Syndrome. Kidney Int Rep 2023; 8:2117-2125. [PMID: 37850022 PMCID: PMC10577367 DOI: 10.1016/j.ekir.2023.07.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Frasier syndrome (FS) is a rare Mendelian form of nephrotic syndrome (NS) caused by variants which disrupt the proper splicing of WT1. This key transcription factor gene is alternatively spliced at exon 9 to produce 2 isoforms ("KTS+" and "KTS-"), which are normally expressed in the kidney at a ∼2:1 (KTS+:KTS-) ratio. FS results from variants that reduce this ratio by disrupting the splice donor of the KTS+ isoform. FS is extremely rare, and it is unclear whether any variants beyond the 8 already known could cause FS. Methods To prospectively identify other splicing-disruptive variants, we leveraged a massively parallel splicing assay. We tested every possible single nucleotide variant (n = 519) in and around WT1 exon 9 for effects upon exon inclusion and KTS+/- ratio. Results Splice disruptive variants (SDVs) made up 11% of the tested point variants overall and were tightly concentrated near the canonical acceptor and the KTS+/- alternate donors. Our map successfully identified all 8 known FS or focal segmental glomerulosclerosis (FSGS) variants and 16 additional novel variants which were comparably disruptive to these known pathogenic variants. We also identified 19 variants that, conversely, increased the KTS+/KTS- ratio, of which 2 are observed in unrelated individuals with 46,XX ovotesticular disorder of sex development (46,XX OTDSD). Conclusion This splicing effect map can serve as functional evidence to guide the clinical interpretation of newly observed variants in and around WT1 exon 9.
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Affiliation(s)
- Cathy Smith
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bala Bharathi Burugula
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ian Dunn
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Jacob O. Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jennifer Lai Yee
- Department of Pediatrics, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
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Xiang Y, Xu C, Xu Y, Zhou L, Tang S, Xu X. Novel compound heterozygous synonymous and missense variants in the MYO7A gene identified by next-generation sequencing in a Chinese family with nonsyndromic hearing loss. J Clin Lab Anal 2022; 36:e24708. [PMID: 36164746 DOI: 10.1002/jcla.24708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/28/2022] [Accepted: 09/06/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Variants in the MYO7A gene are increasingly identified among patients suffering from Usher syndrome type 1B (USH1B). However, such mutations are less commonly detected among patients suffering from nonsyndromic hearing loss (NSHL), including autosomal recessive deafness (DFNB2) and autosomal dominant deafness (DFNA11). This research attempts to clarify the genetic base of DFNB2 in a Chinese family and determine the pathogenicity of the identified mutations. METHOD Targeted next-generation sequencing (TGS) of 127 known deafness genes was performed for the 14-year-old proband. Then, Sanger sequencing was performed on the available family members. A minigene splicing assay was performed to verify the impact of the novel MYO7A synonymous variant. After performing targeted next-generation sequencing (TGS) of 127 existing hearing loss-related genes in a 14-year-old proband, Sanger sequencing was carried out on the available family members. Then, to confirm the influence of the novel MYO7A synonymous variants, a minigene splicing assay was performed. RESULTS Two heteroallelic mutants of MYO7A (NM_000260.3) were identified: a maternally inherited synonymous variant c.2904G > A (p.Glu968=) in exon 23 and a paternally inherited missense variant c.5994G > T (p.Trp1998Cys) in exon 44. The in vitro minigene expression indicated that c.2904G > A may result in skipping of exon 23 resulting in a truncated protein. CONCLUSIONS We reported a novel missense (c.5994G > T) and identified, for the first time, a novel pathogenic synonymous (c.2904G > A) variant within MYO7A in a patient with DFNB2. These findings enrich our understanding of the MYO7A variant spectrum of DFNB2 and can contribute to accurate genetic counseling and diagnosis of NSHL patients.
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Affiliation(s)
- Yanbao Xiang
- Department of Genetics, Key Laboratory of Birth Defects of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Chenyang Xu
- Department of Genetics, Key Laboratory of Birth Defects of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Yunzhi Xu
- Department of Genetics, Key Laboratory of Birth Defects of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Lili Zhou
- Department of Genetics, Key Laboratory of Birth Defects of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Shaohua Tang
- Department of Genetics, Key Laboratory of Birth Defects of Wenzhou, Wenzhou Central Hospital, Wenzhou, China.,Department of Clinical Laboratory Medicine, Key Laboratory of Precision Medicine of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
| | - Xueqin Xu
- Department of Genetics, Key Laboratory of Birth Defects of Wenzhou, Wenzhou Central Hospital, Wenzhou, China.,Department of Clinical Laboratory Medicine, Key Laboratory of Precision Medicine of Wenzhou, Wenzhou Central Hospital, Wenzhou, China
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5
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Guo Q, Zhang P, Ying W, Wang Y, Zhu J, Li G, Wang H, Wang X, Lei C, Zhou W, Sun J, Wu B. Intron retention by a novel intronic mutation in DKC1 gene caused recurrent still birth and early death in a Chinese family. Mol Genet Genomic Med 2022; 10:e1934. [PMID: 35384376 PMCID: PMC9184655 DOI: 10.1002/mgg3.1934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 02/09/2022] [Accepted: 03/14/2022] [Indexed: 11/06/2022] Open
Abstract
Background DKC1, the dyskerin encoding gene, functions in telomerase activity and telomere maintenance. DKC1 mutations cause a multisystem disease, dyskeratosis congenita (DC), which is associated with immunodeficiency and bone marrow failure. Methods In this research, we reported a novel intronic mutation of DKC1 causing dyskerin functional loss in a Chinese family. Whole exome sequence (WES) of the proband and validation by sanger sequencing help us identify a pathogenic DKC1 mutation. Minigene splicing assays were performed to evaluate functional change of DKC1. Results A pathogenic DKC1 intronic mutation(c.84 + 7A > G) was identified in the proband, which was inherited from heterozygous mother and not reported before. We detected the novel transcript with a 7 bp intron retention through minigene splicing assay. The newly spliced transcript is so short that would be degraded by nonsense‐mediated mRNA decay in vitro and we infer that the novel DKC1 mutation would influences normal physiological function of dyskerin. Conclusions Our study identified a novel intronic mutation, which expands the spectrum of pathogenic DKC1 gene mutations and can be used in molecular diagnosis. The mutant allele was transmitted to the next generation with high frequency in the family and causes still birth or early death.
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Affiliation(s)
- Qiufang Guo
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Berry Genomics Co., Beijing, China
| | - Ping Zhang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenjing Ying
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yaqiong Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jitao Zhu
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gang Li
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaochuan Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Caixia Lei
- Prenatal Diagnosis Center, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jinqiao Sun
- Department of Allergy and Clinical Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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Wang D, Dong X, Xiong Y, Li Z, Xie Y, Liang S, Huang T. Identification of a novel TBX5 c.755 + 1 G > A variant and related pathogenesis in a family with Holt-Oram syndrome. Am J Med Genet A 2022; 188:58-70. [PMID: 34490705 PMCID: PMC9290998 DOI: 10.1002/ajmg.a.62488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023]
Abstract
The proband with congenital heart disease and abnormal thumb was clinically diagnosed as Holt-Oram syndrome (HOS). A novel variant, T-box transcription factor 5 (TBX5) c.755 + 1 G > A, was identified in the proband via whole exome sequencing and validated using Sanger sequencing. Pedigree analysis and clinical examinations revealed three/seven individuals over three generations within the family, with features suggestive of HOS. Deep amplicon sequencing confirmed that the allele frequencies of the novel variant in the proband (III-1), her brother (III-2), and her mother (II-2) were 50%, 48.3%, and 38.1%, respectively, indicating that III-1 and III-2 harbored heterozygous variants, while II-2 harbored mosaic heterozygous variants. The minigene splicing assay showed that the novel variant affected the normal splicing of exon 7, resulting in the production of abnormal TBX5 transcripts. Reverse transcription-quantitative polymerase chain reaction and western blot analyses revealed that the novel variant upregulated TBX5 expression at the transcriptional and translational levels. Nuclear localization assay demonstrated impaired nuclear localization of the mutant TBX5. Cell viability assay revealed the inhibition of cell activity by the mutant TBX5. Our findings indicate that the novel variant was potentially induced HOS, probably by causing aberrant splicing, reducing the enrichment of nuclear TBX5 protein, and inhibiting cellular proliferation.
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Affiliation(s)
- De‐Gang Wang
- Research Center for Reproductive Medicine, Shantou University Medical College, Shantou, China
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xing‐Sheng Dong
- Prenatal Diagnosis CenterBoai Hospital of ZhongshanZhongshanChina
| | - Yi Xiong
- Prenatal Diagnosis CenterBoai Hospital of ZhongshanZhongshanChina
- The Second School of Clinical Medicine, Southern Medical UniversityGuangzhouChina
| | - Zhi‐Ming Li
- Prenatal Diagnosis CenterBoai Hospital of ZhongshanZhongshanChina
| | - Ying‐Jun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong ProvinceThe Third Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Shu‐Hua Liang
- The Second School of Clinical Medicine, Southern Medical UniversityGuangzhouChina
| | - Tian‐Hua Huang
- Research Center for Reproductive Medicine, Shantou University Medical College, Shantou, China
- Chengdu Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu, China
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Yuan M, Guo Y, Xia H, Xu H, Deng H, Yuan L. Novel SCN5A and GPD1L Variants Identified in Two Unrelated Han-Chinese Patients With Clinically Suspected Brugada Syndrome. Front Cardiovasc Med 2021; 8:758903. [PMID: 34957250 PMCID: PMC8692717 DOI: 10.3389/fcvm.2021.758903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022] Open
Abstract
Brugada syndrome (BrS) is a complexly genetically patterned, rare, malignant, life-threatening arrhythmia disorder. It is autosomal dominant in most cases and characterized by identifiable electrocardiographic patterns, recurrent syncope, nocturnal agonal respiration, and other symptoms, including sudden cardiac death. Over the last 2 decades, a great number of variants have been identified in more than 36 pathogenic or susceptibility genes associated with BrS. The present study used the combined method of whole exome sequencing and Sanger sequencing to identify pathogenic variants in two unrelated Han-Chinese patients with clinically suspected BrS. Minigene splicing assay was used to evaluate the effects of the splicing variant. A novel heterozygous splicing variant c.2437-2A>C in the sodium voltage-gated channel alpha subunit 5 gene (SCN5A) and a novel heterozygous missense variant c.161A>T [p.(Asp54Val)] in the glycerol-3-phosphate dehydrogenase 1 like gene (GPD1L) were identified in these two patients with BrS-1 and possible BrS-2, respectively. Minigene splicing assay indicated the deletion of 15 and 141 nucleotides in exon 16, resulting in critical amino acid deletions. These findings expand the variant spectrum of SCN5A and GPD1L, which can be beneficial to genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Meng Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yi Guo
- Department of Medical Information, School of Life Sciences, Central South University, Changsha, China
| | - Hong Xia
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China
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Lin JH, Wu H, Zou WB, Masson E, Fichou Y, Le Gac G, Cooper DN, Férec C, Liao Z, Chen JM. Splicing Outcomes of 5' Splice Site GT>GC Variants That Generate Wild-Type Transcripts Differ Significantly Between Full-Length and Minigene Splicing Assays. Front Genet 2021; 12:701652. [PMID: 34422003 PMCID: PMC8375439 DOI: 10.3389/fgene.2021.701652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022] Open
Abstract
Combining data derived from a meta-analysis of human disease-associated 5' splice site GT>GC (i.e., +2T>C) variants and a cell culture-based full-length gene splicing assay (FLGSA) of forward engineered +2T>C substitutions, we recently estimated that ∼15-18% of +2T>C variants can generate up to 84% wild-type transcripts relative to their wild-type counterparts. Herein, we analyzed the splicing outcomes of 20 +2T>C variants that generate some wild-type transcripts in two minigene assays. We found a high discordance rate in terms of the generation of wild-type transcripts, not only between FLGSA and the minigene assays but also between the different minigene assays. In the pET01 context, all 20 wild-type minigene constructs generated the expected wild-type transcripts; of the 20 corresponding variant minigene constructs, 14 (70%) generated wild-type transcripts. In the pSPL3 context, only 18 of the 20 wild-type minigene constructs generated the expected wild-type transcripts whereas 8 of the 18 (44%) corresponding variant minigene constructs generated wild-type transcripts. Thus, in the context of a particular type of variant, we raise awareness of the limitations of minigene splicing assays and emphasize the importance of sequence context in regulating splicing. Whether or not our findings apply to other types of splice-altering variant remains to be investigated.
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Affiliation(s)
- Jin-Huan Lin
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Hao Wu
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
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Li L, Cao Y, Zhao F, Mao B, Ren X, Wang Y, Guan Y, You Y, Li S, Yang T, Zhao X. Validation and Classification of Atypical Splicing Variants Associated With Osteogenesis Imperfecta. Front Genet 2019; 10:979. [PMID: 31737030 PMCID: PMC6832110 DOI: 10.3389/fgene.2019.00979] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/13/2019] [Indexed: 01/17/2023] Open
Abstract
Osteogenesis Imperfecta (OI) is a rare inherited bone dysplasia, which is mainly caused by mutations in genes encoding type I collagen including COL1A1 and COL1A2. It has been well established to identify the classical variants as well as consensus splicing-site-variants in these genes in our previous studies. However, how atypical variants affect splicing in OI patients remains unclear. From a cohort of 867 OI patients, we collected blood samples from 34 probands which contain 29 variants that are located close to splice donor/acceptor sites in either COL1A1 or COL1A2. By conducting minigene assay and sequencing analysis, we found that 17 out of 29 variants led to aberrant splicing effects, while no remarkable aberrant splicing effect was observed in the remaining 12 variants. Among the 17 variants that affect splicing, 14 variants led to single splicing influence: 9 led to exon skipping, 2 resulted in truncated exon, and 3 caused intron retention. There were three complicated cases showing more than one mutant transcript caused by recognition of several different splice sites. This functional study expands our knowledge of atypical splicing variants, and emphasizes the importance of clarifying the splicing effect for variants near exon/intron boundaries in OI.
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Affiliation(s)
- Lulu Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yixuan Cao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Feiyue Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Bin Mao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiuzhi Ren
- Department of Orthopaedics, The People's Hospital of Wuqing District, Tianjin, China
| | - Yanzhou Wang
- Department of Pediatric Orthopaedics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Yun Guan
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, United States
| | - Yi You
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shan Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Tao Yang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
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