1
|
Bharti N, Santos L, Davyt M, Behrmann S, Eichholtz M, Jimenez-Sanchez A, Hong JS, Rab A, Sorscher EJ, Albers S, Ignatova Z. Translation velocity determines the efficacy of engineered suppressor tRNAs on pathogenic nonsense mutations. Nat Commun 2024; 15:2957. [PMID: 38580646 PMCID: PMC10997658 DOI: 10.1038/s41467-024-47258-9] [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: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/07/2024] Open
Abstract
Nonsense mutations - the underlying cause of approximately 11% of all genetic diseases - prematurely terminate protein synthesis by mutating a sense codon to a premature stop or termination codon (PTC). An emerging therapeutic strategy to suppress nonsense defects is to engineer sense-codon decoding tRNAs to readthrough and restore translation at PTCs. However, the readthrough efficiency of the engineered suppressor tRNAs (sup-tRNAs) largely varies in a tissue- and sequence context-dependent manner and has not yet yielded optimal clinical efficacy for many nonsense mutations. Here, we systematically analyze the suppression efficacy at various pathogenic nonsense mutations. We discover that the translation velocity of the sequence upstream of PTCs modulates the sup-tRNA readthrough efficacy. The PTCs most refractory to suppression are embedded in a sequence context translated with an abrupt reversal of the translation speed leading to ribosomal collisions. Moreover, modeling translation velocity using Ribo-seq data can accurately predict the suppression efficacy at PTCs. These results reveal previously unknown molecular signatures contributing to genotype-phenotype relationships and treatment-response heterogeneity, and provide the framework for the development of personalized tRNA-based gene therapies.
Collapse
Affiliation(s)
- Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Stine Behrmann
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Marie Eichholtz
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | | | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Andras Rab
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany.
| |
Collapse
|
2
|
Shi Y, Shi N, Yang Y, Zheng Z, Xia Q. Unnatural Amino Acid-Based Ionic Liquid Enables Oral Treatment of Nonsense Mutation Disease in Mice. Adv Sci (Weinh) 2024; 11:e2306792. [PMID: 38288517 PMCID: PMC10987103 DOI: 10.1002/advs.202306792] [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] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/08/2024] [Indexed: 04/04/2024]
Abstract
This investigation addresses the challenge of suboptimal unnatural amino acid (UAA) utilization in the site-specific suppression of nonsense mutations through genetic code expansion, which is crucial for protein restoration and precise property tailoring. A facile and economical oral liquid formulation is developed by converting UAAs into ionic liquids, significantly enhancing their bioavailability and tissue accumulation. Empirical data reveal a 10-fold increase in bioavailability and up to a 13-fold rise in focal tissue accumulation, alongside marked improvements in UAA incorporation efficiency. A 4-week oral administration in mdx mice, a model for Duchenne muscular dystrophy (DMD), demonstrates the formulation's unprecedented therapeutic potential, with up to 40% dystrophin expression restoration and 75% recovery of normal fiber functions, surpassing existing treatments and exhibiting substantial long-term safety. This study presents a potent oral dosage form that dramatically improves UAA incorporation into target proteins in vivo, offering a significant advance in the treatment of nonsense mutation-mediated disorders and holding considerable promise for clinical translation.
Collapse
Affiliation(s)
- Yujie Shi
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100191China
- Department of Pharmaceutical AnalysisSchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
- Beijing Key Laboratory of Molecular Pharmaceutics and New Drug Delivery SystemsPeking UniversityBeijing100191China
| | - Ningning Shi
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100191China
- Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - Yuelin Yang
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100191China
- Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - Zhetao Zheng
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100191China
- Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijing100191China
- Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking UniversityBeijing100191China
| |
Collapse
|
3
|
Manjunath LE, Singh A, Devi Kumar S, Vasu K, Kar D, Sellamuthu K, Eswarappa SM. Transcript-specific induction of stop codon readthrough using a CRISPR-dCas13 system. EMBO Rep 2024; 25:2118-2143. [PMID: 38499809 PMCID: PMC11015002 DOI: 10.1038/s44319-024-00115-8] [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: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using a CRISPR-dCas13 system. Using specific guide RNAs, we target dCas13 to the region downstream of canonical stop codons of mammalian AGO1 and VEGFA mRNAs, known to exhibit natural SCR. Readthrough assays reveal enhanced SCR of these mRNAs (both exogenous and endogenous) caused by the dCas13-gRNA complexes. This effect is associated with ribosomal pausing, which has been reported for several SCR events. Our data show that CRISPR-dCas13 can also induce SCR across premature termination codons (PTCs) in the mRNAs of green fluorescent protein and TP53. We demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA and hereditary spherocytosis-causing PTC in SPTA1 mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
Collapse
Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Karthi Sellamuthu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- University of Texas Medical Branch, Galveston, TX, USA
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
| |
Collapse
|
4
|
Mangkalaphiban K, Fu L, Du M, Thrasher K, Keeling KM, Bedwell DM, Jacobson A. Extended stop codon context predicts nonsense codon readthrough efficiency in human cells. Nat Commun 2024; 15:2486. [PMID: 38509072 PMCID: PMC10954755 DOI: 10.1038/s41467-024-46703-z] [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: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Protein synthesis terminates when a stop codon enters the ribosome's A-site. Although termination is efficient, stop codon readthrough can occur when a near-cognate tRNA outcompetes release factors during decoding. Seeking to understand readthrough regulation we used a machine learning approach to analyze readthrough efficiency data from published HEK293T ribosome profiling experiments and compared it to comparable yeast experiments. We obtained evidence for the conservation of identities of the stop codon, its context, and 3'-UTR length (when termination is compromised), but not the P-site codon, suggesting a P-site tRNA role in readthrough regulation. Models trained on data from cells treated with the readthrough-promoting drug, G418, accurately predicted readthrough of premature termination codons arising from CFTR nonsense alleles that cause cystic fibrosis. This predictive ability has the potential to aid development of nonsense suppression therapies by predicting a patient's likelihood of improvement in response to drugs given their nonsense mutation sequence context.
Collapse
Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
- Department of Genomics and Computational Biology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Ming Du
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kari Thrasher
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.
| |
Collapse
|
5
|
Machida R, Ogawa T, Min Soe K, Moriyama K. Nonsense-mediated mRNA decay affects hyperactive root formation in oculo-facio-cardio-dental syndrome via up-frameshift protein 1. J Oral Biosci 2024; 66:225-231. [PMID: 38244688 DOI: 10.1016/j.job.2024.01.008] [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: 09/11/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
OBJECTIVES Oculo-facio-cardio-dental (OFCD) syndrome is a rare X-linked genetic disorder caused by mutations in the BCL6 co-repressor (BCOR) and is mainly characterized by radiculomegaly (elongated dental roots). All BCOR mutations reported to date have been associated with premature termination codons, indicating that nonsense-mediated mRNA decay (NMD) might play a vital role in the pathogenesis of OFCD syndrome. However, the molecular mechanisms underlying NMD remain unclear. In this study, we investigated the involvement of up-frameshift protein 1 (UPF1), which plays a central role in NMD, in the hyperactive root formation caused by BCOR mutations. METHODS Periodontal ligament cells, isolated from a Japanese woman with a c.3668delC frameshift mutation in BCOR, and primary human periodontal ligament fibroblasts (HPdLFs) were used for an RNA immunoprecipitation assay to confirm the binding of UPF1 to mutated BCOR. Additionally, the effects of UPF1 on the BCOR transcription levels and corresponding gene expression were determined by performing relative quantitative real-time polymerase chain reactions. RESULTS RNA immunoprecipitation revealed that UPF1 binds to exon 9 of mutated BCOR. Additionally, UPF1 knockdown via siRNA upregulated the transcription of BCOR, whereas overexpression of wild-type and mutated BCOR with the same frameshift mutation in HPdLFs altered bone morphogenetic protein 2 (BMP2) expression. CONCLUSIONS Our findings indicate that BCOR mutations regulate the transcription of BCOR via UPF1, which may in turn regulate the expression of BMP2. NMD, caused by a c.3668delC mutation, potentially leads to an OFCD syndrome phenotype, including elongated dental roots.
Collapse
Affiliation(s)
- Ryoto Machida
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Takuya Ogawa
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Kyaw Min Soe
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo, 113-8549, Japan.
| |
Collapse
|
6
|
Askarinejad A, Esmaeili S, Dalili M, Biglari A, Kohansal E, Maleki M, Kalayinia S. Catecholaminergic polymorphic ventricular tachycardia (and seizure) caused by a novel homozygous likely pathogenic variant in CASQ2 gene. Gene 2024; 895:148012. [PMID: 37995796 DOI: 10.1016/j.gene.2023.148012] [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: 09/15/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND Although structural heart disease is frequently present among patients who experience sudden cardiac death (SCD), inherited arrhythmia syndromes can also play an important role in the occurrence of SCD. CPVT2, which is the second-most prevalent form of CPVT, arises from an abnormality in the CASQ2 gene. OBJECTIVE We represent a novel CASQ2 variant that causes CPVT2 and conduct a comprehensive review on this topic. METHODS The proband underwent Whole-exome sequencing (WES) in order to ascertain the etiology of CPVT. Subsequently, the process of segregating the available family members was carried out through the utilization of PCR and Sanger Sequencing. We searched the google scholar and PubMed/Medline for studies reporting CASQ2 variants, published up to May 10,2023. We used the following mesh term "Calsequestrin" and using free-text method with terms including "CASQ2","CASQ2 variants", and "CASQ2 mutation". RESULTS The CASQ2 gene was found to contain an autosomal recessive nonsense variant c.268_269insTA:p.Gly90ValfsTer4, which was identified by WES. This variant was determined to be the most probable cause of CPVT in the pedigree under investigation. CONCLUSION CASQ2 variants play an important role in pathogenesis of CPVT2. Notabely, based on results of our study and other findings in the literature the variant in this gene may cause an neurological signs in the patients with CPVT2. Further studies are needed for more details about the role of this gene in CPVT evaluation, diagnosis, and gene therapy.
Collapse
Affiliation(s)
- Amir Askarinejad
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran University of Medical Sciences, Tehran, Iran
| | - Shiva Esmaeili
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran University of Medical Sciences, Tehran, Iran
| | - Mohamad Dalili
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Biglari
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran University of Medical Sciences, Tehran, Iran
| | - Erfan Kohansal
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
7
|
Šilhavý J, Mlejnek P, Šimáková M, Liška F, Malínská H, Marková I, Hüttl M, Miklánková D, Mušálková D, Stránecký V, Kmoch S, Sticová E, Vrbacký M, Mráček T, Pravenec M. Spontaneous nonsense mutation in the tuftelin 1 gene is associated with abnormal hair appearance and amelioration of glucose and lipid metabolism in the rat. Physiol Genomics 2024; 56:65-73. [PMID: 37955133 DOI: 10.1152/physiolgenomics.00084.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/07/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
Recently, we have identified a recessive mutation, an abnormal coat appearance in the BXH6 strain, a member of the HXB/BXH set of recombinant inbred (RI) strains. The RI strains were derived from the spontaneously hypertensive rat (SHR) and Brown Norway rat (BN-Lx) progenitors. Whole genome sequencing of the mutant rats identified the 195875980 G/A mutation in the tuftelin 1 (Tuft1) gene on chromosome 2, which resulted in a premature stop codon. Compared with wild-type BXH6 rats, BXH6-Tuft1 mutant rats exhibited lower body weight due to reduced visceral fat and ectopic fat accumulation in the liver and heart. Reduced adiposity was associated with decreased serum glucose and insulin and increased insulin-stimulated glycogenesis in skeletal muscle. In addition, mutant rats had lower serum monocyte chemoattractant protein-1 and leptin levels, indicative of reduced inflammation. Analysis of the liver proteome identified differentially expressed proteins from fatty acid metabolism and β-oxidation, peroxisomes, carbohydrate metabolism, inflammation, and proteasome pathways. These results provide evidence for the important role of the Tuft1 gene in the regulation of lipid and glucose metabolism and suggest underlying molecular mechanisms.NEW & NOTEWORTHY A new spontaneous mutation, abnormal hair appearance in the rat, has been identified as a nonfunctional tuftelin 1 (Tuft1) gene. The pleiotropic effects of this mutation regulate glucose and lipid metabolism. Analysis of the liver proteome revealed possible molecular mechanisms for the metabolic effects of the Tuft1 gene.
Collapse
Affiliation(s)
- Jan Šilhavý
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslava Šimáková
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - František Liška
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Hana Malínská
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Marková
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Denisa Miklánková
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Dita Mušálková
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Viktor Stránecký
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Stanislav Kmoch
- Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Eva Sticová
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- Department of Pathology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marek Vrbacký
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Mráček
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| |
Collapse
|
8
|
Iwanaga Y, Tsuji K, Nishimura A, Tateishi K, Kakiuchi M, Tsuji T. A nonsense mutation in mouse Adamtsl2 causes uterine hypoplasia and an irregular estrous cycle. Mamm Genome 2023; 34:559-571. [PMID: 37656189 PMCID: PMC10627917 DOI: 10.1007/s00335-023-10016-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
The spontaneous mutation stubby (stb) in mice causes chondrodysplasia and male infertility due to impotence through autosomal recessive inheritance. In this study, we conducted linkage analysis to localize the stb locus within a 1.6 Mb region on mouse chromosome 2 and identified a nonsense mutation in Adamtsl2 of stb/stb mice. Histological analysis revealed disturbed endochondral ossification with a reduced hypertrophic chondrocyte layer and stiff skin with a thickened dermal layer. These phenotypes are similar to those observed in humans and mice with ADAMTSL2/Adamtsl2 mutations. Moreover, stb/stb female mice exhibited severe uterine hypoplasia at 5 weeks of age and irregular estrous cycles at 10 weeks of age. In normal mice, Adamtsl2 was more highly expressed in the ovary and pituitary gland than in the uterus, and this expression was decreased in stb/stb mice. These findings suggest that Adamtsl2 may function in these organs rather than in the uterus. Thus, we analyzed Gh expression in the pituitary gland and plasma estradiol and IGF1 levels, which are required for the development of the female reproductive tract. There was no significant difference in Gh expression and estradiol levels, whereas IGF1 levels in stb/stb mice were significantly reduced to 54-59% of those in +/+ mice. We conclude that Adamtsl2 is required for the development of the uterus and regulation of the estrous cycle in female mice, and decreased IGF1 may be related to these abnormalities.
Collapse
Affiliation(s)
- Yuka Iwanaga
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Kaori Tsuji
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Ayaka Nishimura
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Kouji Tateishi
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Misa Kakiuchi
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
| | - Takehito Tsuji
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.
| |
Collapse
|
9
|
Carrard J, Lejeune F. Nonsense-mediated mRNA decay, a simplified view of a complex mechanism. BMB Rep 2023; 56:625-632. [PMID: 38052423 PMCID: PMC10761751] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a quality control mechanism and a gene regulation pathway. It has been studied for more than 30 years, with an accumulation of many mechanistic details that have often led to debate and hence to different models of NMD activation, particularly in higher eukaryotes. Two models seem to be opposed, since the first requires intervention of the exon junction complex (EJC) to recruit NMD factors downstream of the premature termination codon (PTC), whereas the second involves an EJC-independent mechanism in which NMD factors concentrate in the 3'UTR to initiate NMD in the presence of a PTC. In this review we describe both models, giving recent molecular details and providing experimental arguments supporting one or the other model. In the end it is certainly possible to imagine that these two mechanisms co-exist, rather than viewing them as mutually exclusive. [BMB Reports 2023; 56(12): 625-632].
Collapse
Affiliation(s)
- Julie Carrard
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
| |
Collapse
|
10
|
Mention K, Cavusoglu-Doran K, Joynt AT, Santos L, Sanz D, Eastman AC, Merlo C, Langfelder-Schwind E, Scallan MF, Farinha CM, Cutting GR, Sharma N, Harrison PT. Use of adenine base editing and homology-independent targeted integration strategies to correct the cystic fibrosis causing variant, W1282X. Hum Mol Genet 2023; 32:3237-3248. [PMID: 37649273 PMCID: PMC10656707 DOI: 10.1093/hmg/ddad143] [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: 05/09/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023] Open
Abstract
Small molecule drugs known as modulators can treat ~90% of people with cystic fibrosis (CF), but do not work for premature termination codon variants such as W1282X (c.3846G>A). Here we evaluated two gene editing strategies, Adenine Base Editing (ABE) to correct W1282X, and Homology-Independent Targeted Integration (HITI) of a CFTR superexon comprising exons 23-27 (SE23-27) to enable expression of a CFTR mRNA without W1282X. In Flp-In-293 cells stably expressing a CFTR expression minigene bearing W1282X, ABE corrected 24% of W1282X alleles, rescued CFTR mRNA from nonsense mediated decay and restored protein expression. However, bystander editing at the adjacent adenine (c.3847A>G), caused an amino acid change (R1283G) that affects CFTR maturation and ablates ion channel activity. In primary human nasal epithelial cells homozygous for W1282X, ABE corrected 27% of alleles, but with a notably lower level of bystander editing, and CFTR channel function was restored to 16% of wild-type levels. Using the HITI approach, correct integration of a SE23-27 in intron 22 of the CFTR locus in 16HBEge W1282X cells was detected in 5.8% of alleles, resulting in 7.8% of CFTR transcripts containing the SE23-27 sequence. Analysis of a clonal line homozygous for the HITI-SE23-27 produced full-length mature protein and restored CFTR anion channel activity to 10% of wild-type levels, which could be increased three-fold upon treatment with the triple combination of CF modulators. Overall, these data demonstrate two different editing strategies can successfully correct W1282X, the second most common class I variant, with a concomitant restoration of CFTR function.
Collapse
Affiliation(s)
- Karen Mention
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Kader Cavusoglu-Doran
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Anya T Joynt
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Lúcia Santos
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - David Sanz
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Alice C Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, 1800 Orleans St, Baltimore, MD 21287, United States
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Lenox Hill Hospital, 100 E. 77th Street, 4E, New York, NY 10075, United States
| | - Martina F Scallan
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Carlos M Farinha
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Patrick T Harrison
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| |
Collapse
|
11
|
Palomar-Siles M, Yurevych V, Bykov VJN, Wiman KG. Pharmacological induction of translational readthrough of nonsense mutations in the retinoblastoma (RB1) gene. PLoS One 2023; 18:e0292468. [PMID: 37917619 PMCID: PMC10621805 DOI: 10.1371/journal.pone.0292468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023] Open
Abstract
The retinoblastoma protein (Rb) is encoded by the RB1 tumor suppressor gene. Inactivation of RB1 by inherited or somatic mutation occurs in retinoblastoma and various other types of tumors. A significant fraction (25.9%) of somatic RB1 mutations are nonsense substitutions leading to a premature termination codon (PTC) in the RB1 coding sequence and expression of truncated inactive Rb protein. Here we show that aminoglycoside G418, a known translational readthrough inducer, can induce full-length Rb protein in SW1783 astrocytoma cells with endogenous R579X nonsense mutant RB1 as well as in MDA-MB-436 breast carcinoma cells transiently transfected with R251X, R320X, R579X or Q702X nonsense mutant RB1 cDNA. Readthrough was associated with increased RB1 mRNA levels in nonsense mutant RB1 cells. Induction of full-length Rb protein was potentiated by the cereblon E3 ligase modulator CC-90009. These results suggest that pharmacological induction of translational readthrough could be a feasible strategy for therapeutic targeting of tumors with nonsense mutant RB1.
Collapse
Affiliation(s)
- Mireia Palomar-Siles
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Yurevych
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir J. N. Bykov
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Klas G. Wiman
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
12
|
Asif M, Chiou CC, Hussain MF, Hussain M, Sajid Z, Gulsher M, Raheem A, Khan A, Nasreen N, Kloczkowski A, Hassan M, Iqbal F, Chen CC. Homozygous Mutations in GDAP1 and MFN2 Genes Resulted in Autosomal Recessive Forms of Charcot-Marie-Tooth Disease in Consanguineous Pakistani Families. DNA Cell Biol 2023; 42:697-708. [PMID: 37797217 DOI: 10.1089/dna.2023.0169] [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] [Indexed: 10/07/2023] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is a heritable neurodegenerative disease of peripheral nervous system diseases in which more than 100 genes and their mutations are associated. Two consanguineous families Dera Ghazi Khan (PAK-CMT1-DG KHAN) and Layyah (PAK-CMT2-LAYYAH) with multiple CMT-affected subjects were enrolled from Punjab province in Pakistan. Basic epidemiological data were collected for the subjects. Nerve conduction study (NCS) and electromyography (EMG) were performed for the patients. Whole-exome sequencing (WES) followed by Sanger sequencing was applied to report the genetic basic of CMT. The NCS findings revealed that sensory and motor nerve conduction velocities for both families were <38 m/s. EMG presented denervation, neuropathic motor unit potential, and reduced interference pattern of peripheral nerves. WES identified that a novel nonsense mutation (c. 226 G>T) in GADP1 gene and a previously known missense mutation in MFN2 gene (c. 334 G>A) cause CMT4A (Charcot-Marie-Tooth disease type 4A) in the PAK-CMT1-DG KHAN family and CMT2A (Charcot-Marie-Tooth disease type 2A) in the PAK-CMT2-LAYYAH family, respectively. Mutations followed Mendelian pattern with autosomal recessive mode of inheritance. Multiple sequence alignment by Clustal Omega indicated that mutation-containing domain in both genes is highly conserved, and in situ analysis revealed that both mutations are likely to be pathogenic. We reported that a novel nonsense mutation and a previously known missense mutation in GAPD1 gene and MFN2 gene, respectively, cause CMT in consanguineous Pakistani families.
Collapse
Affiliation(s)
- Muhammad Asif
- Institute of Molecular Biology and Biotechnology. Bahauddin Zakariya University, Multan, Pakistan
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Chien-Chun Chiou
- Department of Dermatology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | | | - Manzoor Hussain
- Orthopedic Unit 1, Nishter Medical University Multan, Pakistan
| | - Zureesha Sajid
- Institute of Molecular Biology and Biotechnology. Bahauddin Zakariya University, Multan, Pakistan
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Baghdad-ul-Jadeed Campus, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Gulsher
- Children Hospital and Institute of Child Health, Multan, Pakistan
| | - Afifa Raheem
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Adil Khan
- Department of Botany and Zoology, Bacha Khan University, Charsadda, Pakistan
| | - Nasreen Nasreen
- Department of Zoology, Abdul Wali Khan University, Mardan, Pakistan
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Furhan Iqbal
- Institute of Zoology, Bahauddin Zakariya University, Multan, Pakistan
| | - Chien-Chin Chen
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
- Ph.D. Program in Translational Medicine, Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| |
Collapse
|
13
|
Wittenstein A, Caspi M, Rippin I, Elroy-Stein O, Eldar-Finkelman H, Thoms S, Rosin-Arbesfeld R. Nonsense mutation suppression is enhanced by targeting different stages of the protein synthesis process. PLoS Biol 2023; 21:e3002355. [PMID: 37943958 PMCID: PMC10684085 DOI: 10.1371/journal.pbio.3002355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023] Open
Abstract
The introduction of premature termination codons (PTCs), as a result of splicing defects, insertions, deletions, or point mutations (also termed nonsense mutations), lead to numerous genetic diseases, ranging from rare neuro-metabolic disorders to relatively common inheritable cancer syndromes and muscular dystrophies. Over the years, a large number of studies have demonstrated that certain antibiotics and other synthetic molecules can act as PTC suppressors by inducing readthrough of nonsense mutations, thereby restoring the expression of full-length proteins. Unfortunately, most PTC readthrough-inducing agents are toxic, have limited effects, and cannot be used for therapeutic purposes. Thus, further efforts are required to improve the clinical outcome of nonsense mutation suppressors. Here, by focusing on enhancing readthrough of pathogenic nonsense mutations in the adenomatous polyposis coli (APC) tumor suppressor gene, we show that disturbing the protein translation initiation complex, as well as targeting other stages of the protein translation machinery, enhances both antibiotic and non-antibiotic-mediated readthrough of nonsense mutations. These findings strongly increase our understanding of the mechanisms involved in nonsense mutation readthrough and facilitate the development of novel therapeutic targets for nonsense suppression to restore protein expression from a large variety of disease-causing mutated transcripts.
Collapse
Affiliation(s)
- Amnon Wittenstein
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Rippin
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Elroy-Stein
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Eldar-Finkelman
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sven Thoms
- Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
14
|
Ali G, Sadia S, Ain-ul- Batool S, Azeem Z, Awan NB, Kazmi SAR, Ur- Rehman Z, Anjum Z, Ur- Rehman F, Wali A, Khan K, Zaman N, Ayub M, Sajid M, Hassan N. A Recurrent Nonsense Mutation in NECTIN4 Underlying Ectodermal Dysplasia-Syndactyly Syndrome with a Novel Phenotype in a Consanguineous Kashmiri Family. Genet Res (Camb) 2023; 2023:9999660. [PMID: 37829154 PMCID: PMC10567209 DOI: 10.1155/2023/9999660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 10/14/2023] Open
Abstract
EDSS1, a syndrome characterized by ectodermal dysplasia-syndactyly, is inherited in an autosomal recessive manner due to mutations in the NECTIN4/PVRL4 gene. Clinical manifestations of the syndrome include defective nail plate, sparse to absent scalp and body hair, spaced teeth with enamel hypoplasia, and bilateral cutaneous syndactyly in the fingers and toes. Here, we report a consanguineous family of Kashmiri origin presenting features of EDSS1. Using whole exome sequencing, we found a recurrent nonsense mutation (NM_030916: c.181C > T, p.(Gln61 ∗)) in the NECTIN4 gene. The variant segregated perfectly with the disorder within the family. The candidate variant was absent in 50 in-house exomes pertaining to other disorders from the same population. In addition to the previously reported clinical phenotype, an upper lip cleft was found in one of the affected members as a novel phenotype that is not reported by previous studies in EDSS1 patients. Therefore, the study presented here, which was conducted on the Kashmiri population, is the first to document a NECTIN4 mutation associated with the upper lip cleft as a novel phenotype. This finding broadens the molecular and phenotypic spectrum of EDSS1.
Collapse
Affiliation(s)
- Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Sadia Sadia
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Syeda Ain-ul- Batool
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Zahid Azeem
- Department of Biochemistry, Azad Jammu and Kashmir Medical College, Muzaffarabad, Pakistan
| | - Naheed Bashir Awan
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | | | - Zia- Ur- Rehman
- Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Zeeshan Anjum
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Fazal- Ur- Rehman
- Department of Microbiology, Faculty of Life Sciences, University of Balochistan, Quetta, Pakistan
| | - Abdul Wali
- Department of Biotechnology, Faculty of Life Sciences and Informatics, BUITEMS, 87100, Quetta, Pakistan
| | - Kafaitullah Khan
- Department of Microbiology, Faculty of Life Sciences, University of Balochistan, Quetta, Pakistan
| | - Nasib Zaman
- Centre for Biotechnology and Microbiology University of Swat, Swat, Pakistan
| | - Muhammad Ayub
- Institute of Biochemistry, University of Balochistan, Quetta, Pakistan
| | - Muhammad Sajid
- Department of Pathology, College of Veterinary and Animal Sciences, Jhang Sub Campus of University of Veterinary and Animal Sciences Lahore, Lahore, Pakistan
| | - Noor Hassan
- Institute of Biochemistry, University of Balochistan, Quetta, Pakistan
| |
Collapse
|
15
|
Tan L, Guo Y, Zhong MM, Zhao YQ, Zhao J, Aimee DM, Feng Y, Ye Q, Hu J, Ou-Yang ZY, Chen NX, Su XL, Zhang Q, Liu Q, Yuan H, Wang MY, Feng YZ, Zhang FY. Tooth ultrastructure changes induced by a nonsense mutation in the FAM83H gene: insights into the diversity of amelogenesis imperfecta. Clin Oral Investig 2023; 27:6111-6123. [PMID: 37615776 DOI: 10.1007/s00784-023-05228-3] [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: 06/09/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
OBJECTIVES The current research on single-nucleotide polymorphism (SNP) mutation sites at different positions of the FAM83H gene and their phenotypic changes leading to amelogenesis imperfecta (AI) is inconsistent. We identified a previously reported heterozygous nonsense mutation c.1192C>T (p.Q398*) in the FAM83H gene and conducted a comprehensive analysis of the dental ultrastructure and chemical composition changes induced by this mutation. Additionally, we predicted the protein feature affected by this mutation site. The aim was to further deepen our understanding of the diversity of AI caused by different mutation sites in the FAM83H gene. METHODS Whole-exome sequencing (WES) and Sanger sequencing were used to confirm the mutation sites. Physical features of the patient's teeth were investigated using various methods including cone beam computer tomography (CBCT), scanning electron microscopy (SEM), contact profilometry (roughness measurement), and a nanomechanical tester (nanoindentation measurement). The protein features of wild-type and mutant FAM83H were predicted using bioinformatics methods. RESULTS One previously discovered FAM83H heterozygous nonsense mutation c.1192C>T (p.Q398*) was detected in the patient. SEM revealed inconsistent dentinal tubules, and EDS showed that calcium and phosphorus were lower in the patient's dentin but higher in the enamel compared to the control tooth. Roughness measurements showed that AI patients' teeth had rougher occlusal surfaces than those of the control tooth. Nanoindentation measurements showed that the enamel and dentin hardness values of the AI patients' teeth were both significantly reduced compared to those of the control tooth. Compared to the wild-type FAM83H protein, the mutant FAM83H protein shows alterations in stability, hydrophobicity, secondary structure, and tertiary structure. These changes could underlie functional differences and AI phenotype variations caused by this mutation site. CONCLUSIONS This study expands the understanding of the effects of FAM83H mutations on tooth structure. CLINICAL RELEVANCE Our study enhances our understanding of the genetic basis of AI and may contribute to improved diagnostics and personalized treatment strategies for patients with FAM83H-related AI.
Collapse
Affiliation(s)
- Li Tan
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Yue Guo
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Meng-Mei Zhong
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Ya-Qiong Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Jie Zhao
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Dusenge Marie Aimee
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Yao Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Qin Ye
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Jing Hu
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Ze-Yue Ou-Yang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Ning-Xin Chen
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Xiao-Lin Su
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Qian Zhang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Qiong Liu
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Hui Yuan
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Min-Yuan Wang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Yun-Zhi Feng
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Feng-Yi Zhang
- Department of Stomatology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, People's Republic of China.
| |
Collapse
|
16
|
Hajra B, Abdullah, Bibi N, Syed F, Ullah A, Ahmad W, Umm-E-Kalsoom. A novel homozygous nonsense mutation in NECTIN4 gene in a Pakistani family with ectodermal dysplasia syndactyly syndrome 1. An Bras Dermatol 2023; 98:580-586. [PMID: 37183149 PMCID: PMC10404504 DOI: 10.1016/j.abd.2022.07.009] [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: 03/22/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 05/16/2023] Open
Abstract
BACKGROUND Ectodermal dysplasia syndactyly syndrome 1 (EDSS1) is a rare hereditary disorder characterized by defects in teeth, hair, and nails in association with a fusion of the digits. Genetically, the disease phenotypes are caused by homozygous and compound heterozygous variants in NECTIN4 gene. OBJECTIVE The main objective of the study was to identify the pathogenic sequence variant(s) for family screening and identification of carriers. METHODS In the present study, the authors have investigated a large consanguineous family of Pakistani origin segregating autosomal recessive EDSS1. All the coding exons of the NECTIN4 gene were directly sequenced using gene-specific primers. RESULTS The affected individuals presented the classical EDSS1 clinical features including sparse hair, hypoplastic nails with thick flat discolored nail plates, peg-shaped, conical, and widely spaced teeth with enamel hypoplasia, proximal cutaneous syndactyly of fingers and toes. Sequence analysis of the coding region of the NECTIN4 identified a novel nonsense variant [c.163C>T; p.(Arg55*)] in exon-2 of the gene. Computational analysis of protein structure revealed that the variant induced premature termination at Arg55 located in Ig-like V-loop region leading to loss of Ig-C2 type domains and transmembrane region, and most likely Nectin-4 function will be lost. STUDY LIMITATION Gene expression studies are absent that would have strengthened the findings of computational analysis. CONCLUSION The present study expanded the phenotypic and mutation spectrum of the NECTIN4 gene. Further, the study would assist in carrier testing and prenatal diagnosis of the affected families.
Collapse
Affiliation(s)
- Bibi Hajra
- Department of Biochemistry, Faculty of Biological and Health Sciences, Hazara University, Mansehra, KP, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Nousheen Bibi
- Department of Bioinformatics, Shaheed Benazir Bhutto Women University, Peshawar, KP, Pakistan
| | - Fibhaa Syed
- Department of General Medicine, Shaheed Zulfiqar Ali Bhutto Medical University, PIMS, Islamabad, Pakistan
| | - Asmat Ullah
- Department of General Medicine, Shaheed Zulfiqar Ali Bhutto Medical University, PIMS, Islamabad, Pakistan; Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Umm-E-Kalsoom
- Department of Biochemistry, Faculty of Biological and Health Sciences, Hazara University, Mansehra, KP, Pakistan.
| |
Collapse
|
17
|
Valášek LS, Kučerová M, Zeman J, Beznosková P. Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line. RNA 2023; 29:1379-1387. [PMID: 37221013 PMCID: PMC10573299 DOI: 10.1261/rna.079688.123] [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] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
Under certain circumstances, any of the three termination codons can be read through by a near-cognate tRNA; i.e., a tRNA whose two out of three anticodon nucleotides base pair with those of the stop codon. Unless programed to synthetize C-terminally extended protein variants with expanded physiological roles, readthrough represents an undesirable translational error. On the other side of a coin, a significant number of human genetic diseases is associated with the introduction of nonsense mutations (premature termination codons [PTCs]) into coding sequences, where stopping is not desirable. Here, the tRNA's ability to induce readthrough opens up the intriguing possibility of mitigating the deleterious effects of PTCs on human health. In yeast, the UGA and UAR stop codons were described to be read through by four readthrough-inducing rti-tRNAs-tRNATrp and tRNACys, and tRNATyr and tRNAGln, respectively. The readthrough-inducing potential of tRNATrp and tRNATyr was also observed in human cell lines. Here, we investigated the readthrough-inducing potential of human tRNACys in the HEK293T cell line. The tRNACys family consists of two isoacceptors, one with ACA and the other with GCA anticodons. We selected nine representative tRNACys isodecoders (differing in primary sequence and expression level) and tested them using dual luciferase reporter assays. We found that at least two tRNACys can significantly elevate UGA readthrough when overexpressed. This indicates a mechanistically conserved nature of rti-tRNAs between yeast and human, supporting the idea that they could be used in the PTC-associated RNA therapies.
Collapse
MESH Headings
- Humans
- Codon, Terminator/genetics
- Cysteine/genetics
- Cysteine/metabolism
- HEK293 Cells
- Saccharomyces cerevisiae/genetics
- RNA, Transfer, Cys/metabolism
- RNA, Transfer, Trp/metabolism
- RNA, Transfer, Tyr
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Anticodon
- Codon, Nonsense/genetics
- Protein Biosynthesis
Collapse
Affiliation(s)
- Leoš Shivaya Valášek
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, the Czech Republic
| | - Michaela Kučerová
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, the Czech Republic
| | - Jakub Zeman
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, the Czech Republic
| | - Petra Beznosková
- Laboratory of Regulation of Gene Expression, Institute of Microbiology ASCR, 142 20 Prague, the Czech Republic
| |
Collapse
|
18
|
Trexler M, Bányai L, Kerekes K, Patthy L. Evolution of termination codons of proteins and the TAG-TGA paradox. Sci Rep 2023; 13:14294. [PMID: 37653005 PMCID: PMC10471768 DOI: 10.1038/s41598-023-41410-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
In most eukaryotes and prokaryotes TGA is used at a significantly higher frequency than TAG as termination codon of protein-coding genes. Although this phenomenon has been recognized several years ago, there is no generally accepted explanation for the TAG-TGA paradox. Our analyses of human mutation data revealed that out of the eighteen sense codons that can give rise to a nonsense codon by single base substitution, the CGA codon is exceptional: it gives rise to the TGA stop codon at an order of magnitude higher rate than the other codons. Here we propose that the TAG-TGA paradox is due to methylation and hypermutabilty of CpG dinucleotides. In harmony with this explanation, we show that the coding genomes of organisms with strong CpG methylation have a significant bias for TGA whereas those from organisms that lack CpG methylation use TGA and TAG termination codons with similar probability.
Collapse
Affiliation(s)
- Mária Trexler
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - László Bányai
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - Krisztina Kerekes
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary
| | - László Patthy
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117, Hungary.
| |
Collapse
|
19
|
Song Z, Zhang G, Huang S, Liu Y, Li G, Zhou X, Sun J, Gao P, Chen Y, Huang X, Liu J, Wang X. PE-STOP: A versatile tool for installing nonsense substitutions amenable for precise reversion. J Biol Chem 2023; 299:104942. [PMID: 37343700 PMCID: PMC10365944 DOI: 10.1016/j.jbc.2023.104942] [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: 04/03/2023] [Revised: 06/08/2023] [Accepted: 06/11/2023] [Indexed: 06/23/2023] Open
Abstract
The rapid advances in genome editing technologies have revolutionized the study of gene functions in cell or animal models. The recent generation of double-stranded DNA cleavage-independent base editors has been suitably adapted for interrogation of protein-coding genes on the basis of introducing premature stop codons or disabling the start codons. However, such versions of stop/start codon-oriented genetic tools still present limitations on their versatility, base-level precision, and target specificity. Here, we exploit a newly developed prime editor (PE) that differs from base editors by its adoption of a reverse transcriptase activity, which enables incorporation of various types of precise edits templated by a specialized prime editing guide RNA. Based on such a versatile platform, we established a prime editing-empowered method (PE-STOP) for installation of nonsense substitutions, providing a complementary approach to the present gene-targeting tools. PE-STOP is bioinformatically predicted to feature substantially expanded coverage in the genome space. In practice, PE-STOP introduces stop codons with good efficiencies in human embryonic kidney 293T and N2a cells (with medians of 29% [ten sites] and 25% [four sites] editing efficiencies, respectively), while exhibiting minimal off-target effects and high on-target precision. Furthermore, given the fact that PE installs prime editing guide RNA-templated mutations, we introduce a unique strategy for precise genetic rescue of PE-STOP-dependent nonsense mutation via the same PE platform. Altogether, the present work demonstrates a versatile and specific tool for gene inactivation and for functional interrogation of nonsense mutations.
Collapse
Affiliation(s)
- Ziguo Song
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guiquan Zhang
- Zhejiang Lab, Hangzhou, Zhejiang, China; State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center at Medical School of Nanjing University, Nanjing, China
| | - Shuhong Huang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Liu
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianhui Zhou
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayuan Sun
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Pengfei Gao
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Chen
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingxu Huang
- Zhejiang Lab, Hangzhou, Zhejiang, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Jianghuai Liu
- State Key Laboratory of Pharmaceutical Biotechnology and MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center at Medical School of Nanjing University, Nanjing, China.
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi, China.
| |
Collapse
|
20
|
Albers S, Allen EC, Bharti N, Davyt M, Joshi D, Perez-Garcia CG, Santos L, Mukthavaram R, Delgado-Toscano MA, Molina B, Kuakini K, Alayyoubi M, Park KJJ, Acharya G, Gonzalez JA, Sagi A, Birket SE, Tearney GJ, Rowe SM, Manfredi C, Hong JS, Tachikawa K, Karmali P, Matsuda D, Sorscher EJ, Chivukula P, Ignatova Z. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 2023; 618:842-848. [PMID: 37258671 PMCID: PMC10284701 DOI: 10.1038/s41586-023-06133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 07/31/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
Collapse
Affiliation(s)
- Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | | | | | | | | | | | | | | | - Amit Sagi
- Arcturus Therapeutics, San Diego, CA, USA
| | - Susan E Birket
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MA, Cambridge, USA
| | - Steven M Rowe
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Candela Manfredi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | | | | | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | | | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| |
Collapse
|
21
|
Carollo PS, Tutone M, Culletta G, Fiduccia I, Corrao F, Pibiri I, Di Leonardo A, Zizzo MG, Melfi R, Pace A, Almerico AM, Lentini L. Investigating the Inhibition of FTSJ1, a Tryptophan tRNA-Specific 2'-O-Methyltransferase by NV TRIDs, as a Mechanism of Readthrough in Nonsense Mutated CFTR. Int J Mol Sci 2023; 24:9609. [PMID: 37298560 PMCID: PMC10253411 DOI: 10.3390/ijms24119609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Cystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the CFTR gene, coding for the CFTR chloride channel. About 10% of the CFTR gene mutations are "stop" mutations that generate a premature termination codon (PTC), thus synthesizing a truncated CFTR protein. A way to bypass PTC relies on ribosome readthrough, which is the ribosome's capacity to skip a PTC, thus generating a full-length protein. "TRIDs" are molecules exerting ribosome readthrough; for some, the mechanism of action is still under debate. We investigate a possible mechanism of action (MOA) by which our recently synthesized TRIDs, namely NV848, NV914, and NV930, could exert their readthrough activity by in silico analysis and in vitro studies. Our results suggest a likely inhibition of FTSJ1, a tryptophan tRNA-specific 2'-O-methyltransferase.
Collapse
Affiliation(s)
| | - Marco Tutone
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (P.S.C.); (G.C.); (I.F.); (F.C.); (I.P.); (A.D.L.); (M.G.Z.); (R.M.); (A.P.); (A.M.A.)
| | | | | | | | | | | | | | | | | | | | - Laura Lentini
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy; (P.S.C.); (G.C.); (I.F.); (F.C.); (I.P.); (A.D.L.); (M.G.Z.); (R.M.); (A.P.); (A.M.A.)
| |
Collapse
|
22
|
Wagner RN, Wießner M, Friedrich A, Zandanell J, Breitenbach-Koller H, Bauer JW. Emerging Personalized Opportunities for Enhancing Translational Readthrough in Rare Genetic Diseases and Beyond. Int J Mol Sci 2023; 24:6101. [PMID: 37047074 PMCID: PMC10093890 DOI: 10.3390/ijms24076101] [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: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Nonsense mutations trigger premature translation termination and often give rise to prevalent and rare genetic diseases. Consequently, the pharmacological suppression of an unscheduled stop codon represents an attractive treatment option and is of high clinical relevance. At the molecular level, the ability of the ribosome to continue translation past a stop codon is designated stop codon readthrough (SCR). SCR of disease-causing premature termination codons (PTCs) is minimal but small molecule interventions, such as treatment with aminoglycoside antibiotics, can enhance its frequency. In this review, we summarize the current understanding of translation termination (both at PTCs and at cognate stop codons) and highlight recently discovered pathways that influence its fidelity. We describe the mechanisms involved in the recognition and readthrough of PTCs and report on SCR-inducing compounds currently explored in preclinical research and clinical trials. We conclude by reviewing the ongoing attempts of personalized nonsense suppression therapy in different disease contexts, including the genetic skin condition epidermolysis bullosa.
Collapse
Affiliation(s)
- Roland N. Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Michael Wießner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Andreas Friedrich
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Johanna Zandanell
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| |
Collapse
|
23
|
Zheng Z, Shi N, Xia Q. Adeno-associated viral delivery of engineered tRNA-enzyme pairs into nonsense mutation mouse models. STAR Protoc 2023; 4:101950. [PMID: 36527714 PMCID: PMC9792948 DOI: 10.1016/j.xpro.2022.101950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/06/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
In this protocol, we describe how to utilize the unnatural amino acid (UAA) incorporation system to read through endogenous premature termination codons in a Duchenne muscular dystrophy mouse model. We detail how to screen and optimize tRNA-enzyme pairs for efficient UAA incorporation, deliver the system intraperitoneally or intramuscularly in pathogenic mice by an adeno-associated viral (AAV) vector, and evaluate the restoration of endogenous dystrophin and increase in muscle strength after AAV injection. For complete details on the use and execution of this protocol, please refer to Shi et al. (2021).1.
Collapse
Affiliation(s)
- Zhetao Zheng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ningning Shi
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Qing Xia
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China.
| |
Collapse
|
24
|
Adachi H, Pan Y, He X, Chen JL, Klein B, Platenburg G, Morais P, Boutz P, Yu YT. Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes. Mol Cell 2023; 83:637-651.e9. [PMID: 36764303 PMCID: PMC9975048 DOI: 10.1016/j.molcel.2023.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 11/25/2022] [Revised: 12/18/2022] [Accepted: 01/05/2023] [Indexed: 02/11/2023]
Abstract
Nonsense mutations create premature termination codons (PTCs), activating the nonsense-mediated mRNA decay (NMD) pathway to degrade most PTC-containing mRNAs. The undegraded mRNA is translated, but translation terminates at the PTC, leading to no production of the full-length protein. This work presents targeted PTC pseudouridylation, an approach for nonsense suppression in human cells. Specifically, an artificial box H/ACA guide RNA designed to target the mRNA PTC can suppress both NMD and premature translation termination in various sequence contexts. Targeted pseudouridylation exhibits a level of suppression comparable with that of aminoglycoside antibiotic treatments. When targeted pseudouridylation is combined with antibiotic treatment, a much higher level of suppression is observed. Transfection of a disease model cell line (carrying a chromosomal PTC) with a designer guide RNA gene targeting the PTC also leads to nonsense suppression. Thus, targeted pseudouridylation is an RNA-directed gene-specific approach that suppresses NMD and concurrently promotes PTC readthrough.
Collapse
Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Yi Pan
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Xueyang He
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jonathan L Chen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Bart Klein
- ProQR Therapeutics, Leiden, the Netherlands
| | | | | | - Paul Boutz
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA; Center for Biomedical Informatics and Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA.
| |
Collapse
|
25
|
Staszewski J, Lazarewicz N, Konczak J, Migdal I, Maciaszczyk-Dziubinska E. UPF1-From mRNA Degradation to Human Disorders. Cells 2023; 12:cells12030419. [PMID: 36766761 PMCID: PMC9914065 DOI: 10.3390/cells12030419] [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: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Up-frameshift protein 1 (UPF1) plays the role of a vital controller for transcripts, ready to react in the event of an incorrect translation mechanism. It is well known as one of the key elements involved in mRNA decay pathways and participates in transcript and protein quality control in several different aspects. Firstly, UPF1 specifically degrades premature termination codon (PTC)-containing products in a nonsense-mediated mRNA decay (NMD)-coupled manner. Additionally, UPF1 can potentially act as an E3 ligase and degrade target proteins independently from mRNA decay pathways. Thus, UPF1 protects cells against the accumulation of misfolded polypeptides. However, this multitasking protein may still hide many of its functions and abilities. In this article, we summarize important discoveries in the context of UPF1, its involvement in various cellular pathways, as well as its structural importance and mutational changes related to the emergence of various pathologies and disease states. Even though the state of knowledge about this protein has significantly increased over the years, there are still many intriguing aspects that remain unresolved.
Collapse
Affiliation(s)
- Jacek Staszewski
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Institute of Genetics and Development of Rennes, CNRS UMR 6290, University of Rennes 1, 35000 Rennes, France
| | - Julia Konczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Iwona Migdal
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| |
Collapse
|
26
|
Katsioudi G, Dreos R, Arpa ES, Gaspari S, Liechti A, Sato M, Gabriel CH, Kramer A, Brown SA, Gatfield D. A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway. Sci Adv 2023; 9:eade2828. [PMID: 36638184 PMCID: PMC9839329 DOI: 10.1126/sciadv.ade2828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Nonsense-mediated messenger RNA (mRNA) decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or RNA processing errors. While additional roles in physiological control of mRNA stability have emerged, possible functions in mammalian physiology in vivo remain unclear. Here, we created a conditional mouse allele that allows converting the NMD effector nuclease SMG6 from wild-type to nuclease domain-mutant protein. We find that NMD down-regulation affects the function of the circadian clock, a system known to require rapid mRNA turnover. Specifically, we uncover strong lengthening of free-running circadian periods for liver and fibroblast clocks and direct NMD regulation of Cry2 mRNA, encoding a key transcriptional repressor within the rhythm-generating feedback loop. Transcriptome-wide changes in daily mRNA accumulation patterns in the entrained liver, as well as an altered response to food entrainment, expand the known scope of NMD regulation in mammalian gene expression and physiology.
Collapse
Affiliation(s)
- Georgia Katsioudi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Enes S. Arpa
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sevasti Gaspari
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Miho Sato
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Christian H. Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Steven A. Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
27
|
Beryozkin A, Nagel-Wolfum K, Banin E, Sharon D. Factors Affecting Readthrough of Natural Versus Premature Termination Codons. Adv Exp Med Biol 2023; 1415:149-155. [PMID: 37440028 DOI: 10.1007/978-3-031-27681-1_23] [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] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Nonsense mutations occur within the open-reading frame of a gene resulting in a premature termination codon (PTC). PTC-containing mRNAs can either be degeraded or cause premature translation termination producing a truncated protein that can be either nonfunctional or toxic. Translational readthrough inducing drugs (TRIDs) are small molecules that are able to induce readthrough, resulting in the restoration of full-length protein expression. The re-expressed proteins usually harbor a missense change. The effciency of individual TRIDs is variable and varies between different genes and even different nonsense mutations in the same gene. This review summarizes factors, including the sequences located upstream and downstream the disease-causing mutation and the type of PTC, affecting the translational readthrough process by modulating the type of amino acid insertion and the efficiency of the process during readthrough following TRIDs treatments.
Collapse
Affiliation(s)
- Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kerstin Nagel-Wolfum
- Institute of Molecular Physiology & Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University of Mainz, Mainz, Germany
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
| |
Collapse
|
28
|
Sheriff A, Guri I, Zebrowska P, Llopis-Hernandez V, Brooks IR, Tekkela S, Subramaniam K, Gebrezgabher R, Naso G, Petrova A, Balon K, Onoufriadis A, Kujawa D, Kotulska M, Newby G, Łaczmański Ł, Liu DR, McGrath JA, Jacków J. ABE8e adenine base editor precisely and efficiently corrects a recurrent COL7A1 nonsense mutation. Sci Rep 2022; 12:19643. [PMID: 36385635 PMCID: PMC9666996 DOI: 10.1038/s41598-022-24184-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
Base editing introduces precise single-nucleotide edits in genomic DNA and has the potential to treat genetic diseases such as the blistering skin disease recessive dystrophic epidermolysis bullosa (RDEB), which is characterized by mutations in the COL7A1 gene and type VII collagen (C7) deficiency. Adenine base editors (ABEs) convert A-T base pairs to G-C base pairs without requiring double-stranded DNA breaks or donor DNA templates. Here, we use ABE8e, a recently evolved ABE, to correct primary RDEB patient fibroblasts harboring the recurrent RDEB nonsense mutation c.5047 C > T (p.Arg1683Ter) in exon 54 of COL7A1 and use a next generation sequencing workflow to interrogate post-treatment outcomes. Electroporation of ABE8e mRNA into a bulk population of RDEB patient fibroblasts resulted in remarkably efficient (94.6%) correction of the pathogenic allele, restoring COL7A1 mRNA and expression of C7 protein in western blots and in 3D skin constructs. Off-target DNA analysis did not detect off-target editing in treated patient-derived fibroblasts and there was no detectable increase in A-to-I changes in the RNA. Taken together, we have established a highly efficient pipeline for gene correction in primary fibroblasts with a favorable safety profile. This work lays a foundation for developing therapies for RDEB patients using ex vivo or in vivo base editing strategies.
Collapse
Affiliation(s)
- Adam Sheriff
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Ina Guri
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Paulina Zebrowska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Virginia Llopis-Hernandez
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Imogen R Brooks
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Stavroula Tekkela
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Kavita Subramaniam
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Ruta Gebrezgabher
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Gaetano Naso
- Molecular and Cellular Immunology Unit, UCL GOS Institute of Child Health, London, UK
| | - Anastasia Petrova
- Molecular and Cellular Immunology Unit, UCL GOS Institute of Child Health, London, UK
| | - Katarzyna Balon
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Alexandros Onoufriadis
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Dorota Kujawa
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Martyna Kotulska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Gregory Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Łukasz Łaczmański
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - John A McGrath
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK
| | - Joanna Jacków
- St John's Institute of Dermatology, Faculty of Life Sciences and Medicine, King's College London, 9th Floor Tower Wing, Guy's Hospital, Great Maze Pond Road, London, SE1 9RT, UK.
| |
Collapse
|
29
|
Kim JH, Modena MS, Sehgal E, Courney A, Neudorf C, Arribere J. SMG-6 mRNA cleavage stalls ribosomes near premature stop codons in vivo. Nucleic Acids Res 2022; 50:8852-8866. [PMID: 35950494 PMCID: PMC9410879 DOI: 10.1093/nar/gkac681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/29/2022] [Accepted: 07/26/2022] [Indexed: 12/24/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) protects cells from the toxic and potentially dominant effects of truncated proteins. Targeting of mRNAs with early stop codons is mediated by the ribosome and spatiotemporally aligned with translation termination. Previously we identified a novel NMD intermediate: ribosomes stalled on cleaved stop codons, raising the possibility that NMD begins even prior to ribosome removal from the stop codon. Here we show that this intermediate is the result of mRNA cleavage by the endonuclease SMG-6. Our work supports a model in which ribosomes stall secondary to SMG-6 mRNA cleavage in Caenorhabditis elegans and humans, i.e. that the novel NMD intermediate occurs after a prior ribosome elicits NMD. Our genetic analysis of C. elegans' SMG-6 supports a central role for SMG-6 in metazoan NMD, and provides a context for evaluating its function in other metazoans.
Collapse
Affiliation(s)
- John H Kim
- Department of MCD Biology, UC Santa Cruz, California, USA
| | | | - Enisha Sehgal
- Department of MCD Biology, UC Santa Cruz, California, USA
| | - Annie Courney
- Department of MCD Biology, UC Santa Cruz, California, USA
| | - Celine W Neudorf
- Department of Biomolecular Engineering, UC Santa Cruz, California, USA
| | | |
Collapse
|
30
|
Cho H, Abshire ET, Popp MW, Pröschel C, Schwartz JL, Yeo GW, Maquat LE. AKT constitutes a signal-promoted alternative exon-junction complex that regulates nonsense-mediated mRNA decay. Mol Cell 2022; 82:2779-2796.e10. [PMID: 35675814 PMCID: PMC9357146 DOI: 10.1016/j.molcel.2022.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 02/10/2022] [Revised: 04/21/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022]
Abstract
Despite a long appreciation for the role of nonsense-mediated mRNA decay (NMD) in destroying faulty, disease-causing mRNAs and maintaining normal, physiologic mRNA abundance, additional effectors that regulate NMD activity in mammalian cells continue to be identified. Here, we describe a haploid-cell genetic screen for NMD effectors that has unexpectedly identified 13 proteins constituting the AKT signaling pathway. We show that AKT supersedes UPF2 in exon-junction complexes (EJCs) that are devoid of RNPS1 but contain CASC3, defining an unanticipated insulin-stimulated EJC. Without altering UPF1 RNA binding or ATPase activity, AKT-mediated phosphorylation of the UPF1 CH domain at T151 augments UPF1 helicase activity, which is critical for NMD and also decreases the dependence of helicase activity on ATP. We demonstrate that upregulation of AKT signaling contributes to the hyperactivation of NMD that typifies Fragile X syndrome, as exemplified using FMR1-KO neural stem cells derived from induced pluripotent stem cells.
Collapse
Affiliation(s)
- Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Elizabeth T Abshire
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Maximilian W Popp
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Stem Cell and Regenerative Medicine Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| |
Collapse
|
31
|
Has C, Sayar SB, Zheng S, Chacón-Solano E, Condrat I, Yadav A, Roberge M, Larcher Laguzzi F. Read-Through for Nonsense Mutations in Type XVII Collagen‒Deficient Junctional Epidermolysis Bullosa. J Invest Dermatol 2022; 142:1227-1230.e4. [PMID: 34673051 DOI: 10.1016/j.jid.2021.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Cristina Has
- Department of Dermatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Saliha Beyza Sayar
- Department of Dermatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Shuangshuang Zheng
- Department of Dermatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Esteban Chacón-Solano
- Epithelial Biomedicine Division, CIEMAT-CIBERER (Centre for Biomedical Research on Rare Diseases), Madrid, Spain; Department of Bioengineering, Universidad Carlos III de Madrid, Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Irina Condrat
- Department of Dermatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Department of Dermatology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ayushi Yadav
- Department of Dermatology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michel Roberge
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Larcher Laguzzi
- Epithelial Biomedicine Division, CIEMAT-CIBERER (Centre for Biomedical Research on Rare Diseases), Madrid, Spain; Department of Bioengineering, Universidad Carlos III de Madrid, Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| |
Collapse
|
32
|
McElheny CL, Fowler EL, Iovleva A, Shields RK, Doi Y. In Vitro Evolution of Cefiderocol Resistance in an NDM-Producing Klebsiella pneumoniae Due to Functional Loss of CirA. Microbiol Spectr 2021; 9:e0177921. [PMID: 34756080 PMCID: PMC8579844 DOI: 10.1128/spectrum.01779-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 11/20/2022] Open
Abstract
By serially exposing an NDM-producing Klebsiella pneumoniae clinical strain to cefiderocol, we obtained a mutant with cefiderocol MIC of >128 μg/ml. The mutant contained an early stop codon in the iron transporter gene cirA, and its complementation fully restored susceptibility. The cirA-deficient mutant was competed out by the parental strain in vitro, suggesting reduced fitness. IMPORTANCE Cefiderocol, a newly approved cephalosporin agent with an extensive spectrum of activity against Gram-negative bacteria, is a siderophore cephalosporin that utilizes iron transporters to access the bacterial periplasm. Loss of functional CirA, an iron transporter, has been associated with cefiderocol resistance. Here, we show that such genetic change can be selected under selective pressure and cause high-level cefiderocol resistance, but with a high fitness cost. Whether these resistant mutants can survive beyond selective pressure will inform stewardship of this agent in the clinic.
Collapse
Affiliation(s)
- Christi L. McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Erin L. Fowler
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alina Iovleva
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ryan K. Shields
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Innovative Antimicrobial Therapy, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| |
Collapse
|
33
|
Hernández G, Ferrer-Cortès X, Venturi V, Musri M, Pilquil MF, Torres PMM, Rodríguez IH, Mínguez MÀR, Kelleher NJ, Pelucchi S, Piperno A, Alberca EP, Ricós GG, Giró EC, Pérez-Montero S, Tornador C, Villà-Freixa J, Sánchez M. New Mutations in HFE2 and TFR2 Genes Causing Non HFE-Related Hereditary Hemochromatosis. Genes (Basel) 2021; 12:genes12121980. [PMID: 34946929 PMCID: PMC8702017 DOI: 10.3390/genes12121980] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 01/04/2023] Open
Abstract
Hereditary hemochromatosis (HH) is an iron metabolism disease clinically characterized by excessive iron deposition in parenchymal organs such as liver, heart, pancreas, and joints. It is caused by mutations in at least five different genes. HFE hemochromatosis is the most common type of hemochromatosis, while non-HFE related hemochromatosis are rare cases. Here, we describe six new patients of non-HFE related HH from five different families. Two families (Family 1 and 2) have novel nonsense mutations in the HFE2 gene have novel nonsense mutations (p.Arg63Ter and Asp36ThrfsTer96). Three families have mutations in the TFR2 gene, one case has one previously unreported mutation (Family A-p.Asp680Tyr) and two cases have known pathogenic mutations (Family B and D-p.Trp781Ter and p.Gln672Ter respectively). Clinical, biochemical, and genetic data are discussed in all these cases. These rare cases of non-HFE related hereditary hemochromatosis highlight the importance of an earlier molecular diagnosis in a specialized center to prevent serious clinical complications.
Collapse
Affiliation(s)
- Gonzalo Hernández
- Iron Metabolism: Regulation and Diseases Group, Department of Basic Sciences, Universitat Internacional de Catalunya (UIC), 08195 Sant Cugat del Vallès, Spain; (G.H.); (X.F.-C.); (V.V.)
- BloodGenetics S.L., Diagnostics in Inherited Blood Diseases, 08950 Esplugues de Llobregat, Spain; (M.M.); (S.P.-M.); (C.T.)
| | - Xenia Ferrer-Cortès
- Iron Metabolism: Regulation and Diseases Group, Department of Basic Sciences, Universitat Internacional de Catalunya (UIC), 08195 Sant Cugat del Vallès, Spain; (G.H.); (X.F.-C.); (V.V.)
- BloodGenetics S.L., Diagnostics in Inherited Blood Diseases, 08950 Esplugues de Llobregat, Spain; (M.M.); (S.P.-M.); (C.T.)
| | - Veronica Venturi
- Iron Metabolism: Regulation and Diseases Group, Department of Basic Sciences, Universitat Internacional de Catalunya (UIC), 08195 Sant Cugat del Vallès, Spain; (G.H.); (X.F.-C.); (V.V.)
| | - Melina Musri
- BloodGenetics S.L., Diagnostics in Inherited Blood Diseases, 08950 Esplugues de Llobregat, Spain; (M.M.); (S.P.-M.); (C.T.)
| | - Martin Floor Pilquil
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain; (M.F.P.); (P.M.M.T.); (J.V.-F.)
- Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic—Universitat Central de Catalunya, 08500 Vic, Spain
| | - Pau Marc Muñoz Torres
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain; (M.F.P.); (P.M.M.T.); (J.V.-F.)
| | | | - Maria Àngels Ruiz Mínguez
- Department of Laboratory Medicine/Fundació Hospital de l’Esperit Sant, 08923 Santa Coloma de Gramenet, Spain;
| | | | - Sara Pelucchi
- Department of Medicine and Surgery, University of Milano-Bicocca, 20126 Monza, Italy; (S.P.); (A.P.)
| | - Alberto Piperno
- Department of Medicine and Surgery, University of Milano-Bicocca, 20126 Monza, Italy; (S.P.); (A.P.)
- Medical Genetics—ASST-Monza, S. Gerardo Hospital, 20900 Monza, Italy
- Centre for Rare Diseases—Disorders of Iron Metabolism—ASST-Monza, San Gerardo Hospital, 20900 Monza, Italy
| | - Esther Plensa Alberca
- Hematologia i Hemoteràpia, Consorci Sanitari del Maresme, Institut Català d’Oncologia, 08304 Mataró, Spain; (E.P.A.); (G.G.R.); (E.C.G.)
| | - Georgina Gener Ricós
- Hematologia i Hemoteràpia, Consorci Sanitari del Maresme, Institut Català d’Oncologia, 08304 Mataró, Spain; (E.P.A.); (G.G.R.); (E.C.G.)
| | - Eloi Cañamero Giró
- Hematologia i Hemoteràpia, Consorci Sanitari del Maresme, Institut Català d’Oncologia, 08304 Mataró, Spain; (E.P.A.); (G.G.R.); (E.C.G.)
| | - Santiago Pérez-Montero
- BloodGenetics S.L., Diagnostics in Inherited Blood Diseases, 08950 Esplugues de Llobregat, Spain; (M.M.); (S.P.-M.); (C.T.)
| | - Cristian Tornador
- BloodGenetics S.L., Diagnostics in Inherited Blood Diseases, 08950 Esplugues de Llobregat, Spain; (M.M.); (S.P.-M.); (C.T.)
| | - Jordi Villà-Freixa
- Department of Basic Sciences, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Spain; (M.F.P.); (P.M.M.T.); (J.V.-F.)
- Department of Biosciences, Faculty of Sciences and Technology, Universitat de Vic—Universitat Central de Catalunya, 08500 Vic, Spain
| | - Mayka Sánchez
- Iron Metabolism: Regulation and Diseases Group, Department of Basic Sciences, Universitat Internacional de Catalunya (UIC), 08195 Sant Cugat del Vallès, Spain; (G.H.); (X.F.-C.); (V.V.)
- BloodGenetics S.L., Diagnostics in Inherited Blood Diseases, 08950 Esplugues de Llobregat, Spain; (M.M.); (S.P.-M.); (C.T.)
- Correspondence:
| |
Collapse
|
34
|
Della Marina A, Arlt A, Schara-Schmidt U, Depienne C, Gangfuß A, Kölbel H, Sickmann A, Freier E, Kohlschmidt N, Hentschel A, Weis J, Czech A, Grüneboom A, Roos A. Phenotypical and Myopathological Consequences of Compound Heterozygous Missense and Nonsense Variants in SLC18A3. Cells 2021; 10:cells10123481. [PMID: 34943989 PMCID: PMC8700530 DOI: 10.3390/cells10123481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Presynaptic forms of congenital myasthenic syndromes (CMS) due to pathogenic variants in SLC18A3 impairing the synthesis and recycling of acetylcholine (ACh) have recently been described. SLC18A3 encodes the vesicular ACh transporter (VAChT), modulating the active transport of ACh at the neuromuscular junction, and homozygous loss of VAChT leads to lethality. Methods: Exome sequencing (ES) was carried out to identify the molecular genetic cause of the disease in a 5-year-old male patient and histological, immunofluorescence as well as electron- and CARS-microscopic studies were performed to delineate the muscle pathology, which has so far only been studied in VAChT-deficient animal models. Results: ES unraveled compound heterozygous missense and nonsense variants (c.315G>A, p.Trp105* and c.1192G>C, p.Asp398His) in SLC18A3. Comparison with already-published cases suggests a more severe phenotype including impaired motor and cognitive development, possibly related to a more severe effect of the nonsense variant. Therapy with pyridostigmine was only partially effective while 3,4 diaminopyridine showed no effect. Microscopic investigation of the muscle biopsy revealed reduced fibre size and a significant accumulation of lipid droplets. Conclusions: We suggest that nonsense variants have a more detrimental impact on the clinical manifestation of SLC18A3-associated CMS. The impact of pathogenic SLC18A3 variants on muscle fibre integrity beyond the effect of denervation is suggested by the build-up of lipid aggregates. This in turn implicates the importance of proper VAChT-mediated synthesis and recycling of ACh for lipid homeostasis in muscle cells. This hypothesis is further supported by the pathological observations obtained in previously published VAChT-animal models.
Collapse
Affiliation(s)
- Adela Della Marina
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45122 Essen, Germany; (U.S.-S.); (A.G.); (H.K.); (A.R.)
- Correspondence:
| | - Annabelle Arlt
- Institute of Clinical Genetics and Tumor Genetics Bonn, 53111 Bonn, Germany; (A.A.); (N.K.)
| | - Ulrike Schara-Schmidt
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45122 Essen, Germany; (U.S.-S.); (A.G.); (H.K.); (A.R.)
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany;
| | - Andrea Gangfuß
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45122 Essen, Germany; (U.S.-S.); (A.G.); (H.K.); (A.R.)
| | - Heike Kölbel
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45122 Essen, Germany; (U.S.-S.); (A.G.); (H.K.); (A.R.)
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., 44139 Dortmund, Germany; (A.S.); (E.F.); (A.H.); (A.C.); (A.G.)
| | - Erik Freier
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., 44139 Dortmund, Germany; (A.S.); (E.F.); (A.H.); (A.C.); (A.G.)
| | - Nicolai Kohlschmidt
- Institute of Clinical Genetics and Tumor Genetics Bonn, 53111 Bonn, Germany; (A.A.); (N.K.)
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., 44139 Dortmund, Germany; (A.S.); (E.F.); (A.H.); (A.C.); (A.G.)
| | - Joachim Weis
- Institute of Neuropathology, University Hospital Aachen, RWTH-Aachen University, 52074 Aachen, Germany;
| | - Artur Czech
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., 44139 Dortmund, Germany; (A.S.); (E.F.); (A.H.); (A.C.); (A.G.)
| | - Anika Grüneboom
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., 44139 Dortmund, Germany; (A.S.); (E.F.); (A.H.); (A.C.); (A.G.)
| | - Andreas Roos
- Department of Pediatric Neurology, Centre for Neuromuscular Disorders, Centre for Translational Neuro- and Behavioral Sciences, University Duisburg-Essen, 45122 Essen, Germany; (U.S.-S.); (A.G.); (H.K.); (A.R.)
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| |
Collapse
|
35
|
Igelman AD, Ku C, da Palma MM, Georgiou M, Schiff ER, Lam BL, Sankila EM, Ahn J, Pyers L, Vincent A, Ferraz Sallum JM, Zein WM, Oh JK, Maldonado RS, Ryu J, Tsang SH, Gorin MB, Webster AR, Michaelides M, Yang P, Pennesi ME. Expanding the clinical phenotype in patients with disease causing variants associated with atypical Usher syndrome. Ophthalmic Genet 2021; 42:664-673. [PMID: 34223797 PMCID: PMC9233901 DOI: 10.1080/13816810.2021.1946704] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
Atypical Usher syndrome (USH) is poorly defined with a broad clinical spectrum. Here, we characterize the clinical phenotype of disease caused by variants in CEP78, CEP250, ARSG, and ABHD12.Chart review evaluating demographic, clinical, imaging, and genetic findings of 19 patients from 18 families with a clinical diagnosis of retinal disease and confirmed disease-causing variants in CEP78, CEP250, ARSG, or ABHD12.CEP78-related disease included sensorineural hearing loss (SNHL) in 6/7 patients and demonstrated a broad phenotypic spectrum including: vascular attenuation, pallor of the optic disc, intraretinal pigment, retinal pigment epithelium mottling, areas of mid-peripheral hypo-autofluorescence, outer retinal atrophy, mild pigmentary changes in the macula, foveal hypo-autofluorescence, and granularity of the ellipsoid zone. Nonsense and frameshift variants in CEP250 showed mild retinal disease with progressive, non-congenital SNHL. ARSG variants resulted in a characteristic pericentral pattern of hypo-autofluorescence with one patient reporting non-congenital SNHL. ABHD12-related disease showed rod-cone dystrophy with macular involvement, early and severe decreased best corrected visual acuity, and non-congenital SNHL ranging from unreported to severe.This study serves to expand the clinical phenotypes of atypical USH. Given the variable findings, atypical USH should be considered in patients with peripheral and macular retinal disease even without the typical RP phenotype especially when SNHL is noted. Additionally, genetic screening may be useful in patients who have clinical symptoms and retinal findings even in the absence of known SNHL given the variability of atypical USH.
Collapse
Affiliation(s)
- Austin D Igelman
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Cristy Ku
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mariana Matioli da Palma
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Ophthalmology and Visual Sciences, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Michalis Georgiou
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Elena R Schiff
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Byron L Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eeva-Marja Sankila
- Department of Ophthalmology, Helsinki University Eye Hospital, Helsinki, Finland
| | - Jeeyun Ahn
- UCLA Stein Eye Institute, Division of Retinal Disorders and Ophthalmic Genetics, Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Ophthalmology, Seoul National University, College of Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Lindsey Pyers
- UCLA Stein Eye Institute, Division of Retinal Disorders and Ophthalmic Genetics, Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, the Hospital for Sick Children, University of Toronto, Canada
- Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology and Visual Sciences, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jin Kyun Oh
- Jonas Children's Vision Care, Departments of Ophthalmology, Pathology & Cell Biology, Columbia Stem Cell Initiative, New York, USA
- College of Medicine, State University of New York at Downstate Medical Center, Brooklyn, NY, USA
| | - Ramiro S Maldonado
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, KY, USA
| | - Joseph Ryu
- Jonas Children's Vision Care, Departments of Ophthalmology, Pathology & Cell Biology, Columbia Stem Cell Initiative, New York, USA
| | - Stephen H Tsang
- Jonas Children's Vision Care, Departments of Ophthalmology, Pathology & Cell Biology, Columbia Stem Cell Initiative, New York, USA
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael B Gorin
- UCLA Stein Eye Institute, Division of Retinal Disorders and Ophthalmic Genetics, Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Paul Yang
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| |
Collapse
|
36
|
Coste T, Hervé D, Neau JP, Jouvent E, Ba F, Bergametti F, Lamy M, Cogez J, Derache N, Schneckenburger R, Grelet M, Gollion C, Lanotte L, Lauer V, Layet V, Urbanczyk C, Didic M, Raynouard I, Delaval L, Dassa J, Florea A, Badiu C, Nguyen K, Tournier-Lasserve E. Heterozygous HTRA1 nonsense or frameshift mutations are pathogenic. Brain 2021; 144:2616-2624. [PMID: 34270682 DOI: 10.1093/brain/awab271] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022] Open
Abstract
Heterozygous missense HTRA1 mutations have been associated with an autosomal dominant cerebral small vessel disease (CSVD) whereas the pathogenicity of heterozygous HTRA1 stop codon variants is unclear. We performed a targeted high throughput sequencing of all known CSVD genes, including HTRA1, in 3853 unrelated consecutive CSVD patients referred for molecular diagnosis. The frequency of heterozygous HTRA1 mutations leading to a premature stop codon in this patient cohort was compared with their frequency in large control databases. An analysis of HTRA1 mRNA was performed in several stop codon carrier patients. Clinical and neuroimaging features were characterized in all probands. Twenty unrelated patients carrying a heterozygous HTRA1 variant leading to a premature stop codon were identified. A highly significant difference was observed when comparing our patient cohort with control databases: gnomAD v3.1.1 [P = 3.12 × 10-17, odds ratio (OR) = 21.9], TOPMed freeze 5 (P = 7.6 × 10-18, OR = 27.1) and 1000 Genomes (P = 1.5 × 10-5). Messenger RNA analysis performed in eight patients showed a degradation of the mutated allele strongly suggesting a haploinsufficiency. Clinical and neuroimaging features are similar to those previously reported in heterozygous missense mutation carriers, except for penetrance, which seems lower. Altogether, our findings strongly suggest that heterozygous HTRA1 stop codons are pathogenic through a haploinsufficiency mechanism. Future work will help to estimate their penetrance, an important information for genetic counselling.
Collapse
Affiliation(s)
- Thibault Coste
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, France
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
| | - Dominique Hervé
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
- AP-HP, CERVCO, Service de Neurologie, Hôpital Lariboisière, France
| | - Jean Philippe Neau
- Centre Hospitalier Universitaire de Poitiers, Service de Neurologie, Poitiers, France
| | - Eric Jouvent
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
- AP-HP, CERVCO, Service de Neurologie, Hôpital Lariboisière, France
| | - Fatoumata Ba
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, France
| | | | - Matthias Lamy
- Centre Hospitalier Universitaire de Poitiers, Service de Neurologie, Poitiers, France
| | - Julien Cogez
- Centre Hospitalier Universitaire de Caen, Service de Neurologie, Caen, France
| | - Nathalie Derache
- Centre Hospitalier Universitaire de Caen, Service de Neurologie, Caen, France
| | | | - Maude Grelet
- Centre Hospitalier Intercommunal de Toulon- La Seyne sur mer, Service de Génétique Médicale, Toulon, France
| | - Cédric Gollion
- Centre Hospitalier Universitaire de Toulouse, Service de Neurologie, Toulouse, France
| | - Livia Lanotte
- Hôpital De Hautepierre, Service de Neurologie, Strasbourg, France
| | - Valérie Lauer
- Hôpital De Hautepierre, Unité Neuro-Vasculaire, Strasbourg, France
| | - Valérie Layet
- Groupe Hospitalier Du havre, Service de Génétique Médicale, Le Havre, France
| | - Cédric Urbanczyk
- Centre Hospitalier Départemental La Roche-Sur-Yon, Service de Neurologie, La Roche-Sur-Yon, France
| | - Mira Didic
- APHM, Hôpital Timone Adultes, Service de Neurologie et Neuropsychologie, Marseille, France
- Aix Marseille Université, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - Igor Raynouard
- Fondation Adolphe de Rothschild, Service de Neurologie, Paris, France
| | - Laure Delaval
- AP-HP, Hôpital Bichat, Service de Médecine Interne, France
| | - Jérémie Dassa
- Centre Hospitalier Emile Roux, Service de Neurologie, Le Puy-en-Velay, France
| | - Alexandru Florea
- Centre Hospitalier Marie Madeleine, Service de Neurologie, Forbach, France
| | - Carmen Badiu
- Centre Hospitalier Metz-Thionville, Service de Neurologie, Metz, France
| | - Karine Nguyen
- APHM, Hôpital Timone Adultes, Département de Génétique, Marseille, France
| | - Elisabeth Tournier-Lasserve
- AP-HP, Service de Génétique Moléculaire Neurovasculaire, Hôpital Saint-Louis, France
- Université de Paris, INSERM UMR-1141 Neurodiderot, Paris F-75019, France
| |
Collapse
|
37
|
Zinshteyn B, Sinha NK, Enam SU, Koleske B, Green R. Translational repression of NMD targets by GIGYF2 and EIF4E2. PLoS Genet 2021; 17:e1009813. [PMID: 34665823 PMCID: PMC8555832 DOI: 10.1371/journal.pgen.1009813] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/29/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Translation of messenger RNAs (mRNAs) with premature termination codons produces truncated proteins with potentially deleterious effects. This is prevented by nonsense-mediated mRNA decay (NMD) of these mRNAs. NMD is triggered by ribosomes terminating upstream of a splice site marked by an exon-junction complex (EJC), but also acts on many mRNAs lacking a splice junction after their termination codon. We developed a genome-wide CRISPR flow cytometry screen to identify regulators of mRNAs with premature termination codons in K562 cells. This screen recovered essentially all core NMD factors and suggested a role for EJC factors in degradation of PTCs without downstream splicing. Among the strongest hits were the translational repressors GIGYF2 and EIF4E2. GIGYF2 and EIF4E2 mediate translational repression but not mRNA decay of a subset of NMD targets and interact with NMD factors genetically and physically. Our results suggest a model wherein recognition of a stop codon as premature can lead to its translational repression through GIGYF2 and EIF4E2.
Collapse
Affiliation(s)
- Boris Zinshteyn
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Niladri K. Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Syed Usman Enam
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Benjamin Koleske
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
| |
Collapse
|
38
|
Abstract
Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.
Collapse
Affiliation(s)
- Jingdong Cheng
- Gene Center and Department for Biochemistry, LMU Munich, München, Germany.
| | - Otto Berninghausen
- Gene Center and Department for Biochemistry, LMU Munich, München, Germany
| | - Roland Beckmann
- Gene Center and Department for Biochemistry, LMU Munich, München, Germany.
| |
Collapse
|
39
|
Dabrowski M, Bukowy-Bieryllo Z, Jackson CL, Zietkiewicz E. Properties of Non-Aminoglycoside Compounds Used to Stimulate Translational Readthrough of PTC Mutations in Primary Ciliary Dyskinesia. Int J Mol Sci 2021; 22:ijms22094923. [PMID: 34066907 PMCID: PMC8125088 DOI: 10.3390/ijms22094923] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/30/2022] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare disease with autosomal recessive inheritance, caused mostly by bi-allelic gene mutations that impair motile cilia structure and function. Currently, there are no causal treatments for PCD. In many disease models, translational readthrough of premature termination codons (PTC-readthrough) induced by aminoglycosides has been proposed as an effective way of restoring functional protein expression and reducing disease symptoms. However, variable outcomes of pre-clinical trials and toxicity associated with long-term use of aminoglycosides prompt the search for other compounds that might overcome these problems. Because a high proportion of PCD-causing variants are nonsense mutations, readthrough therapies are an attractive option. We tested a group of chemical compounds with known PTC-readthrough potential (ataluren, azithromycin, tylosin, amlexanox, and the experimental compound TC007), collectively referred to as non-aminoglycosides (NAGs). We investigated their PTC-readthrough efficiency in six PTC mutations found in Polish PCD patients, in the context of cell and cilia health, and in comparison to the previously tested aminoglycosides. The NAGs did not compromise the viability of the primary nasal respiratory epithelial cells, and the ciliary beat frequency was retained, similar to what was observed for gentamicin. In HEK293 cells transfected with six PTC-containing inserts, the tested compounds stimulated PTC-readthrough but with lower efficiency than aminoglycosides. The study allowed us to select compounds with minimal negative impact on cell viability and function but still the potential to induce PTC-readthrough.
Collapse
Affiliation(s)
- Maciej Dabrowski
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (M.D.); (Z.B.-B.)
| | - Zuzanna Bukowy-Bieryllo
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (M.D.); (Z.B.-B.)
| | - Claire L. Jackson
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK;
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
| | - Ewa Zietkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland; (M.D.); (Z.B.-B.)
- Correspondence:
| |
Collapse
|
40
|
Hosseini-Farahabadi S, Baradaran-Heravi A, Zimmerman C, Choi K, Flibotte S, Roberge M. Small molecule Y-320 stimulates ribosome biogenesis, protein synthesis, and aminoglycoside-induced premature termination codon readthrough. PLoS Biol 2021; 19:e3001221. [PMID: 33939688 PMCID: PMC8118496 DOI: 10.1371/journal.pbio.3001221] [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] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 05/13/2021] [Accepted: 04/09/2021] [Indexed: 11/18/2022] Open
Abstract
Premature termination codons (PTC) cause over 10% of genetic disease cases. Some aminoglycosides that bind to the ribosome decoding center can induce PTC readthrough and restore low levels of full-length functional proteins. However, concomitant inhibition of protein synthesis limits the extent of PTC readthrough that can be achieved by aminoglycosides like G418. Using a cell-based screen, we identified a small molecule, the phenylpyrazoleanilide Y-320, that potently enhances TP53, DMD, and COL17A1 PTC readthrough by G418. Unexpectedly, Y-320 increased cellular protein levels and protein synthesis, measured by SYPRO Ruby protein staining and puromycin labeling, as well as ribosome biogenesis measured using antibodies to rRNA and ribosomal protein S6. Y-320 did not increase the rate of translation elongation and it exerted its effects independently of mTOR signaling. At the single cell level, exposure to Y-320 and G418 increased ribosome content and protein synthesis which correlated strongly with PTC readthrough. As a single agent, Y-320 did not affect translation fidelity measured using a luciferase reporter gene but it enhanced misincorporation by G418. RNA-seq data showed that Y-320 up-regulated the expression of CXC chemokines CXCL10, CXCL8, CXCL2, CXCL11, CXCL3, CXCL1, and CXCL16. Several of these chemokines exert their cellular effects through the receptor CXCR2 and the CXCR2 antagonist SB225002 reduced cellular protein levels and PTC readthrough in cells exposed to Y-320 and G418. These data show that the self-limiting nature of PTC readthrough by G418 can be compensated by Y-320, a potent enhancer of PTC readthrough that increases ribosome biogenesis and protein synthesis. They also support a model whereby increased PTC readthrough is enabled by increased protein synthesis mediated by an autocrine chemokine signaling pathway. The findings also raise the possibility that inflammatory processes affect cellular propensity to readthrough agents and that immunomodulatory drugs like Y-320 might find application in PTC readthrough therapy.
Collapse
Affiliation(s)
- Sara Hosseini-Farahabadi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carla Zimmerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kunho Choi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephane Flibotte
- UBC/LSI Bioinformatics Facility, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| |
Collapse
|
41
|
Yang Y, Tang N, Zhu Y, Zhang L, Cao X, Liu L, Xia W, Li P, Yang Y. A novel homozygous nonsense mutation in the CA2 gene (c.368G>A, p.W123X) linked to carbonic anhydrase II deficiency syndrome in a Chinese family. Metab Brain Dis 2021; 36:589-599. [PMID: 33555497 DOI: 10.1007/s11011-021-00677-9] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/24/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Carbonic anhydrase II deficiency syndrome is an autosomal recessive osteopetrosis with renal tubular acidosis and cerebral calcifications. We tried to detect the causative mutation for carbonic anhydrase II deficiency syndrome in a five-generation Chinese family. MATERIALS AND METHODS Genomic DNA was extracted from whole blood of the proband, his grandmother, parents, aunt, uncle and sister. The exomes were sequenced by whole exon sequencing followed by genetic analysis and Sanger sequencing validation. Then, physical and chemical properties studies and structure analysis were performed on mutated protein. Finally, Minigene model of vector plasmids for wild type and mutant type was constructed and transfected into human embryonic kidney 293T cells to further explore the expression change of CA2 transcript and protein after mutation. RESULTS Sequencing and genetic analysis have revealed the homozygous nonsense mutation of CA2 gene (c.368G > A, p.W123X) in the exon 4 of chromosome 8 of the proband, while it was not found in his grandmother, parents, aunt, uncle and sister. Furthermore, Sanger sequencing in the proband and his parents validated the mutation. Properties and structure of mutated CA2 proteins changed after mutation, especially in change of protein modification and hindrance of zinc ions binding, which may lead to decreased protein expression level of CA2. CONCLUSIONS We found a new homozygous nonsense mutation in CA2 gene (c.368G > A, p.W123X), which may be valuable in the early diagnosis and therapy of carbonic anhydrase II deficiency syndrome.
Collapse
Affiliation(s)
- Yan Yang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Nie Tang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Ying Zhu
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Lei Zhang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Xu Cao
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Limei Liu
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Wei Xia
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Pengqiu Li
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China
| | - Yi Yang
- Department of Endocrinology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, No. 32 the west second section of the first ring road, Qingyang District, Chengdu, Sichuan, 610072, China.
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, 610072, Chengdu, China.
| |
Collapse
|
42
|
Lachgar M, Morín M, Villamar M, del Castillo I, Moreno-Pelayo MÁ. A Novel Truncating Mutation in HOMER2 Causes Nonsyndromic Progressive DFNA68 Hearing Loss in a Spanish Family. Genes (Basel) 2021; 12:411. [PMID: 33809266 PMCID: PMC8001007 DOI: 10.3390/genes12030411] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/02/2022] Open
Abstract
Nonsyndromic hereditary hearing loss is a common sensory defect in humans that is clinically and genetically highly heterogeneous. So far, 122 genes have been associated with this disorder and 50 of them have been linked to autosomal dominant (DFNA) forms like DFNA68, a rare subtype of hearing impairment caused by disruption of a stereociliary scaffolding protein (HOMER2) that is essential for normal hearing in humans and mice. In this study, we report a novel HOMER2 variant (c.832_836delCCTCA) identified in a Spanish family by using a custom NGS targeted gene panel (OTO-NGS-v2). This frameshift mutation produces a premature stop codon that may lead in the absence of NMD to a shorter variant (p.Pro278Alafs*10) that truncates HOMER2 at the CDC42 binding domain (CBD) of the coiled-coil structure, a region that is essential for protein multimerization and HOMER2-CDC42 interaction. c.832_836delCCTCA mutation is placed close to the previously identified c.840_840dup mutation found in a Chinese family that truncates the protein (p.Met281Hisfs*9) at the CBD. Functional assessment of the Chinese mutant revealed decreased protein stability, reduced ability to multimerize, and altered distribution pattern in transfected cells when compared with wild-type HOMER2. Interestingly, the Spanish and Chinese frameshift mutations might exert a similar effect at the protein level, leading to truncated mutants with the same Ct aberrant protein tail, thus suggesting that they can share a common mechanism of pathogenesis. Indeed, age-matched patients in both families display quite similar hearing loss phenotypes consisting of early-onset, moderate-to-profound progressive hearing loss. In summary, we have identified the third variant in HOMER2, which is the first one identified in the Spanish population, thus contributing to expanding the mutational spectrum of this gene in other populations, and also to clarifying the genotype-phenotype correlations of DFNA68 hearing loss.
Collapse
Affiliation(s)
- María Lachgar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.L.); (M.M.); (M.V.); (I.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.L.); (M.M.); (M.V.); (I.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Manuela Villamar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.L.); (M.M.); (M.V.); (I.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.L.); (M.M.); (M.V.); (I.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Miguel Ángel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar km 9.100, 28034 Madrid, Spain; (M.L.); (M.M.); (M.V.); (I.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| |
Collapse
|
43
|
Chen J, Zheng H, Wang Z, Wang J, He F, Zhang C, Xiong F. A female carrier of a novel DMD mutation with slightly skewed X-chromosome inactivation shows a suspected case of Becker muscular dystrophy in a Chinese family. Mol Genet Genomics 2021; 296:541-549. [PMID: 33566169 DOI: 10.1007/s00438-020-01757-8] [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: 06/21/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022]
Abstract
Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are both caused by mutations in DMD gene effecting the expression of dystrophin. Generally female carriers are asymptomatic; however, it has been suggested that carriers may exhibit symptoms. We investigated a 6-year-old Chinese girl exhibiting a suspected BMD phenotype, including persistently elevated creatine kinase and creatine kinase isoenzyme levels. The proband harbored a novel heterozygous mutation, c.3458_3459insAA, within exon 26 of the DMD gene inherited from her mother who had a completely normal phenotype and presented with mosaicism in her lymphocytes with 45, X [17%]/46, XX [83%]. In addition, X-chromosome inactivation (XCI) patterns in the peripheral blood of the child were slightly skewed: proband with 62% (mutant allele)/38% (normal allele) when compared with her mother with 32/68%. Amplification of regions of the cDNA revealed different ratios for the expression of these alleles: proband with 50/50% and her mother with 20/80%. Real-time PCR showed that mRNA expression was significantly decreased in both. We proposed that a frameshift or nonsense mutation may contribute to the development of symptoms in carriers. These phenotypes correlate with nonrandom XCI patterns and are compounded by the locus of the mutation. For incompletely skewed XCI patterns, although the mutant allele could suppress the expression of a normal allele, carriers would remain asymptomatic as long as there was adequate compensation from the normal allele. We also proposed a mechanism where mRNA from the mutant allele may be unstable and easily degraded, allowing for phenotypic compensation by the wildtype allele.
Collapse
Affiliation(s)
- Jianfan Chen
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Hui Zheng
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Zhongju Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Jian Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Fei He
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, Guangdong Province, People's Republic of China
| | - Cheng Zhang
- Department of Neurology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Fu Xiong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China.
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, Guangdong Province, People's Republic of China.
| |
Collapse
|
44
|
Suh S, Choi EH, Leinonen H, Foik AT, Newby GA, Yeh WH, Dong Z, Kiser PD, Lyon DC, Liu DR, Palczewski K. Restoration of visual function in adult mice with an inherited retinal disease via adenine base editing. Nat Biomed Eng 2021; 5:169-178. [PMID: 33077938 PMCID: PMC7885272 DOI: 10.1038/s41551-020-00632-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/17/2020] [Indexed: 12/22/2022]
Abstract
Cytosine base editors and adenine base editors (ABEs) can correct point mutations predictably and independent of Cas9-induced double-stranded DNA breaks (which causes substantial indel formation) and homology-directed repair (which typically leads to low editing efficiency). Here, we show, in adult mice, that a subretinal injection of a lentivirus expressing an ABE and a single-guide RNA targeting a de novo nonsense mutation in the Rpe65 gene corrects the pathogenic mutation with up to 29% efficiency and with minimal formation of indel and off-target mutations, despite the absence of the canonical NGG sequence as a protospacer-adjacent motif. The ABE-treated mice displayed restored RPE65 expression and retinoid isomerase activity, and near-normal levels of retinal and visual functions. Our findings motivate the further testing of ABEs for the treatment of inherited retinal diseases and for the correction of pathological mutations with non-canonical protospacer-adjacent motifs.
Collapse
Affiliation(s)
- Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, Irvine, CA, USA.
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA.
| | - Elliot H Choi
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, Irvine, CA, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA
| | - Henri Leinonen
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, Irvine, CA, USA
| | - Andrzej T Foik
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, USA
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Wei-Hsi Yeh
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, USA
| | - Zhiqian Dong
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, Irvine, CA, USA
| | - Philip D Kiser
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA
| | - David C Lyon
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, Irvine, CA, USA.
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA.
| |
Collapse
|
45
|
Doğan M, Eröz R, Terali K, Gezdirici A, Bolu S. Clinical, radiological and computational studies on two novel GNPTG variants causing mucolipidosis III gamma phenotypes with varying severity. Mol Biol Rep 2021; 48:1465-1474. [PMID: 33507475 DOI: 10.1007/s11033-021-06158-7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
Mucolipidosis III gamma (ML III γ) is a slowly progressive disorder that affects multiple parts of the body such as the skeleton, joints, and connective tissue structures. It is caused by pathogenic variants in the GNPTG gene that provides instructions for producing the γ subunit of GlcNAc-1-phosphotransferase. In this study we aim to characterize clinical findings and biological insights on two novel GNPTG variants causing ML III γ phenotypes with varying severity. We report on two siblings with ML III γ bearing the previously undescribed c.477C > G (p.Y159*) nonsense variant in a homozygous state as well as a patient with ML III γ bearing the novel c.110 + 19_111-17del variant in a homozygous state. These variants were revealed by whole-exome sequencing and Sanger sequencing, respectively. Their parents, who are heterozygotes for the same mutation, are healthy. The clinical and radiographic presentation of ML III γ in our patients who had c.477C > G (p.Y159*) variant is consistent with a relatively severe form of the disease, which is further supported by a working three-dimensional model of the GlcNAc-1-phosphotransferase γ subunit. On the other hand, it is seen that our patient who carries the c.110 + 19_111-17del variant has a milder phenotype. Our findings help broaden the spectrum of GNPTG variants causing ML III γ and offer structural and mechanistic insights into loss of GlcNAc-1-phosphotransferase γ subunit function.
Collapse
Affiliation(s)
- Mustafa Doğan
- Department of Medical Genetics, Malatya Turgut Ozal University Training and Research Hospital, Malatya, Turkey.
| | - Recep Eröz
- Department of Medical Genetics, Faculty of Medicine, Düzce University, Düzce, Turkey
| | - Kerem Terali
- Department of Medical Biochemistry, Faculty of Medicine, Near East University, Nicosia, Cyprus
- Bioinformatics and Computational Biology Research Group, DESAM Institute, Near East University, Nicosia, Cyprus
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, 34480, Istanbul, Turkey
| | - Semih Bolu
- Department of Pediatric Endocrinology, Adıyaman Training and Research Hospital, Adıyaman, Turkey
| |
Collapse
|
46
|
Tang H, Mao J, Xiang J, Liu M, Li H, Wang T. Whole-exome sequencing identified a novel mutation in CHM of a Chinese family. J Genet 2021; 100:49. [PMID: 34282730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Choroideraemia (CHM) is a rare X-linked progressive-inherited retinal disease. In this study, we diagnosed and explored the genetic cause in a Chinese pedigree exhibiting nyctalopia and decreased visual acuity in early life. Clinical data and peripheral blood samples were collected from available family members. Sanger sequencing of RPGR and RP2 genes, and subsequently whole-exome sequencing was carried out to investigate the molecular cause. The proband was initially diagnosed as retinitis pigmentosa and experienced night blindness at an early age and decreased visual acuity in teens. The other affected males in this family suffered from the same problem. Direct sequencing failed to reveal the genetic cause and hence a novel hemizygous mutation c.861_862insGCTT was detected by WES in CHM gene resulting in a premature stop codon and a truncated protein. Subsequently, it was confirmed by Sanger sequencing and cosegregation analysis. We describe a novel mutation c.861_862insGCTT in CHM gene in a Chinese pedigree with choroideraemia. Our study emphasizes the utilization of next-generation sequencing in the diagnosis and genetic analysis of retinal diseases.
Collapse
Affiliation(s)
- Hui Tang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, Jiangsu, People's Republic of China.
| | | | | | | | | | | |
Collapse
|
47
|
Luo H, Xiao X, Li S, Sun W, Yi Z, Wang P, Zhang Q. Spectrum-frequency and genotype-phenotype analysis of rhodopsin variants. Exp Eye Res 2020; 203:108405. [PMID: 33347869 DOI: 10.1016/j.exer.2020.108405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/30/2020] [Revised: 11/23/2020] [Accepted: 12/14/2020] [Indexed: 12/18/2022]
Abstract
Mutations in RHO are the most common cause of autosomal dominant retinitis pigmentosa. However, the pathogenicity of many RHO variants is questionable. This study was designed to investigate the genotype-phenotype correlation for RHO variants. These RHO variants were collected from the in-house exome sequencing data of 7092 probands suffering from different types of eye conditions. The variants were classified using bioinformatics tools, family segregation, and clinical phenotypes. The RHO variants were assessed using multiple online tools and a genotype-phenotype analysis based on the data collected from of ours, gnomAD, and published literature. Totally, 52 heterozygous variants of RHO were detected in the 7092 probands. Of these 52, 17 were potentially pathogenic, were present in 35 families, and comprised 15 missense variants, one inframe deletion and one nonsense variant. All the 15 missense variants were predicted to be damaging by five different online tools. The analysis of the clinical data of the patients from the 35 families revealed certain common features, of an early damage to both the rods and the cones, relatively preserved visual acuity in adulthood, and mid-peripheral tapetoretinal degeneration with pigmentation or RPE atrophy. Our data, the data from gnomAD, and the systematic review of the 246 previously reported variants suggest that approximately two-thirds of the rare missense variants and most of the truncated variants involving upstream of K296 are likely benign. This study provides a brief summary of the characteristics of the pathogenic RHO variants. It emphasizes that the systematic evaluation of these variants at the individual-gene level is crucial in the current era of clinical genetic testing even for a well-known gene such as RHO.
Collapse
Affiliation(s)
- Hualei Luo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
| |
Collapse
|
48
|
Guissart C, Mouzat K, Kantar J, Louveau B, Vilquin P, Polge A, Raoul C, Lumbroso S. Premature termination codons in SOD1 causing Amyotrophic Lateral Sclerosis are predicted to escape the nonsense-mediated mRNA decay. Sci Rep 2020; 10:20738. [PMID: 33244158 PMCID: PMC7691510 DOI: 10.1038/s41598-020-77716-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common and severe adult-onset motoneuron disease and has currently no effective therapy. Approximately 20% of familial ALS cases are caused by dominantly-inherited mutations in the gene encoding Cu/Zn superoxide dismutase (SOD1), which represents one of the most frequent genetic cause of ALS. Despite the overwhelming majority of ALS-causing missense mutations in SOD1, a minority of premature termination codons (PTCs) have been identified. mRNA harboring PTCs are known to be rapidly degraded by nonsense-mediated mRNA decay (NMD), which limits the production of truncated proteins. The rules of NMD surveillance varying with PTC location in mRNA, we analyzed the localization of PTCs in SOD1 mRNA to evaluate whether or not those PTCs can be triggered to degradation by the NMD pathway. Our study shows that all pathogenic PTCs described in SOD1 so far can theoretically escape the NMD, resulting in the production of truncated protein. This finding supports the hypothesis that haploinsufficiency is not an underlying mechanism of SOD1 mutant-associated ALS and suggests that PTCs found in the regions that trigger NMD are not pathogenic. Such a consideration is particularly important since the availability of SOD1 antisense strategies, in view of variant treatment assignment.
Collapse
Affiliation(s)
- Claire Guissart
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nimes, University of Montpellier, Nimes, France.
- The Neuroscience Institute of Montpellier, INM, INSERM, Univ Montpellier, Montpellier, France.
| | - Kevin Mouzat
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nimes, University of Montpellier, Nimes, France
- The Neuroscience Institute of Montpellier, INM, INSERM, Univ Montpellier, Montpellier, France
| | - Jovana Kantar
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nimes, University of Montpellier, Nimes, France
- The Neuroscience Institute of Montpellier, INM, INSERM, Univ Montpellier, Montpellier, France
| | - Baptiste Louveau
- Département de Pharmacologie et de Génomique des Tumeurs Solides, Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Paul Vilquin
- Département de Pharmacologie et de Génomique des Tumeurs Solides, Hôpital Saint Louis, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Anne Polge
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nimes, University of Montpellier, Nimes, France
| | - Cédric Raoul
- The Neuroscience Institute of Montpellier, INM, INSERM, Univ Montpellier, Montpellier, France
| | - Serge Lumbroso
- Laboratoire de Biochimie et Biologie Moléculaire, CHU Nimes, University of Montpellier, Nimes, France
- The Neuroscience Institute of Montpellier, INM, INSERM, Univ Montpellier, Montpellier, France
| |
Collapse
|
49
|
Saadeh FS, Morsi RZ, El-Kurdi A, Nemer G, Mahfouz R, Charafeddine M, Khoury J, Najjar MW, Khoueiry P, Assi HI. Correlation of genetic alterations by whole-exome sequencing with clinical outcomes of glioblastoma patients from the Lebanese population. PLoS One 2020; 15:e0242793. [PMID: 33237934 PMCID: PMC7688136 DOI: 10.1371/journal.pone.0242793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/09/2020] [Indexed: 11/24/2022] Open
Abstract
Introduction Glioblastoma (GBM) is an aggressive brain tumor associated with high degree of resistance to treatment. Given its heterogeneity, it is important to understand the molecular landscape of this tumor for the development of more effective therapies. Because of the different genetic profiles of patients with GBM, we sought to identify genetic variants in Lebanese patients with GBM (LEB-GBM) and compare our findings to those in the Cancer Genome Atlas (TCGA). Methods We performed whole exome sequencing (WES) to identify somatic variants in a cohort of 60 patient-derived GBM samples. We focused our analysis on 50 commonly mutated GBM candidate genes and compared mutation signatures between our population and publicly available GBM data from TCGA. We also cross-tabulated biological covariates to assess for associations with overall survival, time to recurrence and follow-up duration. Results We included 60 patient-derived GBM samples from 37 males and 23 females, with age ranging from 3 to 80 years (mean and median age at diagnosis were 51 and 56, respectively). Recurrent tumor formation was present in 94.8% of patients (n = 55/58). After filtering, we identified 360 somatic variants from 60 GBM patient samples. After filtering, we identified 360 somatic variants from 60 GBM patient samples. Most frequently mutated genes in our samples included ATRX, PCDHX11, PTEN, TP53, NF1, EGFR, PIK3CA, and SCN9A. Mutations in NLRP5 were associated with decreased overall survival among the Lebanese GBM cohort (p = 0.002). Mutations in NLRP5 were associated with decreased overall survival among the Lebanese GBM cohort (p = 0.002). EGFR and NF1 mutations were associated with the frontal lobe and temporal lobe in our LEB-GBM cohort, respectively. Conclusions Our WES analysis confirmed the similarity in mutation signature of the LEB-GBM population with TCGA cohorts. It showed that 1 out of the 50 commonly GBM candidate gene mutations is associated with decreased overall survival among the Lebanese cohort. This study also highlights the need for studies with larger sample sizes to inform clinicians for better prognostication and management of Lebanese patients with GBM.
Collapse
Affiliation(s)
- Fadi S. Saadeh
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Rami Z. Morsi
- Department of Neurology, University of Chicago, Chicago, Illinois, United States of America
| | - Abdallah El-Kurdi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Rami Mahfouz
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Maya Charafeddine
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Jessica Khoury
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Marwan W. Najjar
- Division of Neurosurgery, Department of Surgery, American University of Beirut Medical Center, Beirut, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
- * E-mail: (PK); (HIA)
| | - Hazem I. Assi
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- * E-mail: (PK); (HIA)
| |
Collapse
|
50
|
Christen M, Austel M, Banovic F, Jagannathan V, Leeb T. NSDHL Frameshift Deletion in a Mixed Breed Dog with Progressive Epidermal Nevi. Genes (Basel) 2020; 11:genes11111297. [PMID: 33143176 PMCID: PMC7716214 DOI: 10.3390/genes11111297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/24/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
Loss-of-function variants in the NSDHL gene have been associated with epidermal nevi in humans with congenital hemidysplasia, ichthyosiform nevi, and limb defects (CHILD) syndrome and in companion animals. The NSDHL gene codes for the NAD(P)-dependent steroid dehydrogenase-like protein, which is involved in cholesterol biosynthesis. In this study, a female Chihuahua cross with a clinical and histological phenotype consistent with progressive epidermal nevi is presented. All exons of the NSDHL candidate gene were amplified by PCR and analyzed by Sanger sequencing. A heterozygous frameshift variant, c.718_722delGAACA, was identified in the affected dog. In lesional skin, the vast majority of NSDHL transcripts lacked the five deleted bases. The variant is predicted to produce a premature stop codon truncating 34% of the encoded protein, p.Glu240Profs*17. The mutant allele was absent from 22 additionally genotyped Chihuahuas, as well as from 647 control dogs of diverse breeds and eight wolves. The available experimental data together with current knowledge about NSDHL variants and their functional impact in humans, dogs, and other species prompted us to classify this variant as pathogenic according to the ACMG guidelines that were previously established for human sequence variants. Therefore, we propose the c.718_722delGAACA variant as causative variant for the observed skin lesions in this dog.
Collapse
Affiliation(s)
- Matthias Christen
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Michaela Austel
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (M.A.); (F.B.)
| | - Frane Banovic
- Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (M.A.); (F.B.)
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland; (M.C.); (V.J.)
- Dermfocus, University of Bern, 3001 Bern, Switzerland
- Correspondence: ; Tel.: +41-31-631-2326
| |
Collapse
|