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Hua C, Liu L, Kong X. Prenatal diagnosis of 1408 foetuses at risk of DMD/BMD by MLPA and Sanger sequencing combined with STR linkage analysis. BMC Med Genomics 2023; 16:310. [PMID: 38041114 PMCID: PMC10691095 DOI: 10.1186/s12920-023-01746-x] [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: 02/01/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023] Open
Abstract
OBJECTIVE This study is a retrospective analysis of the prenatal genetic diagnosis results of 1408 foetuses at high risk of DMD/BMD to provide information for clinical genetic counselling. BACKGROUND Duchenne muscular dystrophy (DMD) is a severe neuromuscular disorder characterized by skeletal and cardiac muscle weakness. With the deepening of disease research, some treatments have been applied in clinics. Therefore, early and accurate prenatal diagnosis can inform pregnancy choices for high-risk families. METHODS A total of 1316 unrelated DMD/BMD families with confirmed genetic diagnoses were recruited from the Genetic and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University. Prenatal diagnosis of 1408 high-risk foetuses was performed by MLPA and Sanger sequencing combined with STR linkage analysis for all families. RESULTS Among the 1316 families, large deletions, duplications, and small variants of the DMD gene accounted for 70.4% (927/1316), 8.2% (108/1316), and 21.4% (281/1316), respectively. Among 1316 mothers, 863 (65.6%) were carriers, and 453 (34.4%) were not carriers. The rate of de novo variants was 34.4% (453/1316) in our study. In addition, gonadal mosaicism was observed in 11 pregnant females. Prenatal diagnosis was provided for 1408 high-risk foetuses; 282 foetuses were identified as male patients, 219 foetuses were female carriers, and the remainder had normal genetics. The results of prenatal diagnosis were consistent with the results of follow-up. CONCLUSIONS Accurate and rapid prenatal diagnosis can be achieved using MLPA, Sanger sequencing, and STR linkage analysis. Furthermore, germline mosaicism in DMD should not be ignored; considering this, a prenatal diagnosis for all pregnant women with a family history of DMD/BMD regardless of whether they carried disease-causing variants is proposed. Genetic counselling and targeted prenatal diagnosis will continue to be a cornerstone of DMD/BMD family management in the future.
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Affiliation(s)
- Chunxiao Hua
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Lina Liu
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
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2
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Liu X, Shi X, Xin Q, Liu Z, Pan F, Qiao D, Chen M, Zhang Y, Guo W, Li C, Zhang Y, Shao L, Zhang R. Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay. BMC Genomics 2023; 24:407. [PMID: 37468838 PMCID: PMC10354997 DOI: 10.1186/s12864-023-09444-9] [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: 01/08/2023] [Accepted: 06/11/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenic multisystem disease caused primarily by mutations in the PKD1 gene or PKD2 gene. There is increasing evidence that some of these variants, which are described as missense, synonymous or nonsense mutations in the literature or databases, may be deleterious by affecting the pre-mRNA splicing process. RESULTS This study aimed to determine the effect of these PKD1 and PKD2 variants on exon splicing combined with predictive bioinformatics tools and minigene assay. As a result, among the 19 candidate single nucleotide alterations, 11 variants distributed in PKD1 (c.7866C > A, c.7960A > G, c.7979A > T, c.7987C > T, c.11248C > G, c.11251C > T, c.11257C > G, c.11257C > T, c.11346C > T, and c.11393C > G) and PKD2 (c.1480G > T) were identified to result in exon skipping. CONCLUSIONS We confirmed that 11 variants in the gene of PKD1 and PKD2 affect normal splicing by interfering the recognition of classical splicing sites or by disrupting exon splicing enhancers and generating exon splicing silencers. This is the most comprehensive study to date on pre-mRNA splicing of exonic variants in ADPKD-associated disease-causing genes in consideration of the increasing number of identified variants in PKD1 and PKD2 gene in recent years. These results emphasize the significance of assessing the effect of exon single nucleotide variants in ADPKD at the mRNA level.
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Affiliation(s)
- Xuyan Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Xiaomeng Shi
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Qing Xin
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Zhiying Liu
- Renal Division, Peking University First Hospital, Beijing, China
| | - Fengjiao Pan
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Dan Qiao
- Department of Nephrology, Dalian Medical University, Dalian, China
| | - Mengke Chen
- Department of Nephrology, Shandong First Medical University, Taian, China
| | - Yiyin Zhang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Wencong Guo
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Changying Li
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Yan Zhang
- Department of Nephrology, Weifang Medical University, Weifang, China
| | - Leping Shao
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China.
| | - Ruixiao Zhang
- Department of Emergency, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China.
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Priante G, Ceol M, Gianesello L, Bizzotto D, Braghetta P, Calò LA, Del Prete D, Anglani F. Emerging Perspectives on the Rare Tubulopathy Dent Disease: Is Glomerular Damage a Direct Consequence of ClC-5 Dysfunction? Int J Mol Sci 2023; 24:1313. [PMID: 36674829 PMCID: PMC9864126 DOI: 10.3390/ijms24021313] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/12/2023] Open
Abstract
Dent disease (DD1) is a rare tubulopathy caused by mutations in the CLCN5 gene. Glomerulosclerosis was recently reported in DD1 patients and ClC-5 protein was shown to be expressed in human podocytes. Nephrin and actin cytoskeleton play a key role for podocyte functions and podocyte endocytosis seems to be crucial for slit diaphragm regulation. The aim of this study was to analyze whether ClC-5 loss in podocytes might be a direct consequence of the glomerular damage in DD1 patients. Three DD1 kidney biopsies presenting focal global glomerulosclerosis and four control biopsies were analyzed by immunofluorescence (IF) for nephrin and podocalyxin, and by immunohistochemistry (IHC) for ClC-5. ClC-5 resulted as down-regulated in DD1 vs. control (CTRL) biopsies in both tubular and glomerular compartments (p < 0.01). A significant down-regulation of nephrin (p < 0.01) in DD1 vs. CTRL was demonstrated. CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/Caspase9) gene editing of CLCN5 in conditionally immortalized human podocytes was used to obtain clones with the stop codon mutation p.(R34Efs*14). We showed that ClC-5 and nephrin expression, analyzed by quantitative Reverse Transcription/Polymerase Chain Reaction (qRT/PCR) and In-Cell Western (ICW), was significantly downregulated in mutant clones compared to the wild type ones. In addition, F-actin staining with fluorescent phalloidin revealed actin derangements. Our results indicate that ClC-5 loss might alter podocyte function either through cytoskeleton disorganization or through impairment of nephrin recycling.
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Affiliation(s)
- Giovanna Priante
- Kidney Histomorphology and Molecular Biology Laboratory, Nephrology Unit, Department of Medicine—DIMED, University of Padua, Via Giustiniani n° 2, 35128 Padua, Italy
| | - Monica Ceol
- Kidney Histomorphology and Molecular Biology Laboratory, Nephrology Unit, Department of Medicine—DIMED, University of Padua, Via Giustiniani n° 2, 35128 Padua, Italy
| | - Lisa Gianesello
- Kidney Histomorphology and Molecular Biology Laboratory, Nephrology Unit, Department of Medicine—DIMED, University of Padua, Via Giustiniani n° 2, 35128 Padua, Italy
| | - Dario Bizzotto
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Paola Braghetta
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Lorenzo Arcangelo Calò
- Kidney Histomorphology and Molecular Biology Laboratory, Nephrology Unit, Department of Medicine—DIMED, University of Padua, Via Giustiniani n° 2, 35128 Padua, Italy
| | - Dorella Del Prete
- Kidney Histomorphology and Molecular Biology Laboratory, Nephrology Unit, Department of Medicine—DIMED, University of Padua, Via Giustiniani n° 2, 35128 Padua, Italy
| | - Franca Anglani
- Kidney Histomorphology and Molecular Biology Laboratory, Nephrology Unit, Department of Medicine—DIMED, University of Padua, Via Giustiniani n° 2, 35128 Padua, Italy
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Xin Q, Liu Q, Liu Z, Shi X, Liu X, Zhang R, Hong Y, Zhao X, Shao L. Twelve exonic variants in the SLC12A1 and CLCNKB genes alter RNA splicing in a minigene assay. Front Genet 2022; 13:961384. [PMID: 36092934 PMCID: PMC9452827 DOI: 10.3389/fgene.2022.961384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Bartter syndrome (BS) is a rare renal tubular disease caused by gene variants in SLC12A1, KCNJ1, CLCNKA, CLCNKB, BSND or MAGED2 genes. There is growing evidence that many exonic mutations can affect the pre-mRNA normal splicing and induce exon skipping by altering various splicing regulatory signals. Therefore, the aim of this study was to gain new insights into the consequences of exonic mutations associated with BS on pre-mRNA splicing.Methods: We analyzed all the missense, nonsense and synonymous variants described in six pathogenic genes by bioinformatics programs and identified candidate mutations that may promote exon skipping through a minigene system.Results: Results of the study showed that 12 of 14 candidate variants distributed in SLC12A1 (c.728G>A, C.735C>G, c.904C>T, c.905G>A, c.1304C>T, c.1493C>T, c.2221A>T) and CLCNKB (c.226C>T, c.228A>C, c.229G>A, c.229G>C, c.1979C>A) were identified to induce splicing alterations. These variants may not only disrupt exonic splicing enhancers (ESEs) but also generate new exonic splicing silencers (ESSs), or disturb the classic splicing sites.Conclusion: To our knowledge, this is a comprehensive study regarding alterations in pre-mRNA of exonic variants in BS pathogenic genes. Our results reinforce the necessity of assessing the consequences of exonic variants at the mRNA level.
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Affiliation(s)
- Qing Xin
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Qihua Liu
- Department of Material Supply Management, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Zhiying Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xuyan Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Ruixiao Zhang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yefeng Hong
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiangzhong Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Xiangzhong Zhao, ; Leping Shao,
| | - Leping Shao
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- *Correspondence: Xiangzhong Zhao, ; Leping Shao,
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Liu Z, Sui A, Wang S, Cui L, Xin Q, Zhang R, Han Y, Shao L, Zhao X. Double synonymous mutations in exon 9 of the Cullin3 gene restore exon inclusion by abolishing hnRNPs inhibition. Hum Mol Genet 2022; 31:4006-4018. [PMID: 35796549 DOI: 10.1093/hmg/ddac148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/06/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
All mutations in exon 9 of the Cullin3 gene associated with pseudohypoaldosteronism type II (PHA II) contribute to exon skipping to different degrees, but the specific molecular mechanism of this aberrant splicing is still unclear. The aims of this study were to investigate the regulatory mechanism underlying two synonymous splicing events, c.1221A > G (p. Glu407Glu) and c.1236G > A (p. Leu412Leu), and to discover a therapeutic strategy for correcting this aberrant splicing by targeting potential regulatory sites. Through a series of RNA pulldown, silver staining, western blotting, siRNA knockdown, in vitro overexpression and single or double site-directed mutagenesis experiments, we first explored the pathogenesis of exon 9 skipping caused by mutations in the CUL3 gene and verified that the main splicing regulators associated with the synonymous c.1221A > G and c.1236G > A mutations were heterogeneous nuclear ribonucleoproteins (hnRNPs). In addition, we verified that introducing another synonymous mutation, c.1224A > G (A18G), significantly rescued the abnormal splicing caused by c.1221A > G and c.1236G > A, highlighting the therapeutic potential for the treatment of PHA II.
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Affiliation(s)
- Zhiying Liu
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, 266555, China.,Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266071, China
| | - Aihua Sui
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, 266555, China
| | - Sai Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266071, China.,Department of Dermatology, Peking University First Hospital, Beijing, 100034, China
| | - Li Cui
- Department of Nephrology, The Affiliated Hospital of Qingdao University, Qingdao, 266555, China
| | - Qing Xin
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, 266555, China.,Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266071, China
| | - Ruixiao Zhang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266071, China
| | - Yue Han
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266071, China
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, 266071, China
| | - Xiangzhong Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, 266555, China
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6
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Singh S, Singh T, Kunja C, Dhoat NS, Dhania NK. Gene-editing, immunological and iPSCs based therapeutics for muscular dystrophy. Eur J Pharmacol 2021; 912:174568. [PMID: 34656607 DOI: 10.1016/j.ejphar.2021.174568] [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: 06/24/2021] [Revised: 09/25/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Muscular dystrophy is a well-known genetically heterogeneous group of rare muscle disorders. This progressive disease causes the breakdown of skeletal muscles over time and leads to grave weakness. This breakdown is caused by a diverse pattern of mutations in dystrophin and dystrophin associated protein complex. These mutations lead to the production of altered proteins in response to which, the body stimulates production of various cytokines and immune cells, particularly reactive oxygen species and NFκB. Immune cells display/exhibit a dual role by inducing muscle damage and muscle repair. Various anti-oxidants, anti-inflammatory and glucocorticoid drugs serve as potent therapeutics for muscular dystrophy. Along with the above mentioned therapeutics, induced pluripotent stem cells also serve as a novel approach paving a way for personalized treatment. These pluripotent stem cells allow regeneration of large numbers of regenerative myogenic progenitors that can be administered in muscular dystrophy patients which assist in the recovery of lost muscle fibers. In this review, we have summarized gene-editing, immunological and induced pluripotent stem cell based therapeutics for muscular dystrophy treatment.
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Affiliation(s)
- Shagun Singh
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda-151001, Punjab, India
| | - Tejpal Singh
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda-151001, Punjab, India
| | - Chaitanya Kunja
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda-151001, Punjab, India
| | - Navdeep S Dhoat
- Department of Pediatrics Surgery, All India Institute of Medical Sciences, Bathinda, 151001, Punjab, India
| | - Narender K Dhania
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda-151001, Punjab, India.
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7
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Wu J, Zhang J, Liu L, Zhang B, Yamamura T, Nozu K, Matsuo M, Zhao J. A disease-causing variant of COL4A5 in a Chinese family with Alport syndrome: a case series. BMC Nephrol 2021; 22:380. [PMID: 34774011 PMCID: PMC8590243 DOI: 10.1186/s12882-021-02585-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Alport syndrome (AS), which is a rare hereditary disease caused by mutations of genes including COL4A3, COL4A4 and COL4A5, has a wide spectrum of phenotypes. Most disease-causing variants of AS are located in the exons or the conservative splicing sites of these genes, while little is known about the intronic disease-causing variants. METHODS A Chinese AS family was recruited in this study. All the clinical data of AS patient were collected from medical records. After pedigree analysis, the pathogenic variants were studied by the whole exome sequencing (WES). Minigene assay and in vivo RT-PCR analysis were performed to validate the functions of the variants. RESULTS Renal biopsy showed a typical histopathology changes of AS. WES revealed compound heterozygous substitution, NM_033380 c.991-14(IVS17) A > G, in the intron 17 of the COL4A5 gene, which were confirmed by Sanger sequencing. Moreover, the variant was co-segregated with the phenotype in this family. Minigene assay in cultured cell lines showed that a splicing error was induced by this intronic variant, which further confirmed by in vivo RT-PCR analysis. CONCLUSION A novel intronic disease-causing variant in COL4A5 gene was identified by WES, which was the molecular pathogenic basis of AS.
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Affiliation(s)
- Jing Wu
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Jun Zhang
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Li Liu
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Bo Zhang
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, 518, Arise, Ikawadani-cho, Nishi, Kobe, Hyogo, 651-2180, Japan
| | - Jinghong Zhao
- Department of Nephrology, the key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Kidney Center of PLA, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, 400037, China.
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8
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Zhang R, Chen Z, Song Q, Wang S, Liu Z, Zhao X, Shi X, Guo W, Lang Y, Bottillo I, Shao L. Identification of seven exonic variants in the SLC4A1, ATP6V1B1, and ATP6V0A4 genes that alter RNA splicing by minigene assay. Hum Mutat 2021; 42:1153-1164. [PMID: 34157794 DOI: 10.1002/humu.24246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/02/2021] [Accepted: 06/19/2021] [Indexed: 12/25/2022]
Abstract
Primary distal renal tubular acidosis (dRTA) is a rare tubular disease associated with variants in SLC4A1, ATP6V0A4, ATP6V1B1, FOXⅠ1, or WDR72 genes. Currently, there is growing evidence that all types of exonic variants can alter splicing regulatory elements, affecting the precursor messenger RNA (pre-mRNA) splicing process. This study was to determine the consequences of variants associated with dRTA on pre-mRNA splicing combined with predictive bioinformatics tools and minigene assay. As a result, among the 15 candidate variants, 7 variants distributed in SLC4A1 (c.1765C>T, p.Arg589Cys), ATP6V1B1 (c.368G>T, p.Gly123Val; c.370C>T, p.Arg124Trp; c.484G>T, p.Glu162* and c.1102G>A, p.Glu368Lys) and ATP6V0A4 genes (c.322C>T, p.Gln108* and c.1572G>A, p.Pro524Pro) were identified to result in complete or incomplete exon skipping by either disruption of exonic splicing enhancers (ESEs) and generation of exonic splicing silencers, or interference with the recognition of the classic splicing site, or both. To our knowledge, this is the first study on pre-mRNA splicing of exonic variants in the dRTA-related genes. These results highlight the importance of assessing the effects of exonic variants at the mRNA level and suggest that minigene analysis is an effective tool for evaluating the effects of splicing on variants in vitro.
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Affiliation(s)
- Ruixiao Zhang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Zeqing Chen
- Academy for Engineering and Technology, Fudan University, Shanghai, China
| | - Qijing Song
- Emergency Center, People's Hospital of Jimo District, Qingdao, China
| | - Sai Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China.,Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Zhiying Liu
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiangzhong Zhao
- Central Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Wencong Guo
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yanhua Lang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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Saint-Martin C, Cauchois-Le Mière M, Rex E, Soukarieh O, Arnoux JB, Buratti J, Bouvet D, Frébourg T, Gaildrat P, Shyng SL, Bellanné-Chantelot C, Martins A. Functional characterization of ABCC8 variants of unknown significance based on bioinformatics predictions, splicing assays, and protein analyses: Benefits for the accurate diagnosis of congenital hyperinsulinism. Hum Mutat 2021; 42:408-420. [PMID: 33410562 DOI: 10.1002/humu.24164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
Abstract
ABCC8 encodes the SUR1 subunit of the β-cell ATP-sensitive potassium channel whose loss of function causes congenital hyperinsulinism (CHI). Molecular diagnosis is critical for optimal management of CHI patients. Unfortunately, assessing the impact of ABCC8 variants on RNA splicing remains very challenging as this gene is poorly expressed in leukocytes. Here, we performed bioinformatics analysis and cell-based minigene assays to assess the impact on splicing of 13 ABCC8 variants identified in 20 CHI patients. Next, channel properties of SUR1 proteins expected to originate from minigene-detected in-frame splicing defects were analyzed after ectopic expression in COSm6 cells. Out of the analyzed variants, seven induced out-of-frame splicing defects and were therefore classified as recessive pathogenic, whereas two led to skipping of in-frame exons. Channel functional analysis of the latter demonstrated their pathogenicity. Interestingly, the common rs757110 SNP increased exon skipping in our system suggesting that it may act as a disease modifier factor. Our strategy allowed determining the pathogenicity of all selected ABCC8 variants, and CHI-inheritance pattern for 16 out of the 20 patients. This study highlights the value of combining RNA and protein functional approaches in variant interpretation and reveals the minigene splicing assay as a new tool for CHI molecular diagnostics.
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Affiliation(s)
- Cécile Saint-Martin
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Marine Cauchois-Le Mière
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Emily Rex
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Omar Soukarieh
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Jean-Baptiste Arnoux
- Department of Inherited Metabolic Disease, Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Julien Buratti
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Delphine Bouvet
- Department of Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Thierry Frébourg
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | | | - Alexandra Martins
- Inserm U1245, UFR de Médecine et Pharmacie, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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10
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Torella A, Zanobio M, Zeuli R, del Vecchio Blanco F, Savarese M, Giugliano T, Garofalo A, Piluso G, Politano L, Nigro V. The position of nonsense mutations can predict the phenotype severity: A survey on the DMD gene. PLoS One 2020; 15:e0237803. [PMID: 32813700 PMCID: PMC7437896 DOI: 10.1371/journal.pone.0237803] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/03/2020] [Indexed: 12/23/2022] Open
Abstract
A nonsense mutation adds a premature stop signal that hinders any further translation of a protein-coding gene, usually resulting in a null allele. To investigate the possible exceptions, we used the DMD gene as an ideal model. First, because dystrophin absence causes Duchenne muscular dystrophy (DMD), while its reduction causes Becker muscular dystrophy (BMD). Second, the DMD gene is X-linked and there is no second allele that can interfere in males. Third, databases are accumulating reports on many mutations and phenotypic data. Finally, because DMD mutations may have important therapeutic implications. For our study, we analyzed large databases (LOVD, HGMD and ClinVar) and literature and revised critically all data, together with data from our internal patients. We totally collected 2593 patients. Positioning these mutations along the dystrophin transcript, we observed a nonrandom distribution of BMD-associated mutations within selected exons and concluded that the position can be predictive of the phenotype. Nonsense mutations always cause DMD when occurring at any point in fifty-one exons. In the remaining exons, we found milder BMD cases due to early 5’ nonsense mutations, if reinitiation can occur, or due to late 3’ nonsense when the shortened product retains functionality. In the central part of the gene, all mutations in some in-frame exons, such as in exons 25, 31, 37 and 38 cause BMD, while mutations in exons 30, 32, 34 and 36 cause DMD. This may have important implication in predicting the natural history and the efficacy of therapeutic use of drug-stimulated translational readthrough of premature termination codons, also considering the action of internal natural rescuers. More in general, our survey confirm that a nonsense mutation should be not necessarily classified as a null allele and this should be considered in genetic counselling.
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Affiliation(s)
- Annalaura Torella
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Mariateresa Zanobio
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Roberta Zeuli
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | | | - Marco Savarese
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Folkhälsan Research Center, Medicum, University of Helsinki, Helsinki, Finland
| | - Teresa Giugliano
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Arcomaria Garofalo
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Giulio Piluso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Luisa Politano
- Dipartimento di Medicina Sperimentale, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
| | - Vincenzo Nigro
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, Napoli, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
- * E-mail:
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11
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Increasing the Genetic Diagnosis Yield in Inherited Retinal Dystrophies: Assigning Pathogenicity to Novel Non-canonical Splice Site Variants. Genes (Basel) 2020; 11:genes11040378. [PMID: 32244552 PMCID: PMC7231145 DOI: 10.3390/genes11040378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 12/11/2022] Open
Abstract
Aims: We aimed to validate the pathogenicity of genetic variants identified in inherited retinal dystrophy (IRD) patients, which were located in non-canonical splice sites (NCSS). Methods: After next generation sequencing (NGS) analysis (target gene panels or whole exome sequencing (WES)), NCSS variants were prioritized according to in silico predictions. In vivo and in vitro functional tests were used to validate their pathogenicity. Results: Four novel NCSS variants have been identified. They are located in intron 33 and 34 of ABCA4 (c.4774-9G>A and c.4849-8C>G, respectively), intron 2 of POC1B (c.101-3T>G) and intron 3 of RP2 (c.884-14G>A). Functional analysis detected different aberrant splicing events, including intron retention, exon skipping and intronic nucleotide addition, whose molecular effect was either the disruption or the elongation of the open reading frame of the corresponding gene. Conclusions: Our data increase the genetic diagnostic yield of IRD patients and expand the landscape of pathogenic variants, which will have an impact on the genotype–phenotype correlations and allow patients to opt for the emerging gene and cell therapies.
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Exon skipping induced by nonsense/frameshift mutations in DMD gene results in Becker muscular dystrophy. Hum Genet 2020; 139:247-255. [PMID: 31919629 PMCID: PMC6981323 DOI: 10.1007/s00439-019-02107-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 12/27/2019] [Indexed: 01/13/2023]
Abstract
Duchenne muscular dystrophy (DMD) is caused by a nonsense or frameshift mutation in the DMD gene, while its milder form, Becker muscular dystrophy (BMD) is caused by an in-frame deletion/duplication or a missense mutation. Interestingly, however, some patients with a nonsense mutation exhibit BMD phenotype, which is mostly attributed to the skipping of the exon containing the nonsense mutation, resulting in in-frame deletion. This study aims to find BMD cases with nonsense/frameshift mutations in DMD and to investigate the exon skipping rate of those nonsense/frameshift mutations. We searched for BMD cases with nonsense/frameshift mutations in DMD in the Japanese Registry of Muscular Dystrophy. For each DMD mutation identified, we constructed minigene plasmids containing one exon with/without a mutation and its flanking intronic sequence. We then introduced them into HeLa cells and measured the skipping rate of transcripts of the minigene by RT-qPCR. We found 363 cases with a nonsense/frameshift mutation in DMD gene from a total of 1497 dystrophinopathy cases in the registry. Among them, 14 had BMD phenotype. Exon skipping rates were well correlated with presence or absence of dystrophin, suggesting that 5% exon skipping rate is critical for the presence of dystrophin in the sarcolemma, leading to milder phenotypes. Accurate quantification of the skipping rate is important in understanding the exact functions of the nonsense/frameshift mutations in DMD and for interpreting the phenotypes of the BMD patients.
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