1
|
Morita S, Nomura S, Azuma K, Chida-Nagai A, Furutani Y, Inai K, Inoue T, Niimi Y, Iizuka Y, Tsutsumi Y, Ishizaki R, Yamagishi H, Kawamata T, Akagawa H. Functional characterization of variants found in Japanese patients with hereditary hemorrhagic telangiectasia. Clin Genet 2024; 105:543-548. [PMID: 38225712 DOI: 10.1111/cge.14483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/28/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024]
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant form of vascular dysplasia. Genetic diagnosis is made by identifying loss-of-function variants in genes, such as ENG and ACVRL1. However, the causal mechanisms of various variants of unknown significance remains unclear. In this study, we analyzed 12 Japanese patients from 11 families who were clinically diagnosed with HHT. Sequencing analysis identified 11 distinct variants in ACVRL1 and ENG. Three of the 11 were truncating variants, leading to a definitive diagnosis, whereas the remaining eight were splice-site and missense variants that required functional analyses. In silico splicing analyses demonstrated that three variants, c.526-3C > G and c.598C > G in ACVRL1, and c.690-1G > A in ENG, caused aberrant splicing, as confirmed by a minigene assay. The five remaining missense variants were p.Arg67Gln, p.Ile256Asn, p.Leu285Pro, and p.Pro424Leu in ACVRL and p.Pro165His in ENG. Nanoluciferase-based bioluminescence analyses demonstrated that these ACVRL1 variants impaired cell membrane trafficking, resulting in the loss of bone morphogenetic protein 9 (BMP9) signal transduction. In contrast, the ENG mutation impaired BMP9 signaling despite normal cell membrane expression. The updated functional analysis methods performed in this study will facilitate effective genetic testing and appropriate medical care for patients with HHT.
Collapse
Affiliation(s)
- Shuhei Morita
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Shunsuke Nomura
- Department of Neurosurgery, Tokyo Women's Medical University Yachiyo Medical center, Yachiyo, Japan
- Krembil Brain Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Kenko Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Ayako Chida-Nagai
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Kei Inai
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Tatsuya Inoue
- Department of Neurosurgery, St. Luke's International Hospital, Tokyo, Japan
| | - Yasunari Niimi
- Department of Neuroendovascular Therapy, St. Luke's International Hospital, Tokyo, Japan
| | - Yuo Iizuka
- Department of Neuroradiology, Kashiwa Tanaka Hospital, Kashiwa, Japan
| | - Yoshiyuki Tsutsumi
- Department of Radiology, National Center for Child Health and Development, Tokyo, Japan
| | - Reina Ishizaki
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroyuki Yamagishi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| |
Collapse
|
2
|
Liu L, Wang Y, Zhang Z, Yu C, Chen J. Identification of a novel TSC1 gene variant in a patient with atypical vitiligo-like skin lesions: Unveiling the hidden tuberous sclerosis complex. Mol Genet Genomic Med 2024; 12:e2403. [PMID: 38439608 PMCID: PMC10912791 DOI: 10.1002/mgg3.2403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/04/2024] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Tuberous sclerosis complex (TSC), an autosomal-dominant disorder, is characterized by hamartomas affecting multiple organ systems. The underlying etiology of TSC is the pathogenic variations of the TSC1 or TSC2 genes. The phenotype variability of TSC could lead to missed diagnosis; therefore, the latest molecular diagnostic criteria for identifying a heterozygous pathogenic variant in either the TSC1 or TSC2 gene filled this gap. Furthermore, the pathogenicity of numerous variants remains unverified, potentially leading to misinterpretations of their functional consequences. METHODS In this study, a single patient presenting with atypical vitiligo-like skin lesions suspected to have TSC was enrolled. Targeted next-generation sequencing and Sanger sequencing were employed to identify a pathogenic variant. Additionally, a minigene splicing assay was conducted to assess the impact of TSC1 c.1030-2A>T, located in intron 10, on RNA splicing. RESULTS A novel TSC1: c.1030-2A>T heterozygosis variant was identified in intron 10. In vitro minigene assay revealed that the c.1030-2A>T variant caused exon 11 skipping, resulting in a frameshift in the absence of 112 base pairs of mature messenger RNA and premature termination after 174 base pairs (p.Ala344Glnfs*59). CONCLUSION The detection of this novel pathogenic TSC1 variant in the patient with atypical vitiligo-like skin lesions enrolled in our study ultimately resulted in the diagnosis of TSC. As a result, our study contributes to expanding the mutational spectrum of the TSC1 gene and refining the genotype-phenotype map of TSC.
Collapse
Affiliation(s)
- Linli Liu
- Department of DermatologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
- Department of DermatologySuining Central HospitalSuiningSichuanChina
| | - Yanbo Wang
- Department of DermatologyLangzhong People's HospitalNanchongSichuanChina
| | - Zhengzhong Zhang
- Department of DermatologyAffiliated Hospital of North Sichuan Medical CollegeNanchongSichuanChina
| | - Chunshui Yu
- Department of DermatologySuining Central HospitalSuiningSichuanChina
| | - Jin Chen
- Department of DermatologyThe First Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| |
Collapse
|
3
|
Ferese R, Scala S, Suppa A, Campopiano R, Asci F, Zampogna A, Chiaravalloti MA, Griguoli A, Storto M, Pardo AD, Giardina E, Zampatti S, Fornai F, Novelli G, Fanelli M, Zecca C, Logroscino G, Centonze D, Gambardella S. Cohort analysis of novel SPAST variants in SPG4 patients and implementation of in vitro and in vivo studies to identify the pathogenic mechanism caused by splicing mutations. Front Neurol 2023; 14:1296924. [PMID: 38145127 PMCID: PMC10748595 DOI: 10.3389/fneur.2023.1296924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction Pure hereditary spastic paraplegia (SPG) type 4 (SPG4) is caused by mutations of SPAST gene. This study aimed to analyze SPAST variants in SPG4 patients to highlight the occurrence of splicing mutations and combine functional studies to assess the relevance of these variants in the molecular mechanisms of the disease. Methods We performed an NGS panel in 105 patients, in silico analysis for splicing mutations, and in vitro minigene assay. Results and discussion The NGS panel was applied to screen 105 patients carrying a clinical phenotype corresponding to upper motor neuron syndrome (UMNS), selectively affecting motor control of lower limbs. Pathogenic mutations in SPAST were identified in 12 patients (11.42%), 5 missense, 3 frameshift, and 4 splicing variants. Then, we focused on the patients carrying splicing variants using a combined approach of in silico and in vitro analysis through minigene assay and RNA, if available. For two splicing variants (i.e., c.1245+1G>A and c.1414-2A>T), functional assays confirm the types of molecular alterations suggested by the in silico analysis (loss of exon 9 and exon 12). In contrast, the splicing variant c.1005-1delG differed from what was predicted (skipping exon 7), and the functional study indicates the loss of frame and formation of a premature stop codon. The present study evidenced the high splice variants in SPG4 patients and indicated the relevance of functional assays added to in silico analysis to decipher the pathogenic mechanism.
Collapse
Affiliation(s)
| | | | - Antonio Suppa
- IRCCS Neuromed, Pozzilli, Italy
- Department of Human Neurosciences, Sapienza University of Rome, Rome, Italy
| | | | | | | | | | | | | | | | - Emiliano Giardina
- Genomic Medicine Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Stefania Zampatti
- Genomic Medicine Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesco Fornai
- IRCCS Neuromed, Pozzilli, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Giuseppe Novelli
- IRCCS Neuromed, Pozzilli, Italy
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, Rome, Italy
| | - Mirco Fanelli
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino, Italy
| | - Chiara Zecca
- Center for Neurodegenerative Diseases and the Aging Brain, Department of Clinical Research in Neurology of the University of Bari “Aldo Moro” at “Pia Fondazione Card G. Panico” Hospital Tricase, Lecce, Italy
| | - Giancarlo Logroscino
- Center for Neurodegenerative Diseases and the Aging Brain, Department of Clinical Research in Neurology of the University of Bari “Aldo Moro” at “Pia Fondazione Card G. Panico” Hospital Tricase, Lecce, Italy
| | - Diego Centonze
- IRCCS Neuromed, Pozzilli, Italy
- Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Stefano Gambardella
- IRCCS Neuromed, Pozzilli, Italy
- Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Urbino, Italy
| |
Collapse
|
4
|
Dong Y, Li W, Meng J, Wang P, Sun M, Zhou F, Li D, Shu J, Cai C. Pathogenicity analysis and splicing rescue of a classical splice site variant (c.1343+1G>T) of CNOT1 gene associated with neurodevelopmental disorders. Am J Med Genet A 2023; 191:2775-2782. [PMID: 37507849 DOI: 10.1002/ajmg.a.63360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/03/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Mutations in the CNOT1 gene lead to an incurable rare neurological disorder mainly manifested as a clinical spectrum of intellectual disability, developmental delay, seizures, and behavioral problems. In this study, we investigated a classical splice site variant of CNOT1 (c.1343+1G>T) associated with neurodevelopmental disorders, which was a master regulator, orchestrating gene expression, RNA deadenylation, and protein ubiquitination. To link CNOT1 dysfunction with the neurodevelopmental phenotype observed in a patient, in vitro minigene assay was used to verify the effect of CNOT1 gene splice site variant c.1343+1G>T on mRNA splicing. We also explored the impact of transient transfection introducing modified U1 snRNA on correcting the splicing variant. Through minigene expression in mammalian cells, we demonstrated that the variant induced complete exon 12 skipping, which explained the patient's clinical condition and provided additional genetic diagnosis evidence for the clinical significance of the variant. Moreover, we confirmed that the aberrant splice pattern could be partially corrected by the modified U1 snRNA at the mRNA level, which provided strong evidence for the therapeutic potential of modified U1 snRNA in neutralizing the hazardous effect of incorrect splicing patterns.
Collapse
Affiliation(s)
- Yan Dong
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Weiran Li
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Jing Meng
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Department of Neurology, Tianjin Children's Hospital, Tianjin, China
| | - Ping Wang
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Tianjin Pediatric Research Institute, Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Mei Sun
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Feiyu Zhou
- Graduate College of Tianjin Medical University, Tianjin, China
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
| | - Dong Li
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Department of Neurology, Tianjin Children's Hospital, Tianjin, China
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Tianjin Pediatric Research Institute, Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, China
- Tianjin Pediatric Research Institute, Tianjin, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| |
Collapse
|
5
|
Shchagina O, Orlova M, Murtazina A, Filatova A, Skoblov M, Dadali E. Evaluation of Pathogenicity and Causativity of Variants in the MPZ and SH3TC2 Genes in a Family Case of Hereditary Peripheral Neuropathy. Int J Mol Sci 2023; 24:9786. [PMID: 37372933 DOI: 10.3390/ijms24129786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
The implementation of NGS methods into clinical practice allowed researchers effectively to establish the molecular cause of a disorder in cases of a genetically heterogeneous pathology. In cases of several potentially causative variants, we need additional analysis that can help in choosing a proper causative variant. In the current study, we described a family case of hereditary motor and sensory neuropathy (HMSN) type 1 (Charcot-Marie-Tooth disease). DNA analysis revealed two variants in the SH3TC2 gene (c.279G>A and c.1177+5G>A), as well as a previously described variant c.449-9C>T in the MPZ gene, in a heterozygous state. This family segregation study was incomplete because of the proband's father's unavailability. To evaluate the variants' pathogenicity, minigene splicing assay was carried out. This study showed no effect of the MPZ variant on splicing, but the c.1177+5G>A variant in the SH3TC2 gene leads to the retention of 122 nucleotides from intron 10 in the RNA sequence, causing a frameshift and an occurrence of a premature stop codon (NP_078853.2:p.Ala393GlyfsTer2).
Collapse
Affiliation(s)
- Olga Shchagina
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | - Mariya Orlova
- Research Centre for Medical Genetics, Moscow 115522, Russia
| | | | | | | | - Elena Dadali
- Research Centre for Medical Genetics, Moscow 115522, Russia
| |
Collapse
|
6
|
Bodenbender JP, Marino V, Bethge L, Stingl K, Haack TB, Biskup S, Kohl S, Kühlewein L, Dell’Orco D, Weisschuh N. Biallelic Variants in TULP1 Are Associated with Heterogeneous Phenotypes of Retinal Dystrophy. Int J Mol Sci 2023; 24:ijms24032709. [PMID: 36769033 PMCID: PMC9916573 DOI: 10.3390/ijms24032709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Biallelic pathogenic variants in TULP1 are mostly associated with severe rod-driven inherited retinal degeneration. In this study, we analyzed clinical heterogeneity in 17 patients and characterized the underlying biallelic variants in TULP1. All patients underwent thorough ophthalmological examinations. Minigene assays and structural analyses were performed to assess the consequences of splice variants and missense variants. Three patients were diagnosed with Leber congenital amaurosis, nine with early onset retinitis pigmentosa, two with retinitis pigmentosa with an onset in adulthood, one with cone dystrophy, and two with cone-rod dystrophy. Seventeen different alleles were identified, namely eight missense variants, six nonsense variants, one in-frame deletion variant, and two splice site variants. For the latter two, minigene assays revealed aberrant transcripts containing frameshifts and premature termination codons. Structural analysis and molecular modeling suggested different degrees of structural destabilization for the missense variants. In conclusion, we report the largest cohort of patients with TULP1-associated IRD published to date. Most of the patients exhibited rod-driven disease, yet a fraction of the patients exhibited cone-driven disease. Our data support the hypothesis that TULP1 variants do not fold properly and thus trigger unfolded protein response, resulting in photoreceptor death.
Collapse
Affiliation(s)
- Jan-Philipp Bodenbender
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: (J.-P.B.); (N.W.)
| | - Valerio Marino
- Section of Biological Chemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Leon Bethge
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Katarina Stingl
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Saskia Biskup
- Praxis für Humangenetik, 72076 Tübingen, Germany
- CeGaT GmbH, 72076 Tübingen, Germany
| | - Susanne Kohl
- Department for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Laura Kühlewein
- Department for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany
| | - Daniele Dell’Orco
- Section of Biological Chemistry, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37124 Verona, Italy
| | - Nicole Weisschuh
- Department for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
- Correspondence: (J.-P.B.); (N.W.)
| |
Collapse
|
7
|
Chang H, Zhang X, Xu K, Li N, Xie Y, Yan W, Li Y. Phenotype-Based Genetic Analysis Reveals Missing Heritability of KIF11-Related Retinopathy: Clinical and Genetic Findings. Genes (Basel) 2023; 14:212. [PMID: 36672954 PMCID: PMC9858922 DOI: 10.3390/genes14010212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
The purpose of this study was to detect the missing heritability of patients with KIF11-related retinopathy and to describe their clinical and genetic characteristics. We enrolled 10 individuals from 7 unrelated families harboring a pathogenic monoallelic variant in KIF11. All subjects underwent ophthalmic assessment and extraocular phenotype evaluations, as well as comprehensive molecular genetic analyses using next-generation sequencing. Minigene assays were performed to observe the effects of one novel deep intron variant (DIV) and one novel synonymous variant on pre-mRNA splicing. We detected 6 novel different disease-causing variants of KIF11 in the seven pedigrees. Co-segregation analysis and ultra-deep sequencing results indicated that 5 variants arose de novo in 5 families (71%). Functional validation revealed that the synonymous variant leads to an exon skip, while the DIV causes a pseudoexon (PE) inclusion. The patients presented with high variations in their phenotype, and two families exhibited incomplete penetrance. Ocular manifestations and characteristic facial features were observed in all patients, as well as microcephaly in seven patients, intellectual disability in five patients, and lymphedema in one patient. The key retinal features for KIF11-related retinopathy were retinal folds, tractional retinal detachment, and chorioretinal dysplasia. All seven probands had more severe visual detects than other affected family members. Our findings widen the genetic spectrum of KIF11 variants. DIV explained rare unresolved cases with KIF11-related retinopathy. The patients displayed a variable phenotype expressivity and incomplete penetrance, indicating the importance of genetic analysis for patients with KIF11-related retinopathy.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yang Li
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100051, China
| |
Collapse
|
8
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
9
|
Liang L, Wu H, Cai Z, Zhao J. Molecular dynamics and minigene assay of new splicing variant c.4298-20T>A of COL4A5 gene that cause Alport syndrome. Front Genet 2023; 14:1059322. [PMID: 36923787 PMCID: PMC10009158 DOI: 10.3389/fgene.2023.1059322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Introduction: Alport syndrome (AS; OMIM#308940) is a progressive hereditary kidney disease characterized by hearing loss and ocular abnormalities. According to the mode of inheritance, AS has three subtypes: X-linked (XL; OMIM#301050), autosomal recessive (AR; OMIM#203780), and autosomal dominant (AD; OMIM#104200). XLAS is caused by a pathogenic variant in COL4A5 (OMIM*303630) gene encoding type IV collagen (Col-IV) α5 chain, while ADAS and ARAS are consequences of a variant in COL4A3 (OMIM*120070) and COL4A4 (OMIM*120131) genes that encode Col-IV α3 and α4 chains, respectively. Usually, diagnosis of AS requires hereditary or pathological examinations. Splicing variants are hard to be determined as pathogenic or non-pathogenic based on the results of gene sequencing. Methods: This study focused on a splicing variant in COL4A5 gene, termed NM_000495.5: c.4298-20T>A, and to analyzed its authenticity and damaged α5 chain. In vitro minigene splicing assay was applied to investigate the effect of splicing variant, c.4298-20T>A, on COL4A5 mRNA synthesis. Molecular dynamics method was used to predict the capability of the responsible α5(IV) to form a triple helix. Results: The intron 46 of COL4A5 mRNA retained 18 bp, resulting in insertion of six amino acids behind the amino acid at position 1,433 of α5(IV). The predicted protein effect of this variant: p. (Pro1432_Gly1433insAspTyrPheValGluIle). As a consequence, the stability of α5(IV) secondary structure was impaired, probably leading to the unusual configuration of α345(IV). Discussion: Normally, splicing variant in COL4A5 gene can lead to phenotypes of XLAS, and the effect is associated with the extent of splicing. The patient reported here carried a c.4298-20T>A splicing variant in COL4A5 gene, and AS was highly suspected based on the pathology results. However, the patient did not manifest any ocular or ear abnormalities. We therefore present the c.4298-20T>A splicing variant in COL4A5 gene as likely-pathogenic splicing variant that leads to XLAS with mild phenotypes.
Collapse
Affiliation(s)
- Lei Liang
- Center for Prenatal Diagnosis and Medical Genetics, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Haotian Wu
- School of Public Health, Inner Mongolia Medical University, Hohhot, China
| | - Zeyu Cai
- Department of Nephrology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Jianrong Zhao
- Department of Nephrology, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| |
Collapse
|
10
|
Sun L, Lin Z, Zhang J, Shen J, Wang X, Yang J. Genetic etiological analysis of auditory neuropathy spectrum disorder by next-generation sequencing. Front Neurol 2022; 13:1026695. [PMID: 36570450 PMCID: PMC9772003 DOI: 10.3389/fneur.2022.1026695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Objective Auditory neuropathy spectrum disease (ANSD) is caused by both environmental and genetic causes and is defined by a failure in peripheral auditory neural transmission but normal outer hair cells function. To date, 13 genes identified as potentially causing ANSD have been documented. To study the etiology of ANSD, we collected 9 probands with ANSD diagnosed in the clinic and performed targeted next-generation sequencing. Methods Nine probands have been identified as ANSD based on the results of the ABR tests and DPOAE/CMs. Genomic DNA extracted from their peripheral blood was examined by next-generation sequencing (NGS) for a gene panel to identify any potential causal variations. For candidate pathogenic genes, we performed co-segregation among all family members of the pedigrees. Subsequently, using a mini-gene assay, we examined the function of a novel splice site mutant of OTOF. Results We analyzed nine cases of patients with ANSD with normal CMs/DPOAE and abnormal ABR, discovered three novel mutants of the OTOF gene that are known to cause ANSD, and six cases of other gene mutations including TBC1D24, LARS2, TIMM8A, MITF, and WFS1. Conclusion Our results extend the mutation spectrum of the OTOF gene and indicate that the genetic etiology of ANSD may be related to gene mutations of TBC1D24, LARS2, TIMM8A, MITF, and WFS1.
Collapse
Affiliation(s)
- Lianhua Sun
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Jiao Tong University School of Medicine Ear Institute, Shanghai, China,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China,*Correspondence: Lianhua Sun
| | - Zhengyu Lin
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Jiao Tong University School of Medicine Ear Institute, Shanghai, China,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jifang Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Jiao Tong University School of Medicine Ear Institute, Shanghai, China,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jiali Shen
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Jiao Tong University School of Medicine Ear Institute, Shanghai, China,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Xiaowen Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Jiao Tong University School of Medicine Ear Institute, Shanghai, China,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Jun Yang
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Shanghai Jiao Tong University School of Medicine Ear Institute, Shanghai, China,Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China,Jun Yang
| |
Collapse
|
11
|
Chen R, Diaz-Miranda MA, Aref-Eshghi E, Hartman TR, Griffith C, Morrison JL, Wheeler PG, Torti E, Richard G, Kenna M, Dechene ET, Spinner NB, Bai R, Conlin LK, Krantz ID, Amr SS, Luo M. Characterization of a possible founder synonymous variant in TECTA in multiple individuals with autosomal recessive hearing loss. Hum Mutat 2022; 43:1837-1843. [PMID: 35870179 DOI: 10.1002/humu.24443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/15/2022] [Accepted: 07/21/2022] [Indexed: 01/24/2023]
Abstract
Synonymous variants have been shown to alter the correct splicing of pre-mRNAs and generate disease-causing transcripts. These variants are not an uncommon etiology of genetic disease; however, they are frequently overlooked during genetic testing in the absence of functional and clinical data. Here, we describe the occurrence of a synonymous variant [NM_005422.4 (TECTA):c.327C>T, p.(Gly109=)] in seven individuals with hearing loss from six unrelated families. The variant is not located near exonic/intronic boundaries but is predicted to impact splicing by activating a cryptic splicing donor site in exon 4 of TECTA. In vitro minigene assays show that the variant disrupts the reading frame of the canonical transcript, which is predicted to cause a premature termination codon 48 amino acids downstream of the variant, leading to nonsense-mediated decay. The variant is present in population databases, predominantly in Latinos of African ancestry, but is rare in other ethnic groups. Our findings suggest that this synonymous variant is likely pathogenic for TECTA-associated autosomal recessive hearing loss and seems to have arisen as a founder variant in this specific Latino subpopulation. This study demonstrates that synonymous variants need careful splicing assessment and support from additional testing methodologies to determine their clinical impact.
Collapse
Affiliation(s)
- Robert Chen
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Tiffiney R Hartman
- Division of Genetics, Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | | | | | - Margaret Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth T Dechene
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nancy B Spinner
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Laura K Conlin
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ian D Krantz
- Division of Genetics, Roberts Individualized Medical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sami S Amr
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, Massachusetts, USA.,Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
| | - Minjie Luo
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| |
Collapse
|
12
|
Rossanti R, Horinouchi T, Sakakibara N, Yamamura T, Nagano C, Ishiko S, Aoto Y, Kondo A, Nagai S, Awano H, Nagase H, Matsuo M, Iijima K, Nozu K. Detecting pathogenic deep intronic variants in Gitelman syndrome. Am J Med Genet A 2022; 188:2576-2583. [PMID: 35785516 DOI: 10.1002/ajmg.a.62885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/17/2022] [Accepted: 05/30/2022] [Indexed: 01/24/2023]
Abstract
Gitelman syndrome (GS) is a rare, autosomal recessive, salt-losing tubulopathy caused by loss of function in the SLC12A3 gene (NM_000339.2), which encodes the natrium chloride cotransporter. The detection of homozygous or compound heterozygous SLC12A3 variants is expected in GS, but 18%-40% of patients with clinical GS carry only one mutant allele. Previous reports identified some pathogenic deep intronic variants in SLC12A3. Here, we report the screening of SLC12A3 deep intronic variants in 13 patients with suspected GS carrying one mutated SLC12A3 allele. Variant screening used the HaloPlex Target Enrichment System Kit capturing whole introns and the promotor region of SLC12A3, followed by SureCall variant analysis. Rare intronic variants (<1% frequency) were identified, and pathogenicity evaluated by the minigene system. Deep intronic variant screening detected seven rare SLC12A3 variants from six patients. Only one variant showed pathogenicity in the minigene system (c.602-16G>A, intron 4) through activation of a cryptic acceptor site. No variants were detected in the promotor region. Deep intronic screening identified only one pathogenic variant in patients with suspected GS carrying monoallelic SLC12A3 variants. Our results suggest that deep intronic variants partially explain the cause of monoallelic variants in patients with GS.
Collapse
Affiliation(s)
- Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Child Health, Nephrology Division, Dr. Hasan Sadikin General Hospital/Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nana Sakakibara
- 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
| | - 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
| | - Atsushi Kondo
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Sadayuki Nagai
- 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
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Hyogo, Japan
| | - Kazumoto Iijima
- Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan.,Department of Advanced Pediatric Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| |
Collapse
|
13
|
Zhang H, Chen C, Wu X, Lou C, Liang Q, Wu W, Wang X, Ding Q. Effects of 14 F9 synonymous codon variants on hemophilia B expression: Alteration of splicing along with protein expression. Hum Mutat 2022; 43:928-939. [PMID: 35391506 DOI: 10.1002/humu.24377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023]
Abstract
There is growing evidence that synonymous codon variants (SCVs) can cause disease through the disruption of different processes of protein production. The aim of the study is to investigate whether the 14 SCVs reported in the F9 variant database were the pathogenic causes of hemophilia B. The impacts of SCVs on splicing and protein expression were detected using a combination of in silico prediction, in vitro minigene splicing assay and cell expression detection. The splicing transcripts were identified and quantified by co-amplification fluorescent PCR. The mechanism of splicing was verified by a modified pU1snRNA and pU7snRNA approach. Aberrant splicing patterns were found in eight SCVs. Five of the 8 SCVs produced almost all aberrant splicing isoforms, which were expected to truncate protein, three of them presented a partial defect on both splicing and protein secretion, the overall effects were consistent with the residual Factor IX activity of the affected cases. Neither the pre-messenger RNA (mRNA) splicing process nor the protein function was impaired in the rest six SCVs. In conclusion, our study firstly revealed the pathogenic mechanism of the 14 F9 SCVs and highlighted the importance of performing mRNA splicing analysis and protein expression studies of SCVs in inherited disorders.
Collapse
Affiliation(s)
- Huayang Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Can Lou
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| |
Collapse
|
14
|
Stingl K, Baumann B, De Angeli P, Vincent A, Héon E, Cordonnier M, De Baere E, Raskin S, Sato MT, Shiokawa N, Kohl S, Wissinger B. Novel OPN1LW/OPN1MW Exon 3 Haplotype-Associated Splicing Defect in Patients with X-Linked Cone Dysfunction. Int J Mol Sci 2022; 23:ijms23126868. [PMID: 35743313 PMCID: PMC9224739 DOI: 10.3390/ijms23126868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
Certain combinations of common variants in exon 3 of OPN1LW and OPN1MW, the genes encoding the apo-protein of the long- and middle-wavelength sensitive cone photoreceptor visual pigments in humans, induce splicing defects and have been associated with dyschromatopsia and cone dysfunction syndromes. Here we report the identification of a novel exon 3 haplotype, G-C-G-A-T-T-G-G (referring to nucleotide variants at cDNA positions c.453, c.457, c.465, c.511, c.513, c.521, c.532, and c.538) deduced to encode a pigment with the amino acid residues L-I-V-V-A at positions p.153, p.171, p.174, p.178, and p.180, in OPN1LW or OPN1MW or both in a series of seven patients from four families with cone dysfunction. Applying minigene assays for all observed exon 3 haplotypes in the patients, we demonstrated that the novel exon 3 haplotype L-I-V-V-A induces a strong but incomplete splicing defect with 3-5% of residual correctly spliced transcripts. Minigene splicing outcomes were similar in HEK293 cells and the human retinoblastoma cell line WERI-Rb1, the latter retaining a cone photoreceptor expression profile including endogenous OPN1LW and OPN1MW gene expression. Patients carrying the novel L-I-V-V-A haplotype presented with a mild form of Blue Cone Monochromacy or Bornholm Eye Disease-like phenotype with reduced visual acuity, reduced cone electroretinography responses, red-green color vision defects, and frequently with severe myopia.
Collapse
Affiliation(s)
- Katarina Stingl
- Centre for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany;
| | - Britta Baumann
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, 72076 Tübingen, Germany; (B.B.); (P.D.A.); (S.K.)
| | - Pietro De Angeli
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, 72076 Tübingen, Germany; (B.B.); (P.D.A.); (S.K.)
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada; (A.V.); (E.H.)
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1X8, Canada; (A.V.); (E.H.)
| | - Monique Cordonnier
- Department of Ophthalmology, Hôpital Erasme, Cliniques Universitaires de Bruxelles, Université Libre de Bruxelles, 1070 Bruxelles, Belgium;
| | - Elfriede De Baere
- Center for Medical Genetics, Ghent University Hospital, Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium;
| | - Salmo Raskin
- Laboratório Genetika, Curitiba 80730-180, Brazil;
| | - Mario Teruo Sato
- Department of Ophthalmology & Otorhinolaryngology, Federal University of Paraná, Curitiba 80060-900, Brazil;
- Retina and Vitreo Consulting Eye Clinic, Curitiba 80530-010, Brazil;
| | - Naoye Shiokawa
- Retina and Vitreo Consulting Eye Clinic, Curitiba 80530-010, Brazil;
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, 72076 Tübingen, Germany; (B.B.); (P.D.A.); (S.K.)
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, 72076 Tübingen, Germany; (B.B.); (P.D.A.); (S.K.)
- Correspondence:
| |
Collapse
|
15
|
Liu Y, Sheng W, Wu J, Zheng J, Zhi X, Zhang S, Gu C, Guo D, Wang W. Case report: Altered pre-mRNA splicing caused by intronic variant c.1499 + 1G > A in the SLC4A4 gene. Front Pediatr 2022; 10:890147. [PMID: 36061388 PMCID: PMC9428394 DOI: 10.3389/fped.2022.890147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Proximal renal tubular acidosis (pRTA) with ocular abnormalities is an autosomal recessive disease caused by variants in the Solute Carrier Family 4 Member 4 (SLC4A4) gene. Patients present with metabolic acidosis and low plasma bicarbonate concentration (3∼17 mmol/L). In addition, they are often accompanied by ocular abnormalities, intellectual disability, and growth retardation. The patient underwent whole exome sequencing (WES) and bioinformatics analysis of variant pathogenicity in this study. Then, a minigene assay was conducted to analyze the splicing site variant further. Compound heterozygous variants in the SLC4A4 gene (NM_003759.3), c.145C > T (p.Arg49*) and c.1499 + 1G > A, were detected by WES. The minigene assay showed an mRNA splicing aberration caused by the c.1499 + 1G > A variant. Compared with the wild type, the mutant type caused 4-base insertion between exons 10 and 11 of SLC4A4 after expression in HEK293 cells. In conclusion, the c.1499 + 1G > A variant in the SLC4A4 gene may be one of the genetic causes in the patient. Moreover, our study provides the foundation for future gene therapy of such pathogenic variants.
Collapse
Affiliation(s)
- Yan Liu
- Department of Nephrology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| | - Wenchao Sheng
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Jinying Wu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Jie Zheng
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Xiufang Zhi
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Shuyue Zhang
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Chunyu Gu
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Detong Guo
- Graduate College of Tianjin Medical University, Tianjin Medical University, Tianjin, China.,Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Wenhong Wang
- Department of Nephrology, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China
| |
Collapse
|
16
|
Tsuji Y, Yamamura T, Nagano C, Horinouchi T, Sakakibara N, Ishiko S, Aoto Y, Rossanti R, Okada E, Tanaka E, Tsugawa K, Okamoto T, Sawai T, Araki Y, Shima Y, Nakanishi K, Nagase H, Matsuo M, Iijima K, Nozu K. Systematic Review of Genotype-Phenotype Correlations in Frasier Syndrome. Kidney Int Rep 2021; 6:2585-2593. [PMID: 34622098 PMCID: PMC8484119 DOI: 10.1016/j.ekir.2021.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 12/22/2022] Open
Abstract
Introduction Frasier syndrome (FS) is a rare inherited kidney disease caused by intron 9 splicing variants of WT1. For wild-type WT1, 2 active splice donor sites in intron 9 cause a mixture of 2 essential transcripts (with or without lysine-threonine-serine [+/KTS or −KTS]), and imbalance of the +KTS/−KTS ratio results in the development of FS. To date, 6 causative intron 9 variants have been identified; however, detailed transcript analysis has not yet been conducted and the genotype-phenotype correlation also remains to be elucidated. Methods We conducted an in vitro minigene splicing assay for 6 reported causative variants and in vivo RNA sequencing to determine the +KTS/−KTS ratio using patients’ samples. We also performed a systematic review of reported FS cases with a description of the renal phenotype. Results The in vitro assay revealed that although all mutant alleles produced −KTS transcripts only, the wild-type allele produced both +KTS and −KTS transcripts at a 1:1 ratio. In vivo RNA sequencing showed that patients’ samples with all heterozygous variants produced similar ratios of +KTS to −KTS (1:3.2−1:3.5) and wild-type kidney showed almost a 1:1 ratio (1:0.85). A systematic review of 126 cases clarified that the median age of developing ESKD was 16 years in all FS patients, and there were no statistically significant differences between the genotypes or sex chromosome karyotypes in terms of the renal survival period. Conclusion Our study suggested no differences in splicing pattern or renal survival period among reported intron 9 variants causative of FS.
Collapse
Affiliation(s)
- Yurika Tsuji
- 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
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, 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
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eriko Tanaka
- Department of Pediatrics, Kyorin University School of Medicine, Mitaka, Japan
| | - Koji Tsugawa
- Department of Pediatrics, Hirosaki University Hospital, Hirosaki, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Graduate School of Meidicine, Sapporo, Japan
| | - Toshihiro Sawai
- Department of Pediatrics, Shiga University of Medical Science, Shiga, Japan
| | - Yoshinori Araki
- Department of Pediatrics, Hokkaido Medical Center, Sapporo, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Koichi Nakanishi
- Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masafumi Matsuo
- Locomotion Biology Research Center, Kobe Gakuin University, 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
| |
Collapse
|
17
|
Bruni V, Spoleti CB, La Barbera A, Dattilo V, Colao E, Votino C, Bellacchio E, Perrotti N, Giglio S, Iuliano R. A Novel Splicing Variant of COL2A1 in a Fetus with Achondrogenesis Type II: Interpretation of Pathogenicity of In-Frame Deletions. Genes (Basel) 2021; 12:genes12091395. [PMID: 34573377 PMCID: PMC8467821 DOI: 10.3390/genes12091395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/08/2023] Open
Abstract
Achondrogenesis type II (ACG2) is a lethal skeletal dysplasia caused by dominant pathogenic variants in COL2A1. Most of the variants found in patients with ACG2 affect the glycine residue included in the Gly-X-Y tripeptide repeat that characterizes the type II collagen helix. In this study, we reported a case of a novel splicing variant of COL2A1 in a fetus with ACG2. An NGS analysis of fetal DNA revealed a heterozygous variant c.1267-2_1269del located in intron 20/exon 21. The variant occurred de novo since it was not detected in DNA from the blood samples of parents. We generated an appropriate minigene construct to study the effect of the variant detected. The minigene expression resulted in the synthesis of a COL2A1 messenger RNA lacking exon 21, which generated a predicted in-frame deleted protein. Usually, in-frame deletion variants of COL2A1 cause a phenotype such as Kniest dysplasia, which is milder than ACG2. Therefore, we propose that the size and position of an in-frame deletion in COL2A1 may be relevant in determining the phenotype of skeletal dysplasia.
Collapse
Affiliation(s)
- Valentina Bruni
- Medical Genetics Unit, Department of Health Sciences, University “Magna Graecia” of Catanzaro, 88100 Catanzaro, Italy; (V.B.); (C.B.S.); (V.D.); (E.C.); (N.P.)
| | - Cristina Barbara Spoleti
- Medical Genetics Unit, Department of Health Sciences, University “Magna Graecia” of Catanzaro, 88100 Catanzaro, Italy; (V.B.); (C.B.S.); (V.D.); (E.C.); (N.P.)
| | - Andrea La Barbera
- Medical Genetics Unit, Department of Clinical and Experimental Biomedical Sciences “Mario Serio”, University of Florence, 50121 Florence, Italy;
| | - Vincenzo Dattilo
- Medical Genetics Unit, Department of Health Sciences, University “Magna Graecia” of Catanzaro, 88100 Catanzaro, Italy; (V.B.); (C.B.S.); (V.D.); (E.C.); (N.P.)
| | - Emma Colao
- Medical Genetics Unit, Department of Health Sciences, University “Magna Graecia” of Catanzaro, 88100 Catanzaro, Italy; (V.B.); (C.B.S.); (V.D.); (E.C.); (N.P.)
| | | | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Nicola Perrotti
- Medical Genetics Unit, Department of Health Sciences, University “Magna Graecia” of Catanzaro, 88100 Catanzaro, Italy; (V.B.); (C.B.S.); (V.D.); (E.C.); (N.P.)
| | - Sabrina Giglio
- Unit of Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, 09124 Cagliari, Italy;
| | - Rodolfo Iuliano
- Medical Genetics Unit, Department of Health Sciences, University “Magna Graecia” of Catanzaro, 88100 Catanzaro, Italy; (V.B.); (C.B.S.); (V.D.); (E.C.); (N.P.)
- Correspondence: ; Tel.: +39-0961-3695182
| |
Collapse
|
18
|
Takafuji S, Mori T, Nishimura N, Yamamoto N, Uemura S, Nozu K, Terui K, Toki T, Ito E, Muramatsu H, Takahashi Y, Matsuo M, Yamamura T, Iijima K. Usefulness of functional splicing analysis to confirm precise disease pathogenesis in Diamond-Blackfan anemia caused by intronic variants in RPS19. Pediatr Hematol Oncol 2021; 38:515-527. [PMID: 33622161 DOI: 10.1080/08880018.2021.1887984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Diamond-Blackfan anemia (DBA) is mainly caused by pathogenic variants in ribosomal proteins and 22 responsible genes have been identified to date. The most common causative gene of DBA is RPS19 [NM_001022.4]. Nearly 180 RPS19 variants have been reported, including three deep intronic variants outside the splicing consensus sequence (c.72-92A > G, c.356 + 18G > C, and c.411 + 6G > C). We also identified one case with a c.412-3C > G intronic variant. Without conducting transcript analysis, the pathogenicity of these variants is unknown. However, it is difficult to assess transcripts because of their fragility. In such cases, in vitro functional splicing assays can be used to assess pathogenicity. Here, we report functional splicing analysis results of four RPS19 deep intronic variants identified in our case and in previously reported cases. One splicing consensus variant (c.411 + 1G > A) was also examined as a positive control. Aberrant splicing with a 2-bp insertion between exons 5 and 6 was identified in the patient samples and minigene assay results also identified exon 6 skipping in our case. The exon 6 skipping transcript was confirmed by further evaluation using quantitative RT-PCR. Additionally, minigene assay analysis of three reported deep intronic variants revealed that none of them showed aberrant splicing and that these variants were not considered to be pathogenic. In conclusion, the minigene assay is a useful method for functional splicing analysis of inherited disease.
Collapse
Affiliation(s)
- Satoru Takafuji
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takeshi Mori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Noriyuki Nishimura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nobuyuki Yamamoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Suguru Uemura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kiminori Terui
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Tsutomu Toki
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masafumi Matsuo
- Locomotion Biology Research Center, Kobe Gakuin University, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| |
Collapse
|
19
|
Xiong Y, Xia H, Yuan L, Deng S, Ding Z, Deng H. Identification of compound heterozygous DNAH11 variants in a Han-Chinese family with primary ciliary dyskinesia. J Cell Mol Med 2021; 25:9028-9037. [PMID: 34405951 PMCID: PMC8435457 DOI: 10.1111/jcmm.16866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/24/2021] [Accepted: 08/04/2021] [Indexed: 12/13/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a group of genetically and clinically heterogeneous disorders with motile cilia dysfunction. It is clinically characterized by oto‐sino‐pulmonary diseases and subfertility, and half of the patients have situs inversus (Kartagener syndrome). To identify the genetic cause in a Han‐Chinese pedigree, whole‐exome sequencing was conducted in the 37‐year‐old proband, and then, Sanger sequencing was performed on available family members. Minigene splicing assay was applied to verify the impact of the splice‐site variant. Compound heterozygous variants including a splice‐site variant (c.1974‐1G>C, rs1359107415) and a missense variant (c.7787G>A, p.(Arg2596Gln), rs780492669), in the dynein axonemal heavy chain 11 gene (DNAH11) were identified and confirmed as the disease‐associated variants of this lineage. The minigene expression in vitro revealed that the c.1974‐1G>C variant could cause skipping over exon 12, predicted to result in a truncated protein. This discovery may enlarge the DNAH11 variant spectrum of PCD, promote accurate genetic counselling and contribute to PCD diagnosis.
Collapse
Affiliation(s)
- Ying Xiong
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hong Xia
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China
| | - Sheng Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Zerui Ding
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Disease Genome Research Center, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| |
Collapse
|
20
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
21
|
Mauro-Herrera M, Chiang J, Radojevic B, Bennett LD. Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases. Genes (Basel) 2021; 12:993. [PMID: 34209753 DOI: 10.3390/genes12070993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/13/2023] Open
Abstract
Inherited retinal diseases (IRD) comprise a heterogeneous set of clinical and genetic disorders that lead to blindness. Given the emerging opportunities in precision medicine and gene therapy, it has become increasingly important to determine whether DNA variants with uncertain significance (VUS) are responsible for patients’ IRD. This research was performed to assess the functional consequence of six VUS identified in patients with IRD. Clinical assessments included an ophthalmic examination, best-corrected visual acuity, and kinetic perimetry. Imaging was acquired with the Optos ultra-widefield camera and spectral domain optical coherence tomography (SD-OCT). Genetic testing was performed by Molecular Vision Laboratories. VUS that were predicted to alter splicing were analyzed with a minigene assay, which revealed that VUS in the genes OPA1, CNGB1, and CLUAP1 altered spicing mechanisms. Due to emerging gene and cell therapies, these results expand the genotype-phenotype correlations for patients diagnosed with an IRD.
Collapse
|
22
|
Damásio J, Santos D, Morais S, Brás J, Guerreiro R, Sardoeira A, Cavaco S, Carrilho I, Barbot C, Barros J, Sequeiros J. Congenital ataxia due to novel variant in ATP8A2. Clin Genet 2021; 100:79-83. [PMID: 33682124 DOI: 10.1111/cge.13954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/22/2023]
Abstract
Congenital ataxias are a heterogeneous group of disorders characterized by congenital or early-onset ataxia. Here, we describe two siblings with congenital ataxia, who acquired independent gait by age 4 years. After 16 years of follow-up they presented near normal cognition, cerebellar ataxia, mild pyramidal signs, and dystonia. On exome sequencing, a novel homozygous variant (c.1580-18C > G - intron 17) in ATP8A2 was identified. A new acceptor splice site was predicted by bioinformatics tools, and functionally characterized through a minigene assay. Minigene constructs were generated by PCR-amplification of genomic sequences surrounding the variant of interest and cloning into the pCMVdi vector. Altered splicing was evaluated by expressing these constructs in HEK293T cells. The construct with the c.1580-18C > G homozygous variant produced an aberrant transcript, leading to retention of 17 bp of intron 17, by the use of an alternative acceptor splice site, resulting in a premature stop codon by insertion of four amino acids. These results allowed us to establish this as a disease-causing variant and expand ATP8A2-related disorders to include less severe forms of congenital ataxia.
Collapse
Affiliation(s)
- Joana Damásio
- UnIGENe/CGPP - Instituto de Biologia Molecular e Celular, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Serviço Neurologia, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Diana Santos
- UnIGENe/CGPP - Instituto de Biologia Molecular e Celular, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sara Morais
- UnIGENe/CGPP - Instituto de Biologia Molecular e Celular, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - José Brás
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, Michigan, USA
| | - Rita Guerreiro
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, Michigan, USA.,Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, Michigan, USA
| | - Ana Sardoeira
- Serviço Neurologia, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Sara Cavaco
- Unidade Neuropsicologia, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Inês Carrilho
- Unidade Neurologia Pediátrica, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Clara Barbot
- UnIGENe/CGPP - Instituto de Biologia Molecular e Celular, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - José Barros
- Serviço Neurologia, Centro Hospitalar Universitário do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Jorge Sequeiros
- UnIGENe/CGPP - Instituto de Biologia Molecular e Celular, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal
| |
Collapse
|
23
|
Suarez-Artiles L, Perdomo-Ramirez A, Ramos-Trujillo E, Claverie-Martin F. Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease. Genes (Basel) 2018; 9:E15. [PMID: 29300302 DOI: 10.3390/genes9010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
Collapse
|
24
|
Wu H, Boulling A, Cooper DN, Li ZS, Liao Z, Férec C, Chen JM. Analysis of the Impact of Known SPINK1 Missense Variants on Pre-mRNA Splicing and/or mRNA Stability in a Full-Length Gene Assay. Genes (Basel) 2017; 8:genes8100263. [PMID: 28994706 PMCID: PMC5664113 DOI: 10.3390/genes8100263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/25/2017] [Accepted: 10/06/2017] [Indexed: 12/16/2022] Open
Abstract
It is increasingly appreciated that missense variants may not only alter protein structure and function but may also influence pre-mRNA splicing and/or mRNA stability. Here we explore this issue in the context of currently known SPINK1 missense variants using a full-length gene assay. We demonstrated that 4 (17%) out of 24 variants tested significantly reduced pre-mRNA splicing and/or stability as compared with the wild-type. However, since the strongest effect observed was a 23% reduction from normal, the contribution of SPINK1 missense variants to the clinical phenotype through an impact on mRNA processing alone may be relatively minor compared with their effects in relation to protein structure/function.
Collapse
Affiliation(s)
- Hao Wu
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China.
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest 29238, France.
- Etablissement Français du Sang (EFS)-Bretagne, Brest 29200, France.
- Shanghai Institute of Pancreatic Diseases, Shanghai 200433, China.
| | - Arnaud Boulling
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest 29238, France.
- Etablissement Français du Sang (EFS)-Bretagne, Brest 29200, France.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China.
- Shanghai Institute of Pancreatic Diseases, Shanghai 200433, China.
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, The Second Military Medical University, Shanghai 200433, China.
- Shanghai Institute of Pancreatic Diseases, Shanghai 200433, China.
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest 29238, France.
- Etablissement Français du Sang (EFS)-Bretagne, Brest 29200, France.
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest 29238, France.
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest 29200, France.
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest 29238, France.
- Etablissement Français du Sang (EFS)-Bretagne, Brest 29200, France.
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest 29238, France.
| |
Collapse
|
25
|
Álvarez-Satta M, Castro-Sánchez S, Pousada G, Valverde D. Functional analysis by minigene assay of putative splicing variants found in Bardet-Biedl syndrome patients. J Cell Mol Med 2017; 21:2268-2275. [PMID: 28502102 PMCID: PMC5618670 DOI: 10.1111/jcmm.13147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/30/2017] [Indexed: 01/05/2023] Open
Abstract
Bardet–Biedl syndrome (BBS) and Alström syndrome (ALMS) are rare diseases belonging to the group of ciliopathies. Although mutational screening studies of BBS/ALMS cohorts have been extensively reported, little is known about the functional effect of those changes. Thus, splicing variants are estimated to represent 15% of disease‐causing mutations, and there is growing evidence that many exonic changes are really splicing variants misclassified. In this study, we aimed to analyse for the first time several variants in BBS2,ARL6/BBS3,BBS4 and ALMS1 genes predicted to produce aberrant splicing by minigene assay. We found discordance between bioinformatics analysis and experimental data when comparing wild‐type and mutant constructs. Remarkably, we identified nonsense variants presumably resistant to nonsense‐mediated decay, even when a premature termination codon would be introduced in the second amino acid (p.(G2*) mutation in ARL6/BBS3 gene). As a whole, we report one of the first functional studies of BBS/ALMS1 variants using minigene assay, trying to elucidate their role in disease. Functional studies of variants identified in BBS and ALMS patients are essential for their proper classification and subsequent genetic counselling and could also be the start point for new therapeutic approaches, currently based only on symptomatic treatment.
Collapse
Affiliation(s)
- María Álvarez-Satta
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Sheila Castro-Sánchez
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Guillermo Pousada
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Diana Valverde
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| |
Collapse
|
26
|
Claverie-Martin F, Gonzalez-Paredes FJ, Ramos-Trujillo E. Splicing defects caused by exonic mutations in PKD1 as a new mechanism of pathogenesis in autosomal dominant polycystic kidney disease. RNA Biol 2016; 12:369-74. [PMID: 25757501 DOI: 10.1080/15476286.2015.1014291] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The correct splicing of precursor-mRNA depends on the actual splice sites plus exonic and intronic regulatory elements recognized by the splicing machinery. Surprisingly, an increasing number of examples reveal that exonic mutations disrupt the binding of splicing factors to these sequences or generate new splice sites or regulatory elements, causing disease. This contradicts the general assumption that missense mutations disrupt protein function and that synonymous mutations are merely polymorphisms. Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited disorder caused mainly by mutations in the PKD1 gene. Recently, we analyzed a substantial number of PKD1 missense or synonymous mutations to further characterize their consequences on pre-mRNA splicing. Our results showed that one missense and 2 synonymous mutations induce significant defects in pre-mRNA splicing. Thus, it appears that aberrant splicing as a result of exonic mutations is a previously unrecognized cause of ADPKD.
Collapse
Affiliation(s)
- Felix Claverie-Martin
- a Unidad de Investigacion; Hospital Nuestra Señora de Candelaria ; Santa Cruz de Tenerife , Spain
| | | | | |
Collapse
|
27
|
van der Klift HM, Jansen AML, van der Steenstraten N, Bik EC, Tops CMJ, Devilee P, Wijnen JT. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med 2015; 3:327-45. [PMID: 26247049 PMCID: PMC4521968 DOI: 10.1002/mgg3.145] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/05/2015] [Accepted: 03/16/2015] [Indexed: 12/13/2022] Open
Abstract
A subset of DNA variants causes genetic disease through aberrant splicing. Experimental splicing assays, either RT-PCR analyses of patient RNA or functional splicing reporter minigene assays, are required to evaluate the molecular nature of the splice defect. Here, we present minigene assays performed for 17 variants in the consensus splice site regions, 14 exonic variants outside these regions, and two deep intronic variants, all in the DNA mismatch-repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, associated with Lynch syndrome. We also included two deep intronic variants in APC and PKD2. For one variant (MLH1 c.122A>G), our minigene assay and patient RNA analysis could not confirm the previously reported aberrant splicing. The aim of our study was to further investigate the concordance between minigene splicing assays and patient RNA analyses. For 30 variants results from patient RNA analyses were available, either performed by our laboratory or presented in literature. Some variants were deliberately included in this study because they resulted in multiple aberrant transcripts in patient RNA analysis, or caused a splice effect other than the prevalent exon skip. While both methods were completely concordant in the assessment of splice effects, four variants exhibited major differences in aberrant splice patterns. Based on the present and earlier studies, together showing an almost 100% concordance of minigene assays with patient RNA analyses, we discuss the weight given to minigene splicing assays in the current criteria proposed by InSiGHT for clinical classification of MMR variants.
Collapse
Affiliation(s)
- Heleen M van der Klift
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Anne M L Jansen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands
| | | | - Elsa C Bik
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Carli M J Tops
- Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Pathology, Leiden University Medical Center Leiden, The Netherlands
| | - Juul T Wijnen
- Department of Human Genetics, Leiden University Medical Center Leiden, The Netherlands ; Department of Clinical Genetics, Leiden University Medical Center Leiden, The Netherlands
| |
Collapse
|
28
|
Vemula SR, Xiao J, Zhao Y, Bastian RW, Perlmutter JS, Racette BA, Paniello RC, Wszolek ZK, Uitti RJ, Van Gerpen JA, Hedera P, Truong DD, Blitzer A, Rudzińska M, Momčilović D, Jinnah HA, Frei K, Pfeiffer RF, LeDoux MS. A rare sequence variant in intron 1 of THAP1 is associated with primary dystonia. Mol Genet Genomic Med 2014; 2:261-72. [PMID: 24936516 PMCID: PMC4049367 DOI: 10.1002/mgg3.67] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/31/2013] [Accepted: 01/03/2014] [Indexed: 12/16/2022] Open
Abstract
Although coding variants in THAP1 have been causally associated with primary dystonia, the contribution of noncoding variants remains uncertain. Herein, we examine a previously identified Intron 1 variant (c.71+9C>A, rs200209986). Among 1672 subjects with mainly adult-onset primary dystonia, 12 harbored the variant in contrast to 1/1574 controls (P < 0.01). Dystonia classification included cervical dystonia (N = 3), laryngeal dystonia (adductor subtype, N = 3), jaw-opening oromandibular dystonia (N = 1), blepharospasm (N = 2), and unclassified (N = 3). Age of dystonia onset ranged from 25 to 69 years (mean = 54 years). In comparison to controls with no identified THAP1 sequence variants, the c.71+9C>A variant was associated with an elevated ratio of Isoform 1 (NM_018105) to Isoform 2 (NM_199003) in leukocytes. In silico and minigene analyses indicated that c.71+9C>A alters THAP1 splicing. Lymphoblastoid cells harboring the c.71+9C>A variant showed extensive apoptosis with relatively fewer cells in the G2 phase of the cell cycle. Differentially expressed genes from lymphoblastoid cells revealed that the c.71+9C>A variant exerts effects on DNA synthesis, cell growth and proliferation, cell survival, and cytotoxicity. In aggregate, these data indicate that THAP1 c.71+9C>A is a risk factor for adult-onset primary dystonia.
Collapse
Affiliation(s)
- Satya R Vemula
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center Memphis, Tennessee, 38163
| | - Jianfeng Xiao
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center Memphis, Tennessee, 38163
| | - Yu Zhao
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center Memphis, Tennessee, 38163
| | | | - Joel S Perlmutter
- Department of Neurology, Washington University School of Medicine St. Louis, Missouri
| | - Brad A Racette
- Department of Neurology, Washington University School of Medicine St. Louis, Missouri
| | - Randal C Paniello
- Department of Otolaryngology-Head and Neck Surgery, Washington University School of Medicine St. Louis, Missouri
| | | | - Ryan J Uitti
- Department of Neurology, Mayo Clinic Jacksonville, Florida, 32224
| | - Jay A Van Gerpen
- Department of Neurology, Mayo Clinic Jacksonville, Florida, 32224
| | - Peter Hedera
- Department of Neurology, Vanderbilt University Nashville, Tennessee
| | - Daniel D Truong
- Parkinson's & Movement Disorder Institute Fountain Valley, California, 92708
| | - Andrew Blitzer
- New York Center for Voice and Swallowing Disorders New York, New York
| | - Monika Rudzińska
- Department of Neurology, Jagiellonian University Medical College in Krakow Kraków, Poland
| | - Dragana Momčilović
- Clinic for Child Neurology and Psychiatry, Medical Faculty University of Belgrade Belgrade, Serbia
| | - Hyder A Jinnah
- Departments of Neurology, Human Genetics, and Pediatrics, School of Medicine, Emory University Atlanta, Georgia, 30322
| | - Karen Frei
- Department of Neurology, Loma Linda University Health System Loma Linda, California, 92354
| | - Ronald F Pfeiffer
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center Memphis, Tennessee, 38163
| | - Mark S LeDoux
- Departments of Neurology and Anatomy & Neurobiology, University of Tennessee Health Science Center Memphis, Tennessee, 38163
| |
Collapse
|