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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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Zhang Y, Xu S, Jin Q, Luo J, Gao C, Jayaprakash S, Wang H, Zhuang L, He J. Establishment of transgenic pigs overexpressing human PKD2-D511V mutant. Front Genet 2022; 13:1059682. [DOI: 10.3389/fgene.2022.1059682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Numerous missense mutations have been reported in autosomal dominant polycystic kidney disease which is one of the most common renal genetic disorders. The underlying mechanism for cystogenesis is still elusive, partly due to the lack of suitable animal models. Currently, we tried to establish a porcine transgenic model overexpressing human PKD2-D511V (hPKD2-D511V), which is a dominant-negative mutation in the vertebrate in vitro models. A total of six cloned pigs were finally obtained using somatic cell nuclear transfer. However, five with functional hPKD2-D511V died shortly after birth, leaving only one with the dysfunctional transgenic event to survive. Compared with the WT pigs, the demised transgenic pigs had elevated levels of hPKD2 expression at the mRNA and protein levels. Additionally, no renal malformation was observed, indicating that hPKD2-D511V did not alter normal kidney development. RNA-seq analysis also revealed that several ADPKD-related pathways were disturbed when overexpressing hPKD2-D511V. Therefore, our study implies that hPKD2-D511V may be lethal due to the dominant-negative effect. Hence, to dissect how PKD2-D511V drives renal cystogenesis, it is better to choose in vitro or invertebrate models.
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Sarkar A, Panati K, Narala VR. Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108444. [PMID: 36307006 DOI: 10.1016/j.mrrev.2022.108444] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
In eukaryotes, precise pre-mRNA processing, including alternative splicing, is essential to carry out the intricate protein translation process. Both point mutations (that alter the translated protein sequence) and synonymous mutations (that do not alter the translated protein sequence) are capable of affecting the splicing process. Synonymous mutations are known to affect gene expression via altering mRNA stability, mRNA secondary structure, splicing processes, and translational kinetics. In higher eukaryotes, precise splicing is regulated by three weakly conserved cis-elements, 5' and 3' splice sites and the branch site. Many other cis-acting elements (exonic/intronic splicing enhancers and silencers) and trans-acting splicing factors (serine and arginine-rich proteins and heterogeneous nuclear ribonucleoproteins) have also been found to enhance or suppress the splicing process. The appearance of synonymous mutations in cis-acting elements can alter the splicing process by changing the binding pattern of splicing factors to exonic splicing enhancers or silencer motifs. This results in exon skipping, intron retention, and various other forms of alternative splicing, eventually leading to the emergence of a wide range of diseases. The focus of this review is to elucidate the role of synonymous mutations and their impact on abnormal splicing mechanisms. Further, this study highlights the function of synonymous mutation in mediating abnormal splicing in cancer and development of X-linked, and autosomal inherited diseases.
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Affiliation(s)
- Avik Sarkar
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102, India
| | - Kalpana Panati
- Department of Biotechnology, Government College for Men, Kadapa 516004, India
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Cantero MDR, Cantiello HF. Polycystin-2 (TRPP2): Ion channel properties and regulation. Gene 2022; 827:146313. [PMID: 35314260 DOI: 10.1016/j.gene.2022.146313] [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: 09/09/2021] [Revised: 01/19/2022] [Accepted: 02/08/2022] [Indexed: 12/01/2022]
Abstract
Polycystin-2 (TRPP2, PKD2, PC2) is the product of the PKD2 gene, whose mutations cause Autosomal Dominant Polycystic Kidney Disease (ADPKD). PC2 belongs to the superfamily of TRP (Transient Receptor Potential) proteins that generally function as Ca2+-permeable nonselective cation channels implicated in Ca2+ signaling. PC2 localizes to various cell domains with distinct functions that likely depend on interactions with specific channel partners. Functions include receptor-operated, nonselective cation channel activity in the plasma membrane, intracellular Ca2+ release channel activity in the endoplasmic reticulum (ER), and mechanosensitive channel activity in the primary cilium of renal epithelial cells. Here we summarize our current understanding of the properties of PC2 and how other transmembrane and cytosolic proteins modulate this activity, providing functional diversity and selective regulatory mechanisms to its role in the control of cellular Ca2+ homeostasis.
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Affiliation(s)
- María Del Rocío Cantero
- Laboratorio de Canales Iónicos, Instituto Multidisciplinario de Salud, Tecnología y Desarrollo (IMSaTeD, CONICET-UNSE), El Zanjón, Santiago del Estero 4206, Argentina.
| | - Horacio F Cantiello
- Laboratorio de Canales Iónicos, Instituto Multidisciplinario de Salud, Tecnología y Desarrollo (IMSaTeD, CONICET-UNSE), El Zanjón, Santiago del Estero 4206, Argentina
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A Presumed Synonymous Mutation of PKD2 Caused Autosomal Dominant Polycystic Kidney Disease in a Chinese Family. Curr Med Sci 2021; 41:1029-1036. [PMID: 34542828 DOI: 10.1007/s11596-021-2436-9] [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: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by the pathogenic mutation of PKD1 or PKD2 gene and usually affects bilateral kidneys. Synonymous mutations are generally assumed to be neutral as they do not alter amino acids. Herein, we described an extremely rare ADPKD child caused by a heterozygous synonymous mutation of PKD2 gene accompanied by massive proteinuria and congenital solitary kidney. METHODS Clinical characteristics of the patients were summarized. Whole-exome sequencing was performed to screen the disease-causing gene mutation, and reverse transcription polymerase chain reaction (RT-PCR) and Sanger sequencing were applied to analyze the impact of the identified mutation on gene transcription and splicing. RESULTS Polycystic changes were found in the solitary kidney of a girl initially presented with nephrotic-range proteinuria. Thereafter her mother and 2 other family members were diagnosed to be ADPKD. Whole-exome sequencing of the proband identified a heterozygous synonymous mutation (c.1716G>A, p.Lys572=) located in the splicing site of exon 7 in PKD2 gene, which was co-segregated with the PKD phenotype in the family. RT-PCR and direct sequencing of amplified products revealed that this heterozygous synonymous mutation led to exon7 skipping in PKD2 gene. CONCLUSION We reported an extremely rare child case of ADPKD2 in combination with solitary kidney and nephrotic-range proteinuria, and firstly confirmed the pathogenicity of a heterozygous synonymous mutation (c.1716G>A) in PKD2 gene. The results indicate that synonymous mutations should not be excluded from disease-causing if they are located in splicing site of an exon.
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Wang S, Wang Y, Wang J, Liu Z, Zhang R, Shi X, Han Y, Guo W, Bottillo I, Shao L. Six Exonic Variants in the SLC5A2 Gene Cause Exon Skipping in a Minigene Assay. Front Genet 2020; 11:585064. [PMID: 33250922 PMCID: PMC7674938 DOI: 10.3389/fgene.2020.585064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/20/2020] [Indexed: 01/16/2023] Open
Abstract
Background Familial renal glucosuria is a rare renal tubular disorder caused by SLC5A2 gene variants. Most of them are exonic variants and have been classified as missense variants. However, there is growing evidence that some of these variants can be detrimental by affecting the pre-mRNA splicing process. Therefore, we hypothesize that a certain proportion of SLC5A2 exonic variants can result in disease via interfering with the normal splicing process of the pre-mRNA. Methods We used bioinformatics programs to analyze 77 previously described presumed SLC5A2 missense variants and identified candidate variants that may alter the splicing of pre-mRNA through minigene assays. Results Our study indicated six of 7 candidate variants induced splicing alterations. Variants c.216C > A, c.294C > A, c.886G > C, c.932A > G and c.962A > G may disrupt splicing enhancer motifs and generate splicing silencer sequences resulting in the skipping of exon 3. Variants c.305C > T and c.1129G > A probably disturb splice sites leading to exon skipping. Conclusion To our knowledge, we report, for the first time, SLC5A2 exonic variants that produce alterations in pre-mRNA. Our research reinforces the importance of assessing the consequences for putative point variants at the mRNA level. Additionally, we propose that minigenes function analysis may be valuable to evaluate the impact of SLC5A2 exonic variants on pre-mRNA splicing without patients’ RNA samples.
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Affiliation(s)
- Sai Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China.,Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Yixiu Wang
- Department of Hepatic Surgery, Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jinchao Wang
- Yantai Branch of Wenden Osteopathic Hospital, Yantai, China
| | - Zhiying 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
| | - Xiaomeng Shi
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yue Han
- 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
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Italy
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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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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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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Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease. Genes (Basel) 2018; 9:genes9010015. [PMID: 29300302 PMCID: PMC5793168 DOI: 10.3390/genes9010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/11/2017] [Accepted: 12/27/2017] [Indexed: 01/12/2023] Open
Abstract
Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no additional clinical defects. It is not yet understood why some OCRL mutations cause the phenotype of Lowe syndrome, while others develop the milder phenotype of Dent-2 disease. Our goal was to gain new insights into the consequences of OCRL exonic mutations on pre-mRNA splicing. Using predictive bioinformatics tools, we selected thirteen missense mutations and one synonymous mutation based on their potential effects on splicing regulatory elements or splice sites. These mutations were analyzed in a minigene splicing assay. Results of the RNA analysis showed that three presumed missense mutations caused alterations in pre-mRNA splicing. Mutation c.741G>T; p.(Trp247Cys) generated splicing silencer sequences and disrupted splicing enhancer motifs that resulted in skipping of exon 9, while mutations c.2581G>A; p.(Ala861Thr) and c.2581G>C; p.(Ala861Pro) abolished a 5′ splice site leading to skipping of exon 23. Mutation c.741G>T represents the first OCRL exonic variant outside the conserved splice site dinucleotides that results in alteration of pre-mRNA splicing. Our results highlight the importance of evaluating the effects of OCRL exonic mutations at the mRNA level.
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Alternative Splicing in Genetic Diseases: Improved Diagnosis and Novel Treatment Options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 335:85-141. [PMID: 29305015 DOI: 10.1016/bs.ircmb.2017.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alternative splicing is an important mechanism to regulate gene expression and to expand the repertoire of gene products in order to accommodate an increase in complexity of multicellular organisms. It needs to be precisely regulated, which is achieved via RNA structure, splicing factors, transcriptional regulation, and chromatin. Changes in any of these factors can lead to disease. These may include the core spliceosome, splicing enhancer/repressor sequences and their interacting proteins, the speed of transcription by RNA polymerase II, and histone modifications. While the basic principle of splicing is well understood, it is still very difficult to predict splicing outcome, due to the multiple levels of regulation. Current molecular diagnostics mainly uses Sanger sequencing of exons, or next-generation sequencing of gene panels or the whole exome. Functional analysis of potential splicing variants is scarce, and intronic variants are often not considered. This likely results in underestimation of the percentage of splicing variants. Understanding how sequence variants may affect splicing is not only crucial for confirmation of diagnosis and for genetic counseling, but also for the development of novel treatment options. These include small molecules, transsplicing, antisense oligonucleotides, and gene therapy. Here we review the current state of molecular mechanisms of splicing regulation and how deregulation can lead to human disease, diagnostics to detect splicing variants, and novel treatment options based on splicing correction.
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Mutation in an exonic splicing enhancer site causing chronic granulomatous disease. Blood Cells Mol Dis 2017; 66:50-57. [PMID: 28886419 DOI: 10.1016/j.bcmd.2017.08.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 11/24/2022]
Abstract
In a male patient suffering from X-linked chronic granulomatous disease (CGD) we found a c.389G>T mutation in exon 5 of the CYBB gene. We have analyzed why 95% of the transcripts of this gene lacked exon 5, leading to a frameshift and premature termination codon. The mutation was located in a region comprising three putative exonic splicing enhancer binding sites, for SRSF1, SRFS2 and SRFS6, according to the ESEfinder Tool (http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi). With the Analyser Splice Tool we calculated the probability of skipping of exon 5 in CYBB mRNA, and by means of Sroogle the number of putative binding motifs for splicing enhancer and splicing silencer proteins (http://astlab.tau.ac.il/index.php). These analyses clarify why this exon was skipped in the majority of the mRNA. The normally spliced transcript contains an amino acid change p.Arg130Leu. This poorly expressed transcript gives rise to a protein with low expression but presumably normal activity, leading to a respiratory burst activity in the patient's neutrophils of about 15% of normal.
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