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Gwack J, Kim N, Park J. Improving the Yield of Genetic Diagnosis through Additional Genetic Panel Testing in Hereditary Ophthalmic Diseases. Curr Issues Mol Biol 2024; 46:5010-5022. [PMID: 38785568 PMCID: PMC11119902 DOI: 10.3390/cimb46050300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 05/25/2024] Open
Abstract
Numerous hereditary ophthalmic diseases display significant genetic diversity. Consequently, the utilization of gene panel sequencing allows a greater number of patients to receive a genetic diagnosis for their clinical manifestations. We investigated how to improve the yield of genetic diagnosis through additional gene panel sequencing in hereditary ophthalmic diseases. A gene panel sequencing consisting of a customized hereditary retinopathy panel or hereditary retinitis pigmentosa (RP) panel was prescribed and referred to a CAP-accredited clinical laboratory. If no significant mutations associated with hereditary retinopathy and RP were detected in either panel, additional gene panel sequencing was requested for research use, utilizing the remaining panel. After additional gene panel sequencing, a total of 16 heterozygous or homozygous variants were identified in 15 different genes associated with hereditary ophthalmic diseases. Of 15 patients carrying any candidate variants, the clinical symptoms could be tentatively accounted for by genetic mutations in seven patients. However, in the remaining eight patients, given the in silico mutation predictive analysis, variant allele frequency in gnomAD, inheritance pattern, and genotype-phenotype correlation, fully elucidating the clinical manifestations with the identified rare variant was challenging. Our study highlights the utility of gene panel sequencing in achieving accurate diagnoses for hereditary ophthalmic diseases and enhancing the diagnostic yield through additional gene panel sequencing. Thus, gene panel sequencing can serve as a primary tool for the genetic diagnosis of hereditary ophthalmic diseases, even in cases where a single genetic cause is suspected. With a deeper comprehension of the genetic mechanisms underlying these diseases, it becomes feasible.
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Affiliation(s)
- Jin Gwack
- Department of Preventive Medicine, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea;
| | - Namsu Kim
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Department of Laboratory Medicine, Daejeon St. Mary’s Hospital, Daejeon 34943, Republic of Korea
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Huang L, Zhang Y, Fu H, Gu W, Mao J. A missense mutant of ocrl1 promotes apoptosis of tubular epithelial cells and disrupts endocytosis and the cell cycle of podocytes in Dent-2 Disease. Cell Commun Signal 2023; 21:256. [PMID: 38049819 PMCID: PMC10696739 DOI: 10.1186/s12964-023-01272-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/13/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND This study aimed to identify an orcl1 mutation in a patient with Dent-2 Disease and investigate the underlying mechanisms. METHODS The ocrl1 mutation was identified through exome sequencing. Knockdown of orcl1 and overexpression of the orcl1 mutant were performed in HK-2 and MPC5 cells to study its function, while flow cytometry measured reactive oxygen species (ROS), phosphatidylserine levels, and cell apoptosis. Scanning electron microscopy observed crystal adhesion, while transmission electron microscopy examined kidney tissue pathology. Laser scanning confocal microscopy was used to examine endocytosis, and immunohistochemical and immunofluorescence assays detected protein expression. Additionally, podocyte-specific orcl1 knockout mice were generated to investigate the role of orcl1 in vivo. RESULTS We identified a mutation resulting in the replacement of Histidine with Arginine at position 318 (R318H) in ocrl1 in the proband. orcl1 was widely expressed in the kidney. In vitro experiments showed that knockdown of orcl1 and overexpression of ocrl1 mutant increased ROS, phosphatidylserine exocytosis, crystal adhesion, and cell apoptosis in HK-2 cells. Knockdown of orcl1 in podocytes reduced endocytosis and disrupted the cell cycle while increasing cell migration. In vivo studies in mice showed that conditional deletion of orcl1 in podocytes caused glomerular dysfunction, including proteinuria and fibrosis. CONCLUSION This study identified an R318H mutation in orcl1 in a patient with Dent-2 Disease. This mutation may contribute to renal injury by promoting ROS production and inducing cell apoptosis in tubular cells, while disrupting endocytosis and the cell cycle, and promoting cell migration of podocytes. Video Abstract.
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Affiliation(s)
- Limin Huang
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine. National Clinical Research Center for Child Health, Hangzhou, China
| | - Yingying Zhang
- Department of Pediatrics, Clinical Center of Pediatric Nephrology of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haidong Fu
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine. National Clinical Research Center for Child Health, Hangzhou, China
| | - Weizhong Gu
- Department of Pathologyology, Children's Hospital, Zhejiang University School of Medicine. National Clinical Research Center for Child Health, Hangzhou, China
| | - Jianhua Mao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine. National Clinical Research Center for Child Health, Hangzhou, China.
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Mura-Escorche G, Perdomo-Ramírez A, Ramos-Trujillo E, Trujillo-Frías CJ, Claverie-Martín F. Characterization of pre-mRNA Splicing Defects Caused by CLCN5 and OCRL Mutations and Identification of Novel Variants Associated with Dent Disease. Biomedicines 2023; 11:3082. [PMID: 38002082 PMCID: PMC10669864 DOI: 10.3390/biomedicines11113082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Dent disease (DD) is an X-linked renal tubulopathy characterized by low-molecular-weight proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis and progressive renal failure. Two-thirds of cases are associated with inactivating variants in the CLCN5 gene (Dent disease 1, DD1) and a few present variants in the OCRL gene (Dent disease 2, DD2). The aim of the present study was to test the effect on the pre-mRNA splicing process of DD variants, described here or in the literature, and describe the clinical and genotypic features of thirteen unrelated patients with suspected DD. All patients presented tubular proteinuria, ten presented hypercalciuria and five had nephrolithiasis or nephrocalcinosis. CLCN5 and OCRL genes were analyzed by Sanger sequencing. Nine patients showed variants in CLCN5 and four in OCRL; eight of these were new. Bioinformatics tools were used to select fifteen variants with a potential effect on pre-mRNA splicing from our patients' group and from the literature, and were experimentally tested using minigene assays. Results showed that three exonic missense mutations and two intronic variants affect the mRNA splicing process. Our findings widen the genotypic spectrum of DD and provide insight into the impact of variants causing DD.
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Affiliation(s)
- Glorián Mura-Escorche
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
- Departamento de Medicina Interna, Dermatología y Psiquiatría, Facultad de Medicina, Universidad de la Laguna, 38071 Santa Cruz de Tenerife, Spain
| | - Ana Perdomo-Ramírez
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
| | - Elena Ramos-Trujillo
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
- Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de la Laguna, 38071 Santa Cruz de Tenerife, Spain
| | - Carmen Jane Trujillo-Frías
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
| | - Félix Claverie-Martín
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
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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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Shi X, Wang H, Zhang R, Liu Z, Guo W, Wang S, Liu X, Lang Y, Bottillo I, Dong B, Shao L. Minigene splicing assays reveal new insights into exonic variants of the SLC12A3 gene in Gitelman syndrome. Mol Genet Genomic Med 2023; 11:e2128. [PMID: 36597580 PMCID: PMC10094094 DOI: 10.1002/mgg3.2128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/15/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gitelman syndrome (GS) is a type of salt-losing tubular disease, most of which is caused by SLC12A3 gene variants, and missense variants account for the majority. Recently, the phenomenon of exon skipping, in which variants disrupt normal pre-mRNA splicing, has been related to a variety of diseases. Therefore, we hypothesize that a certain proportion of SLC12A3 variants can result in disease via interfering with the normal splicing process. METHODS We analyzed 342 previously presumed SLC12A3 missense variants using bioinformatics programs and identified candidate variants that may alter the splicing of pre-mRNA through minigene assays. RESULTS Our study revealed that, among ten candidate variants, six variants (c.602G>A, c.602G>T, c.1667C>T, c.1925G>A, c.2548G>C, and c.2549G>C) led to complete or incomplete exon skipping by affecting exonic splicing regulatory elements and/or disturbing canonical splice sites. CONCLUSION It is worth mentioning that this is the largest study on pre-mRNA splicing of SLC12A3 exonic variants. In addition, our study emphasizes the importance of detecting splicing function at the mRNA level in GS and indicates that minigene analysis is a valuable tool for splicing functional assays of variants in vitro.
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Affiliation(s)
- Xiaomeng Shi
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Hong Wang
- Department of Nephrology, Qingdao Eighth People's Hospital, Qingdao, China
| | - Ruixiao Zhang
- Department of Nephrology, 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
| | - Wencong Guo
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, 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
| | - Xuyan Liu
- 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, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Bingzi Dong
- Department of Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Leping Shao
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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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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A case of Dent disease type 2 with large deletion of OCRL diagnosed after close examination of a school urinary test. CEN Case Rep 2022; 11:366-370. [PMID: 35098431 DOI: 10.1007/s13730-022-00685-3] [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: 06/14/2021] [Accepted: 01/20/2022] [Indexed: 10/19/2022] Open
Abstract
A 7-year-old boy visited our hospital for a detailed examination of proteinuria identified in a school urinary test. He had short stature, misaligned teeth, and mild intellectual disability. A urinary examination identified mild proteinuria and extremely high levels of beta-2 microglobulin. On blood examination, his protein, albumin, and creatinine levels were found to be normal; however, his lactate dehydrogenase and creatinine phosphokinase levels were slightly elevated. Upon histological examination, no abnormalities in glomeruli or tubules were found. Considering these results, we diagnosed our patient with Dent disease type 2 (DD2). Although the whole exome sequencing revealed large deletion of OCRL, which was seen only in Lowe syndrome and not in DD2 previously, our final diagnosis for the patient is DD2. A phenotypic continuum exists between Dent disease and Lowe syndrome, and several factors modify the phenotypes caused by defects in OCRL. Although patients have thus far been diagnosed with DD2 or Lowe syndrome on the basis of their symptoms, accumulation and analysis of cases with OCRL defects may hereafter enable more accurate diagnoses.
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Sakakibara N, Ijuin T, Horinouchi T, Yamamura T, Nagano C, Okada E, Ishiko S, Aoto Y, Rossanti R, Ninchoji T, Awano H, Nagase H, Minamikawa S, Tanaka R, Matsuyama T, Nagatani K, Kamei K, Jinnouchi K, Ohtsuka Y, Oka M, Araki Y, Tanaka T, Harada MS, Igarashi T, Kitahara H, Morisada N, Nakamura SI, Okada T, Iijima K, Nozu K. Identification of novel OCRL isoforms associated with phenotypic differences between Dent disease-2 and Lowe syndrome. Nephrol Dial Transplant 2021; 37:262-270. [PMID: 34586410 DOI: 10.1093/ndt/gfab274] [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: 06/18/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Although Lowe syndrome and Dent disease-2 are both caused by OCRL mutations, their clinical severities differ substantially, and their molecular mechanisms remain unclear. Truncating mutations in OCRL exons 1 through 7 lead to Dent disease-2, whereas those in exons 8 through 24 lead to Lowe syndrome. Herein, we identified the mechanism underlying the action of novel OCRL protein isoforms. METHODS mRNA samples extracted from cultured urine-derived cells from a healthy control and the Dent disease-2 patient were examined to detect the 5' end of the OCRL isoform. For protein expression and functional analysis, vectors containing (1) the full-length OCRL transcripts, (2) the isoform transcripts, and (3) transcripts with truncating mutations detected in Lowe syndrome and Dent disease-2 patients were transfected into HeLa cells. RESULTS We successfully cloned the novel isoform transcripts from OCRL exons 6-24, including the translation-initiation codons present in exon 8. In vitro protein-expression analysis detected proteins of two different sizes (105 and 80 kDa) translated from full-length OCRL, whereas only one protein (80 kDa) was found from the isoform and Dent disease-2 variants. No protein expression was observed for the Lowe syndrome variants. The isoform enzyme activity was equivalent to that of full-length OCRL; the Dent disease-2 variants retained > 50% enzyme activity, whereas the Lowe syndrome variants retained < 20% activity. CONCLUSIONS We elucidated the molecular mechanism underlying the two different phenotypes in OCRL-related diseases; the functional OCRL isoform translated starting at exon 8 was associated with this mechanism.
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Affiliation(s)
- Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Ijuin
- Division of Biochemistry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Nephrology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Ninchoji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shogo Minamikawa
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | | | - Koji Nagatani
- Department of Pediatrics, Uwajima City Hospital, Uwajima, Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Kumiko Jinnouchi
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasufumi Ohtsuka
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Masafumi Oka
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Yoshinori Araki
- Department of Pediatrics, National Hospital Organization Hokkaido Medical Center, Sapporo, Japan
| | - Toju Tanaka
- Department of Pediatrics, National Hospital Organization Hokkaido Medical Center, Sapporo, Japan
| | - Mari S Harada
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Toru Igarashi
- Department of Pediatrics, Nippon Medical School Hospital, Tokyo, Japan
| | - Hikaru Kitahara
- Department of Pediatrics, Osaka Medical College, Takatsuki, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Shun-Ichi Nakamura
- Division of Biochemistry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Taro Okada
- Division of Biochemistry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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10
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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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11
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Parikh AC, Gadgil P. Lowe Syndrome: A Complex Clinical Diagnosis with a Novel Mutation in the OCRL Gene. JOURNAL OF CHILD SCIENCE 2021. [DOI: 10.1055/s-0041-1724042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
AbstractLowe syndrome (LS) is a rare X-linked condition having a clinical triad of congenital cataracts, intellectual disability, and progressive tubular nephropathy. Although the easily recognizable symptom complex usually evolves by infancy, a unifying diagnosis is often missed. We present a young boy with a prolonged history of multisystem affection, finally leading to the clinical suspicion of LS. The diagnosis was confirmed on genetic analysis as well as a previously unreported mutation in the OCRL gene was discovered. A 9-year-old boy with intellectual disability and recent onset seizures was referred for the evaluation of rickets. In addition, there was a significant past history of neonatal cataracts, infantile glaucoma, persistent albuminuria, and severe short stature with growth hormone deficiency. The characteristic involvement of eyes, brain, and kidneys along with a family history of a maternal uncle being similarly affected led to the clinical suspicion of LS. A whole exome sequencing was performed, which not only confirmed a nonsense mutation, c.2530C > T, in exon 23 of the Lowe gene (OCRL) but also revealed it to be a novel pathogenic variant. This case highlights the importance of piecing together the different facets of a complex clinical syndrome in reaching a challenging diagnosis. Also, LS must be kept as a differential in any child with neonatal cataracts and intellectual disability. Genetic confirmation of LS in our patient partly relieved the parental anxiety, and the child continued to remain under follow-up with multiple specialists, only now with a definite diagnosis.
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Affiliation(s)
- Akanksha C. Parikh
- Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, Maharashtra, India
| | - Pradnya Gadgil
- Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute, Mumbai, Maharashtra, India
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12
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Diagnosis and management of X-linked hypophosphatemia in children and adolescent in the Gulf Cooperation Council countries. Arch Osteoporos 2021; 16:52. [PMID: 33660084 PMCID: PMC7929956 DOI: 10.1007/s11657-021-00879-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/04/2021] [Indexed: 02/03/2023]
Abstract
INTRODUCTION X-linked hypophosphatemia (XLH) is a rare inherited cause of hypophosphatemic rickets and osteomalacia. It is caused by mutations in the phosphate-regulating endopeptidase homolog, X-linked (PHEX). This results in increased plasma fibroblast growth factor-23 (FGF23), which leads to loss of renal sodium-phosphate co-transporter expression leading to chronic renal phosphate excretion. It also leads to low serum 1,25-dihydroxyvitamin D (1,25(OH)2D), resulting in impaired intestinal phosphate absorption. Chronic hypophosphatemia in XLH leads to impaired endochondral mineralization of the growth plates of long bones with bony deformities. XLH in children and adolescents also causes impaired growth, myopathy, bone pain, and dental abscesses. XLH is the most frequent inherited cause of phosphopenic rickets/osteomalacia. Hypophosphatemia is also found in calcipenic rickets/osteomalacia as a result of secondary hyperparathyroidism. Thus, chronic hypophosphatemia is a common etiologic factor in all types of rickets. RESULTS There is considerable overlap between symptoms and signs of phosphopenic and calcipenic rickets/osteomalacia. Wrong diagnosis leads to inappropriate treatment of rickets/osteomalacia. Nutritional rickets and osteomalacia are common in the Gulf Cooperation Council countries which include Saudi Arabia, United Arab Emirates, Kuwait, Qatar, Bahrain, and Oman. Due to high levels of consanguinity in the region, genetic causes of phosphopenic and calcipenic rickets/osteomalacia are also common. CONCLUSION This guideline was developed to provide an approach to the diagnosis of XLH, especially where there is no family history of the disease, and that other related conditions are not mistaken for XLH. We also guide the medical management of XLH with conventional treatment and with burosumab, a recombinant human IgG1 monoclonal antibody to FGF23.
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Le Tertre M, Ka C, Raud L, Berlivet I, Gourlaouen I, Richard G, Uguen K, Chen JM, Férec C, Fichou Y, Le Gac G. Splicing analysis of SLC40A1 missense variations and contribution to hemochromatosis type 4 phenotypes. Blood Cells Mol Dis 2020; 87:102527. [PMID: 33341511 DOI: 10.1016/j.bcmd.2020.102527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 02/09/2023]
Abstract
Hemochromatosis type 4, or ferroportin disease, is considered as the second leading cause of primary iron overload after HFE-related hemochromatosis. The disease, which is predominantly associated with missense variations in the SLC40A1 gene, is characterized by wide clinical heterogeneity. We tested the possibility that some of the reported missense mutations, despite their positions within exons, cause splicing defects. Fifty-eight genetic variants were selected from the literature based on two criteria: a precise description of the nucleotide change and individual evidence of iron overload. The selected variants were investigated by different in silico prediction tools and prioritized for midigene splicing assays. Of the 15 variations tested in vitro, only two were associated with splicing changes. We confirm that the c.1402G>A transition (p.Gly468Ser) disrupts the exon 7 donor site, leading to the use of an exonic cryptic splicing site and the generation of a truncated reading frame. We observed, for the first time, that the p.Gly468Ser substitution has no effect on the ferroportin iron export function. We demonstrate alternative splicing of exon 5 in different cell lines and show that the c.430A>G (p.Asn144Asp) variant promotes exon 5 inclusion. This could be part of a gain-of-function mechanism. We conclude that splicing mutations rarely contribute to hemochromatosis type 4 phenotypes. An in-depth investigation of exon 5 auxiliary splicing sequences may help to elucidate the mechanism by which splicing regulatory proteins regulate the production of the full length SLC40A1 transcript and to clarify its physiological importance.
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Affiliation(s)
- Marlène Le Tertre
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | - Loann Raud
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Association Gaétan Saleün, F-29200, France
| | | | - Isabelle Gourlaouen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | | | - Kévin Uguen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Association Gaétan Saleün, F-29200, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | - Gérald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France.
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14
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Zhou FQ, Wang QW, Liu ZZ, Zhang XL, Wang DN, Dongye MM, Lin HT, Chen WR. Novel mutation in OCRL leading to a severe form of Lowe syndrome. Int J Ophthalmol 2019; 12:1057-1060. [PMID: 31341792 DOI: 10.18240/ijo.2019.07.01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/01/2019] [Indexed: 01/02/2023] Open
Abstract
AIM To investigate the phenotype and genotype of a family with X-linked recessive Lowe syndrome. METHODS All the members in the Chinese pedigree underwent comprehensive ophthalmologic and systemic examinations. Genomic DNA was isolated from peripheral blood of the pedigree members and 100 unrelated healthy Chinese subjects. Direct sequencing was performed to screen the exons and intron boundaries of OCRL. RESULTS The ophthalmological and systemic examinations suggested that the affected individual had Lowe syndrome. The phenotype in the pedigree is severe and consistent among all the affected individuals except for an individual who additionally suffered from congenital heart disease and laryngeal cartilage dysplasia. Directional Sanger sequencing identified a complex mutation c.(2368_2368delG; c.2370A>C) in the Rho-GTPase activating protein domain. This complex mutation causes termination of protein synthesis at amino acid 824 and result in a new peptide with 823 amino acids (p.Ala790ProfsX34). This mutation was not detected in 100 unrelated healthy Chinese subjects. CONCLUSION Our findings expand the phenotypic and genotypic spectrum of Lowe syndrome.
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Affiliation(s)
- Feng-Qi Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China.,New England College of Optometry, Boston, MA 02115, USA
| | - Qi-Wei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Zhen-Zhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Xu-Lin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Dong-Ni Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Mei-Mei Dongye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Hao-Tian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
| | - Wei-Rong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, Guangdong Province, China
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15
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Bitsori M, Vergadi E, Galanakis E. A Novel CLCN5 Splice Site Mutation in a Boy with Incomplete Phenotype of Dent Disease. J Pediatr Genet 2019; 8:235-239. [PMID: 31687264 DOI: 10.1055/s-0039-1692172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/22/2019] [Indexed: 12/15/2022]
Abstract
Dent disease is a rare X-linked renal proximal tubulopathy presenting with low-molecular-weight proteinuria (LMWP), hypercalciuria, and nephrocalcinosis, other signs of incomplete renal Fanconi syndrome, and renal failure. Early identification of patients who harbor disease-associated mutations is important for effective medical care and avoidance of unnecessary interventions. We report the case of an asymptomatic 9-year-old boy who presented with proteinuria in routine examination. Further investigation revealed the presence of nephrotic range proteinuria, mostly LMWP and mild hypercalciuria without nephrocalcinosis, or other features of tubular dysfunction. Renal function, growth, and bone mineral density were within regular limits. The male gender and the presence of LMWP and hypercalciuria even in the absence of other findings prompted us to genetic investigation for Dent disease. A novel splice site mutation (c.416-2A > G) of the chloride voltage-gated channel 5 ( CLCN5 ) gene, responsible for Dent disease type 1 was identified. In silico analysis revealed that this mutation interferes with the mating of exons 4 and 5. Due to early molecular diagnosis, our patient did not undergo a renal biopsy, neither required aggressive pharmacological interventions. This case underscores the diversity and complexity of CLCN5 mutations and highlights the importance of early molecular testing in male patients with incomplete phenotype of Dent disease.
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Affiliation(s)
- Maria Bitsori
- Department of Paediatrics, Heraklion University Hospital, Crete, Greece
| | - Eleni Vergadi
- Department of Paediatrics, School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Emmanouil Galanakis
- Department of Paediatrics, School of Medicine, University of Crete, Heraklion, Crete, Greece
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16
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Perdomo-Ramirez A, Aguirre M, Davitaia T, Ariceta G, Ramos-Trujillo E, Claverie-Martin F. Characterization of two novel mutations in the claudin-16 and claudin-19 genes that cause familial hypomagnesemia with hypercalciuria and nephrocalcinosis. Gene 2019; 689:227-234. [DOI: 10.1016/j.gene.2018.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
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17
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Claverie-Martin F, Trindade A, Garcia-Gonzalez NC, Callejon AC. Novel missense mutation affecting the LIM-A domain of LMX1B in a family with Nail-Patella syndrome. Intractable Rare Dis Res 2019; 8:14-19. [PMID: 30881852 PMCID: PMC6409120 DOI: 10.5582/irdr.2018.01131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Nail-patella syndrome (NPS) is a rare autosomal dominant disease characterized by developmental defects of dorsal limb structures, the kidney, and the eye, that manifest as dysplastic nails, hypoplastic or absent patella, elbow dysplasia, iliac horns, glomerulopathy, and adult-onset glaucoma, respectively. This disorder is inherited in an autosomal dominant mode and is caused by heterozygous loss-of-function mutations in the LMX1B gene, which encodes the LIM homeodomain transcription factor LMX1B. In this study, we report the clinical findings of a Spanish family, from the Canary Islands, with three affected members who displayed varying phenotypes. DNA sequence analysis identified a novel heterozygous missense mutation in LMX1B, c.305A>G, p.(Y102C), that segregated with the disease. The tyrosine residue affected by the mutation is highly conserved in evolution, and is located in the LIM-A domain, next to one of the cysteine residues involved in zinc binding, suggesting that p.(Y102C) affects LMX1B function by disturbing its interactions with other proteins. Our results expand the mutation spectrum of LMX1B and provide insight into the molecular mechanisms of NPS pathology.
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Affiliation(s)
- Felix Claverie-Martin
- Unidad de Investigacion, Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Address correspondence to:Dr. Félix Claverie-Martín, Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain. E-mail:
| | - Amelia Trindade
- Unidad de Investigacion, Hospital Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Present address:Departamento de Medicina, Centro de Ciências Biológicas e da Saude (CCBS), Universidade Federal de São Carlos, São Carlos, Brasil
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18
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Perdomo-Ramirez A, de Armas-Ortiz M, Ramos-Trujillo E, Suarez-Artiles L, Claverie-Martin F. Exonic CLDN16 mutations associated with familial hypomagnesemia with hypercalciuria and nephrocalcinosis can induce deleterious mRNA alterations. BMC MEDICAL GENETICS 2019; 20:6. [PMID: 30621608 PMCID: PMC6325764 DOI: 10.1186/s12881-018-0713-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/30/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Familial hypomagnesaemia with hypercalciuria and nephrocalcinosis type 1 is an autosomal recessive disease characterized by excessive renal magnesium and calcium excretion, bilateral nephrocalcinosis, and progressive chronic renal failure. This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations. The functional consequences of some of these claudin-16 mutant proteins have been analysed after heterologous expression showing indeed a significant loss of function compared to the wild-type claudin-16. We hypothesize that a number of CLDN16 exonic mutations can be responsible for the disease phenotype by disrupting the pre-mRNA splicing process. METHODS We selected 12 previously described presumed CLDN16 missense mutations and analysed their potential effect on pre-mRNA splicing using a minigene assay. RESULTS Our results indicate that five of these mutations induce significant splicing alterations. Mutations c.453G > T and c.446G > T seem to inactivate exonic splicing enhancers and promote the use of an internal cryptic acceptor splice site resulting in inclusion of a truncated exon 3 in the mature mRNA. Mutation c.571G > A affects an exonic splicing enhancer resulting in partial skipping of exon 3. Mutations c.593G > C and c.593G > A disturb the acceptor splice site of intron 3 and cause complete exon 4 skipping. CONCLUSIONS To our knowledge, this is the first report of CLDN16 exonic mutations producing alterations in splicing. We suggest that in the absence of patients RNA samples, splicing functional assays with minigenes could be valuable for evaluating the effect of exonic CLDN16 mutations on pre-mRNA splicing.
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Affiliation(s)
- Ana Perdomo-Ramirez
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Marian de Armas-Ortiz
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Elena Ramos-Trujillo
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Lorena Suarez-Artiles
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
| | - Felix Claverie-Martin
- Unidad de Investigación, Hospital Nuestra Señora de Candelaria, Carretera del Rosario 145, 38010 Santa Cruz de Tenerife, Spain
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19
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Goursaud C, Mallet D, Janin A, Menassa R, Tardy-Guidollet V, Russo G, Lienhardt-Roussie A, Lecointre C, Plotton I, Morel Y, Roucher-Boulez F. Aberrant Splicing Is the Pathogenicity Mechanism of the p.Glu314Lys Variant in CYP11A1 Gene. Front Endocrinol (Lausanne) 2018; 9:491. [PMID: 30233493 PMCID: PMC6134065 DOI: 10.3389/fendo.2018.00491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/06/2018] [Indexed: 12/30/2022] Open
Abstract
Context: The cholesterol side chain cleavage enzyme (CYP11A1) catalyzes the conversion of cholesterol to pregnenolone, the first rate-limiting step of steroidogenesis. CYP11A1 mutations are associated with primary adrenal insufficiency (PAI) as well as disorders of sex development (DSD) in 46,XY patients. Objective: To define the pathogenicity mechanism for the p.Glu314Lys variant, previously reported, and found in four additional patients with CYP11A1 deficiency. Subjects and Methods: DNA of four patients presenting with delayed PAI and/or 46,XY DSD were studied by Sanger or Massively Parallel sequencing. Three CYP11A1 mutations were characterized in vitro and in silico, and one by mRNA analysis on testicular tissue. Results: All patients were compound heterozygous for the previously described p.Glu314Lys variant. In silico studies predicted this mutation as benign with no effect on splicing but mRNA analysis found that it led to incomplete exon 5 skipping. This mechanism was confirmed by minigene experiment. The protein carrying this mutation without exon skipping should conserve almost normal activity, according to in vitro studies. Two other mutations found in trans, the p.Arg120Gln and p.Arg465Trp, had similar activity compared to negative control, consistent with the in silico studies. Conclusions: We provide biological proof that the p. Glu314Lys variant is pathogenic due to its impact on splicing and seems responsible for the moderate phenotype of the four patients reported herein. The present study highlights the importance of considering the potential effect of a missense variant on splicing when it is not predicted to be disease causing.
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Affiliation(s)
- Claire Goursaud
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- *Correspondence: Claire Goursaud
| | - Delphine Mallet
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
| | - Alexandre Janin
- Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Cardiogénétique Moléculaire, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Institut NeuroMyoGène, CNRS UMR 5310 – INSERM U1217, Université de Lyon 1, Lyon, France
| | - Rita Menassa
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
| | - Véronique Tardy-Guidollet
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
- Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Gianni Russo
- Centro di Endocrinologia dell'infanzia e dell'adolescenza, Ospedale San Raffaele, Milan, Italy
| | - Anne Lienhardt-Roussie
- Service de Pédiatrie Médicale, Hôpital de la mère et de l'enfant, CHU de Limoges, Limoges, France
| | | | - Ingrid Plotton
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
- Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Yves Morel
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
- Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Florence Roucher-Boulez
- Laboratoire de Biochimie et Biologie Moléculaire Grand Est, UM Pathologies Endocriniennes Rénales Musculaires et Mucoviscidose, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
- Centre de Référence du Développement Génital: du Fœtus à l'Adulte, Filière Maladies Rares Endocriniennes, Bron, France
- Univ Lyon, Université Claude Bernard Lyon 1, Lyon, France
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