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Ishtiaq H, Siddiqui S, Nawaz R, Jamali KS, Khan AG. Sialuria-Related Intellectual Disability in Children and Adolescent of Pakistan: Tenth Patient Described has a Novel Mutation in the GNE Gene. CNS & NEUROLOGICAL DISORDERS-DRUG TARGETS 2021; 19:127-141. [PMID: 32053088 DOI: 10.2174/1871527319666200213115747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 12/23/2019] [Accepted: 01/01/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Sialuria is a rare inborn error of metabolism caused by excessive synthesis of sialic acid due to the mutation in the binding site of the cytidine monophosphate-sialic acid of UDPGlcNAc 2-Epimerase/ManNAc Kinase (GNE/MNK). OBJECTIVE This is the first study investigating the molecular basis of neuronal disorders exhibiting sialuria in Pakistani children/adolescents. METHODS The current study genotyped GNE SNPs rs121908621, rs121908622 and rs121908623 by using PCR, RFLP, and DNA sequencing methods. Socioeconomic and clinical histories were also recorded. RESULTS Our data suggest that clinical symptoms and financial status play a significant role in conferring sialuria related Intellectual Disability (ID). SNP: rs121908623 showed G/A substitution (R263Q) in the GNE gene. CONCLUSION We have identified one case study in Pakistan, so this makes our research a leap forward towards the identification of the 10th case study worldwide.
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Affiliation(s)
- Hina Ishtiaq
- Department of Neuroscience, Dr. Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Sonia Siddiqui
- Department of Neuroscience, Dr. Panjwani Center For Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.,Department of Biochemistry, Dow University of Health Sciences, Karachi-75290, Pakistan
| | - Rukhsana Nawaz
- Department of Psychology, College of Humanities and Social Sciences, University of UAE, Al-Ain, United Arab Emirates
| | - Khawar Saeed Jamali
- Department of Surgery, Dow University of Health Sciences, Karachi- 75290, Pakistan
| | - Abdul Ghani Khan
- Department of Neuropsychiatry and Rehabilitation, National Institute of Child Health, Jinnah Post Graduate Medical Center, Karachi-75510, Pakistan
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Trochet D, Prudhon B, Beuvin M, Peccate C, Lorain S, Julien L, Benkhelifa-Ziyyat S, Rabai A, Mamchaoui K, Ferry A, Laporte J, Guicheney P, Vassilopoulos S, Bitoun M. Allele-specific silencing therapy for Dynamin 2-related dominant centronuclear myopathy. EMBO Mol Med 2018; 10:239-253. [PMID: 29246969 PMCID: PMC5801507 DOI: 10.15252/emmm.201707988] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 11/14/2017] [Accepted: 11/20/2017] [Indexed: 11/09/2022] Open
Abstract
Rapid advances in allele-specific silencing by RNA interference established a strategy of choice to cure dominant inherited diseases by targeting mutant alleles. We used this strategy for autosomal-dominant centronuclear myopathy (CNM), a rare neuromuscular disorder without available treatment due to heterozygous mutations in the DNM2 gene encoding Dynamin 2. Allele-specific siRNA sequences were developed in order to specifically knock down the human and murine DNM2-mRNA harbouring the p.R465W mutation without affecting the wild-type allele. Functional restoration was achieved in muscle from a knock-in mouse model and in patient-derived fibroblasts, both expressing the most frequently encountered mutation in patients. Restoring either muscle force in a CNM mouse model or DNM2 function in patient-derived cells is an essential breakthrough towards future gene-based therapy for dominant centronuclear myopathy.
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Affiliation(s)
- Delphine Trochet
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Bernard Prudhon
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Maud Beuvin
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Cécile Peccate
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Stéphanie Lorain
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Laura Julien
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Sofia Benkhelifa-Ziyyat
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Aymen Rabai
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, Collège de France, University of Strasbourg, Illkirch, France
| | - Kamel Mamchaoui
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Arnaud Ferry
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, Collège de France, University of Strasbourg, Illkirch, France
| | - Pascale Guicheney
- Institute of Cardiometabolism and Nutrition (ICAN), INSERM UMR_S1166, UPMC Univ Paris 06, Sorbonne Universités, Paris, France
| | - Stéphane Vassilopoulos
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
| | - Marc Bitoun
- Research Center for Myology, UPMC Univ Paris 06 and INSERM UMRS 974, Institute of Myology, Sorbonne Universités, Paris, France
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Klootwijk E, Dufek S, Issler N, Bockenhauer D, Kleta R. Pathophysiology, current treatments and future targets in hereditary forms of renal Fanconi syndrome. Expert Opin Orphan Drugs 2016. [DOI: 10.1080/21678707.2017.1259560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Stephanie Dufek
- Centre for Nephrology, University College London, London, UK
| | - Naomi Issler
- Centre for Nephrology, University College London, London, UK
| | | | - Robert Kleta
- Centre for Nephrology, University College London, London, UK
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Allele-specific Col1a1 silencing reduces mutant collagen in fibroblasts from Brtl mouse, a model for classical osteogenesis imperfecta. Eur J Hum Genet 2013; 22:667-74. [PMID: 24022296 DOI: 10.1038/ejhg.2013.198] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/17/2013] [Accepted: 08/09/2013] [Indexed: 11/08/2022] Open
Abstract
Gene silencing approaches have the potential to become a powerful curative tool for a variety of monogenic diseases caused by gain-of-function mutations. Classical osteogenesis imperfecta (OI), a dominantly inherited bone dysplasia, is characterized in its more severe forms by synthesis of structurally abnormal type I collagen, which exerts a negative effect on extracellular matrix. Specific suppression of the mutant (Mut) allele would convert severe OI forms to the mild type caused by a quantitative defect in normal collagen. Here, we describe the in vitro and ex vivo investigation of a small interfering RNA (siRNA) approach to allele-specific gene silencing using Mut Col1a1 from the Brtl mouse, a well-characterized model for classical human OI. A human embryonic kidney cell line, which expresses the firefly luciferase gene, combined with either wild-type or Mut Brtl Col1a1 exon 23 sequences, was used for the first screening. The siRNAs selected based on their specificity and the corresponding short hairpin RNAs (shRNAs) subcloned in a lentiviral vector were evaluated ex vivo in Brtl fibroblasts for their effect on collagen transcripts and protein. A preferential reduction of the Mut allele of up to 52% was associated with about 40% decrease of the Mut protein, with no alteration of cell proliferation. Interestingly, a downregulation of HSP47, a specific collagen chaperone known to be upregulated in some OI cases, was detected. Our data support further testing of shRNAs and their delivery by lentivirus as a strategy to specifically suppress the Mut allele in mesenchymal stem cells of OI patients for autologous transplantation.
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Gaur U, Li K, Mei S, Liu G. Research progress in allele-specific expression and its regulatory mechanisms. J Appl Genet 2013; 54:271-83. [PMID: 23609142 DOI: 10.1007/s13353-013-0148-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/22/2013] [Accepted: 04/03/2013] [Indexed: 12/12/2022]
Abstract
Although the majority of genes are expressed equally from both alleles, some genes are differentially expressed. Organisms possess characteristics to preferentially express a particular allele under regulatory factors, which is termed allele-specific expression (ASE). It is one of the important genetic factors that lead to phenotypic variation and can be used to identify the variance of gene regulation factors. ASE indicates mechanisms such as DNA methylation, histone modifications, and non-coding RNAs function. Here, we review a broad survey of progress in ASE studies, and what this simple yet very effective approach can offer in functional genomics, and possible implications toward our better understanding of the underlying mechanisms of complex traits.
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Affiliation(s)
- Uma Gaur
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Yaoyuan No. 1, Nanhu, Hongshan District, Wuhan, 430064, People's Republic of China
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Hinderlich S, Weidemann W, Yardeni T, Horstkorte R, Huizing M. UDP-GlcNAc 2-Epimerase/ManNAc Kinase (GNE): A Master Regulator of Sialic Acid Synthesis. Top Curr Chem (Cham) 2013; 366:97-137. [PMID: 23842869 DOI: 10.1007/128_2013_464] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase is the key enzyme of sialic acid biosynthesis in vertebrates. It catalyzes the first two steps of the cytosolic formation of CMP-N-acetylneuraminic acid from UDP-N-acetylglucosamine. In this review we give an overview of structure, biochemistry, and genetics of the bifunctional enzyme and its complex regulation. Furthermore, we will focus on diseases related to UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase.
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Affiliation(s)
- Stephan Hinderlich
- Department of Life Sciences and Technology, Beuth Hochschule für Technik Berlin, University of Applied Sciences, Berlin, Germany,
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7
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Lowery JW, Rosen V. Allele-specific RNA interference in FOP silencing the FOP gene. Gene Ther 2011; 19:701-2. [PMID: 22130446 DOI: 10.1038/gt.2011.190] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Müller GA, Hansen U, Xu Z, Griswold B, Talan MI, McDonnell NB, Briest W. Allele-specific siRNA knockdown as a personalized treatment strategy for vascular Ehlers-Danlos syndrome in human fibroblasts. FASEB J 2011; 26:668-77. [PMID: 22038052 DOI: 10.1096/fj.11-182162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The vascular type of the Ehlers-Danlos syndrome (vEDS) is caused by dominant-negative mutations in the procollagen type III (COL3A1) gene. Patients with this autosomal dominant disorder have a shortened life expectancy due to complications from ruptured vessels or hollow organs. We tested the effectiveness of allele-specific RNA interference (RNAi) to reduce the mutated phenotype in fibroblasts. Small-interfering RNAs (siRNAs) discriminating between wild-type and mutant COL3A1 allele were identified by a luciferase reporter gene assay and in primary fibroblasts from a normal donor and a patient with vEDS. The best discriminative siRNA with the mutation at position 10 resulted in >90% silencing of the mutant allele without affecting the wild-type allele. Transmission and immunogold electron microscopy of extracted extracellular matrices from untreated fibroblasts of the patient with vEDS revealed structurally abnormal fibrils. After siRNA treatment, collagen fibrils became similar to fibrils from fibroblasts of normal and COL3A1 haploinsufficient donors. In addition, it was shown that expression of mutated COL3A1 activates the unfolded protein response and that reduction of the amount of mutated protein by siRNA reduces cellular stress. Taken together, the results provide evidence that allele-specific siRNAs are able to reduce negative effects of mutated COL3A1 proteins. Thus, the application of allele-specific RNAi may be a promising direction for future personalized therapies to reduce the severity of vEDS.
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Affiliation(s)
- Gerd A Müller
- Laboratory of Cardiovascular Sciences, National Institute on Aging, Baltimore, Maryland, USA
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Teng X, Liu JY, Li D, Fang Y, Wang XY, Ma YX, Chen SJ, Zhao YX, Xu WZ, Gu HX. Application of allele-specific RNAi in hepatitis B virus lamivudine resistance. J Viral Hepat 2011; 18:e491-8. [PMID: 21914068 DOI: 10.1111/j.1365-2893.2011.01483.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Understanding the consequences of mutation in the tyrosine-methionine-aspartate-aspartate (YMDD) motif of hepatitis B virus (HBV) genome on replication is critical for treating chronic hepatitis B with lamivudine. Allele-specific gene silencing by RNAi (allele-specific RNAi: ASP-RNAi) is an advanced application of RNAi techniques. Use of this strategy as a means for specifically inhibiting an allele expression of interest suggested that it can specifically suppress the expression of alleles causing disease without inhibiting the expression of corresponding wild-type alleles. However, no studies have used ASP-RNAi to address the issue of HBV lamivudine resistance. In this study, we applied ASP-RNAi into two long-term eukaryotic cell lines of full-length HBV containing either lamivudine-resistant mutants (HBV-YIDD) or wild type (HBV-WT) which we generated in previously. The designed siRNAs were also used in this eukaryotic expression system together with lamivudine. ELISA and real-time PCR were performed to monitor virus-specific protein synthesis and viral DNA replication. The results showed that the base substitutions conferring marked ASP-RNAi appeared to be largely present in positions 1, 3, 6, 11, 12, 15 and 19 of the sense strand of siRNAs which were different from the most sensitive positions of this application in eukaryotes. In addition, siRNA-lamivudine combinations did not possess the prominent anti-HBV activity we expected because of some unknown mechanisms. These findings recapitulated many of the features of ASP-RNAi in hepadnaviruses which provided a new insight into the development of a potent strategy against HBV drug resistance.
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Affiliation(s)
- X Teng
- Department of Microbiology, Harbin Medical University, Harbin, China
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Hickerson RP, Leachman SA, Pho LN, Gonzalez-Gonzalez E, Smith FJD, McLean WHI, Contag CH, Leake D, Milstone LM, Kaspar RL. Development of quantitative molecular clinical end points for siRNA clinical trials. J Invest Dermatol 2010; 131:1029-36. [PMID: 21191405 DOI: 10.1038/jid.2010.372] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is an evolutionarily conserved mechanism that results in specific gene inhibition at the mRNA level. The discovery that short interfering RNAs (siRNAs) are selective, potent, and can largely avoid immune surveillance has resulted in keen interest to develop these inhibitors as therapeutics. A single nucleotide-specific siRNA (K6a_513a.12, also known as TD101) was recently evaluated in a phase 1b clinical trial for the rare skin disorder, pachyonychia congenita (PC). To develop a clinical trial molecular end point for this type of trial, methods were developed to: (1) isolate total RNA containing amplifiable mRNA from human skin and callus material; (2) quantitatively distinguish the single-nucleotide mutant mRNA from wild-type K6a mRNA in both patient-derived keratinocytes and patient callus; and (3) demonstrate that repeated siRNA treatment results in sustained inhibition of mutant K6a mRNA in patient-derived keratinocyte cultures. These methods allow noninvasive sampling and monitoring of gene expression from patient-collected shavings and may be useful in evaluating the effectiveness of RNAi-based therapeutics, including inhibitors that specifically target single-nucleotide mutations.
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Huang H, Qiao R, Zhao D, Zhang T, Li Y, Yi F, Lai F, Hong J, Ding X, Yang Z, Zhang L, Du Q, Liang Z. Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs. Nucleic Acids Res 2010; 37:7560-9. [PMID: 19815667 PMCID: PMC2794185 DOI: 10.1093/nar/gkp835] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Silencing specificity is a critical issue in the therapeutic applications of siRNA, particularly in the treatment of single nucleotide polymorphism (SNP) diseases where discrimination against single nucleotide variation is demanded. However, no generally applicable guidelines are available for the design of such allele-specific siRNAs. In this paper, the issue was approached by using a reporter-based assay. With a panel of 20 siRNAs and 240 variously mismatched target reporters, we first demonstrated that the mismatches were discriminated in a position-dependent order, which was however independent of their sequence contexts using position 4th, 12th and 17th as examples. A general model was further built for mismatch discrimination at all positions using 230 additional reporter constructs specifically designed to contain mismatches distributed evenly along the target regions of different siRNAs. This model was successfully employed to design allele-specific siRNAs targeting disease-causing mutations of PIK3CA gene at two SNP sites. Furthermore, conformational distortion of siRNA-target duplex was observed to correlate with the compromise of gene silencing. In summary, these findings could dramatically simplify the design of allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs.
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Affiliation(s)
- Huang Huang
- Institute of Molecular Medicine, Peking University, Beijing 100871, China
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