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New Drug Targets to Prevent Death Due to Stroke: A Review Based on Results of Protein-Protein Interaction Network, Enrichment, and Annotation Analyses. Int J Mol Sci 2021; 22:ijms222212108. [PMID: 34829993 PMCID: PMC8619767 DOI: 10.3390/ijms222212108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/07/2023] Open
Abstract
This study used established biomarkers of death from ischemic stroke (IS) versus stroke survival to perform network, enrichment, and annotation analyses. Protein-protein interaction (PPI) network analysis revealed that the backbone of the highly connective network of IS death consisted of IL6, ALB, TNF, SERPINE1, VWF, VCAM1, TGFB1, and SELE. Cluster analysis revealed immune and hemostasis subnetworks, which were strongly interconnected through the major switches ALB and VWF. Enrichment analysis revealed that the PPI immune subnetwork of death due to IS was highly associated with TLR2/4, TNF, JAK-STAT, NOD, IL10, IL13, IL4, and TGF-β1/SMAD pathways. The top biological and molecular functions and pathways enriched in the hemostasis network of death due to IS were platelet degranulation and activation, the intrinsic pathway of fibrin clot formation, the urokinase-type plasminogen activator pathway, post-translational protein phosphorylation, integrin cell-surface interactions, and the proteoglycan-integrin extracellular matrix complex (ECM). Regulation Explorer analysis of transcriptional factors shows: (a) that NFKB1, RELA and SP1 were the major regulating actors of the PPI network; and (b) hsa-mir-26-5p and hsa-16-5p were the major regulating microRNA actors. In conclusion, prevention of death due to IS should consider that current IS treatments may be improved by targeting VWF, the proteoglycan-integrin-ECM complex, TGF-β1/SMAD, NF-κB/RELA and SP1.
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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] [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.
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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:
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Alpha-mannosidosis in Tunisian consanguineous families: Potential involvement of variants in GHR and SLC19A3 genes in the variable expressivity of cognitive impairment. PLoS One 2021; 16:e0258202. [PMID: 34614013 PMCID: PMC8494324 DOI: 10.1371/journal.pone.0258202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 09/21/2021] [Indexed: 01/30/2023] Open
Abstract
Alpha-Mannosidosis (AM) is an ultra-rare storage disorder caused by a deficiency of lysosomal alpha-mannosidase encoded by the MAN2B1 gene. Clinical presentation of AM includes mental retardation, recurrent infections, hearing loss, dysmorphic features, and motor dysfunctions. AM has never been reported in Tunisia. We report here the clinical and genetic study of six patients from two Tunisian families with AM. The AM diagnosis was confirmed by an enzymatic activity assay. Genetic investigation was conducted by Sanger sequencing of the mutational hotspots for the first family and by ES analysis for the second one. In the first family, a frameshift duplication p.(Ser802GlnfsTer129) was identified in the MAN2B1 gene. For the second family, ES analysis led to the identification of a missense mutation p.(Arg229Trp) in the MAN2B1 gene in four affected family members. The p.(Ser802GlnfsTer129) mutation induces a premature termination codon which may trigger RNA degradation by the NMD system. The decrease in the levels of MAN2B1 synthesis could explain the severe phenotype observed in the index case. According to the literature, the p.(Arg229Trp) missense variant does not have an impact on MAN2B1 maturation and transportation, which correlates with a moderate clinical sub-type. To explain the intra-familial variability of cognitive impairment, exome analysis allowed the identification of two likely pathogenic variants in GHR and SLC19A3 genes potentially associated to cognitive decline. The present study raises awareness about underdiagnosis of AM in the region that deprives patients from accessing adequate care. Indeed, early diagnosis is critical in order to prevent disease progression and to propose enzyme replacement therapy.
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Cancer predisposition and germline CTNNA1 variants. Eur J Med Genet 2021; 64:104316. [PMID: 34425242 DOI: 10.1016/j.ejmg.2021.104316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/16/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022]
Abstract
Hereditary Diffuse Gastric Cancer (HDGC) is a cancer predisposing syndrome mainly caused by germline inactivating variants in CDH1, encoding E-cadherin. Early-onset diffuse gastric cancer (DGC) and/or invasive lobular breast cancer (LBC) are the main phenotypes in CDH1-associated HDGC. CTNNA1, encoding for α-E-catenin, and E-cadherin-partner in the adherens junction complex, has been recently classified as a HDGC predisposing gene. Nevertheless, little is known about CTNNA1 tumor spectrum in variant carriers and variant-type associated causality. Herein, we systematically reviewed the literature searching for CTNNA1 germline variants carriers, further categorized them according to HDGC clinical criteria (HDGC vs non-HDGC), collected phenotypes, classified variants molecularly and according to CDH1 ACMG/AMP guidelines and performed genotype-phenotype analysis. We found 41 families carrying CTNNA1 germline variants encompassing in total 105 probands and relatives. All probands from 13 HDGC families presented DGC and their average age of onset was 40 ± 17 years; 10/13 (77%) HDGC families carried a pathogenic (P) variant. Most probands from 28 non-HDGC families developed unspecified-BC, as well as most of their relatives; 4/28 (14%) carried a P variant, 16/28 (57%) carried a likely pathogenic (LP) variant, 7/28 (25%) carried variants of unknown significance (VUS) and 1/28 (4%) carried a likely benign variant. Regardless of clinical criteria, 97% (32/33) of probands and relatives from P variant-carrier families had DGC/unspecified-GC. In LP variant-carrier families, 82% (28/34) of probands and relatives had unspecified-BC. Only 2/105 individuals had LBC. A cluster of frameshift and nonsense variants was found in CTNNA1 last exon of non-HDGC families and classified as VUS. In conclusion, current available data confirms an association of CTNNA1 P variants with early-onset DGC, but not with LBC. We demonstrate that in ascertained cohorts, CTNNA1 P variants explain <2% of HDGC families and support the use of ACMG/AMP CDH1 specific variant curation guidelines, while no specific guidelines are developed for CTNNA1 variant classification. Moreover, we demonstrated that truncating variants at the CTNNA1 NMD-incompetent last exon have limited deleteriousness, and that CTNNA1 LP variants have lower actionability than CDH1 LP variants. Current knowledge supports considering only CTNNA1 P variants as clinically actionable in HDGC carrying families.
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Teran NA, Nachun DC, Eulalio T, Ferraro NM, Smail C, Rivas MA, Montgomery SB. Nonsense-mediated decay is highly stable across individuals and tissues. Am J Hum Genet 2021; 108:1401-1408. [PMID: 34216550 DOI: 10.1016/j.ajhg.2021.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022] Open
Abstract
Precise interpretation of the effects of rare protein-truncating variants (PTVs) is important for accurate determination of variant impact. Current methods for assessing the ability of PTVs to induce nonsense-mediated decay (NMD) focus primarily on the position of the variant in the transcript. We used RNA sequencing of the Genotype Tissue Expression v.8 cohort to compute the efficiency of NMD using allelic imbalance for 2,320 rare (genome aggregation database minor allele frequency ≤ 1%) PTVs across 809 individuals in 49 tissues. We created an interpretable predictive model using penalized logistic regression in order to evaluate the comprehensive influence of variant annotation, tissue, and inter-individual variation on NMD. We found that variant position, allele frequency, the inclusion of ultra-rare and singleton variants, and conservation were predictive of allelic imbalance. Furthermore, we found that NMD effects were highly concordant across tissues and individuals. Due to this high consistency, we demonstrate in silico that utilizing peripheral tissues or cell lines provides accurate prediction of NMD for PTVs.
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Xie Z, Jiang J, Cao L, Jiang M, Yang F, Ma Z, Wang Z, Ruan C, Liu H, Zhou L. Nonsense-mediated mRNA decay efficiency influences bleeding severity in ITGA2B c.2659C > T (p.Q887X) knock-in mice. Clin Genet 2021; 100:213-218. [PMID: 33928629 DOI: 10.1111/cge.13975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Glanzmann's thrombasthenia (GT) is a severe hemorrhagic disease. It is caused by mutations in ITGA2B or ITGB3, which are the respective genes encoding integrin αIIb and β3. Despite widespread mutational analysis, the mechanisms underlying the extensive variability in bleeding severity observed among affected individuals remains poorly understood. In order to explore the mechanisms conferring for bleeding heterogeneity, three GT patients with ITGA2B c.2671C > T (p.Q891X) who possessed different bleeding scores were studied. Analysis showed that there was significant difference in nonsense-mediated mRNA decay (NMD) efficiency among the three patients. These differences positively correlated with their bleeding score. Next, a knock-in mouse model (KI mice) with the ITGA2B c.2659C > T (p.Q887X) was generated using CRISPR/Cas9. Importantly, this mutation is homologous to ITGA2B c.2671C > T (p.Q891X) in humans. The bleeding time of KI mice was significantly in comparison to the wide-type mice. Interestingly, bleeding was stopped after treatment with caffeine, which is a known NMD inhibitor. This suggests that NMD efficiency potentially influences bleeding severity in ITGA2B c.2659C > T (p.Q887X) KI mice.
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Affiliation(s)
- Zhanli Xie
- Department of Nuclear Medicine, Institute of Clinical Medicine Research, Suzhou Hospital (West District), Affiliated to Nanjing Medical University, Suzhou Science and Technology Town Hospital, Suzhou, China
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiang Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Cao
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Miao Jiang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fei Yang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenni Ma
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhaoyue Wang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Changgeng Ruan
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Liu
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
| | - Lu Zhou
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
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Schilff M, Sargsyan Y, Hofhuis J, Thoms S. Stop Codon Context-Specific Induction of Translational Readthrough. Biomolecules 2021; 11:biom11071006. [PMID: 34356630 PMCID: PMC8301745 DOI: 10.3390/biom11071006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
Premature termination codon (PTC) mutations account for approximately 10% of pathogenic variants in monogenic diseases. Stimulation of translational readthrough, also known as stop codon suppression, using translational readthrough-inducing drugs (TRIDs) may serve as a possible therapeutic strategy for the treatment of genetic PTC diseases. One important parameter governing readthrough is the stop codon context (SCC)-the stop codon itself and the nucleotides in the vicinity of the stop codon on the mRNA. However, the quantitative influence of the SCC on treatment outcome and on appropriate drug concentrations are largely unknown. Here, we analyze the readthrough-stimulatory effect of various readthrough-inducing drugs on the SCCs of five common premature termination codon mutations of PEX5 in a sensitive dual reporter system. Mutations in PEX5, encoding the peroxisomal targeting signal 1 receptor, can cause peroxisomal biogenesis disorders of the Zellweger spectrum. We show that the stop context has a strong influence on the levels of readthrough stimulation and impacts the choice of the most effective drug and its concentration. These results highlight potential advantages and the personalized medicine nature of an SCC-based strategy in the therapy of rare diseases.
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Affiliation(s)
- Mirco Schilff
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
| | - Yelena Sargsyan
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
| | - Julia Hofhuis
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
- Department of Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615 Bielefeld, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
- Department of Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615 Bielefeld, Germany
- Correspondence: ; Tel.: +49-521-106-86502
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Derksen A, Shih HY, Forget D, Darbelli L, Tran LT, Poitras C, Guerrero K, Tharun S, Alkuraya FS, Kurdi WI, Nguyen CTE, Laberge AM, Si Y, Gauthier MS, Bonkowsky JL, Coulombe B, Bernard G. Variants in LSM7 impair LSM complexes assembly, neurodevelopment in zebrafish and may be associated with an ultra-rare neurological disease. HGG ADVANCES 2021; 2:100034. [PMID: 35047835 PMCID: PMC8756503 DOI: 10.1016/j.xhgg.2021.100034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 11/15/2022] Open
Abstract
Leukodystrophies, genetic neurodevelopmental and/or neurodegenerative disorders of cerebral white matter, result from impaired myelin homeostasis and metabolism. Numerous genes have been implicated in these heterogeneous disorders; however, many individuals remain without a molecular diagnosis. Using whole-exome sequencing, biallelic variants in LSM7 were uncovered in two unrelated individuals, one with a leukodystrophy and the other who died in utero. LSM7 is part of the two principle LSM protein complexes in eukaryotes, namely LSM1-7 and LSM2-8. Here, we investigate the molecular and functional outcomes of these LSM7 biallelic variants in vitro and in vivo. Affinity purification-mass spectrometry of the LSM7 variants showed defects in the assembly of both LSM complexes. Lsm7 knockdown in zebrafish led to central nervous system defects, including impaired oligodendrocyte development and motor behavior. Our findings demonstrate that variants in LSM7 cause misassembly of the LSM complexes, impair neurodevelopment of the zebrafish, and may be implicated in human disease. The identification of more affected individuals is needed before the molecular mechanisms of mRNA decay and splicing regulation are added to the categories of biological dysfunctions implicated in leukodystrophies, neurodevelopmental and/or neurodegenerative diseases.
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Supek F, Lehner B, Lindeboom RG. To NMD or Not To NMD: Nonsense-Mediated mRNA Decay in Cancer and Other Genetic Diseases. Trends Genet 2021; 37:657-668. [DOI: 10.1016/j.tig.2020.11.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
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Xiang X, Zhao X, Pan X, Dong Z, Yu J, Li S, Liang X, Han P, Qu K, Jensen JB, Farup J, Wang F, Petersen TS, Bolund L, Teng H, Lin L, Luo Y. Efficient correction of Duchenne muscular dystrophy mutations by SpCas9 and dual gRNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:403-415. [PMID: 33868784 PMCID: PMC8039775 DOI: 10.1016/j.omtn.2021.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 03/10/2021] [Indexed: 12/17/2022]
Abstract
CRISPR gene therapy is one promising approach for treatment of Duchenne muscular dystrophy (DMD), which is caused by a large spectrum of mutations in the dystrophin gene. To broaden CRISPR gene editing strategies for DMD treatment, we report the efficient restoration of dystrophin expression in induced myotubes by SpCas9 and dual guide RNAs (gRNAs). We first sequenced 32 deletion junctions generated by this editing method and revealed that non-homologous blunt-end joining represents the major indel type. Based on this predictive repair outcome, efficient in-frame deletion of a part of DMD exon 51 was achieved in HEK293T cells with plasmids expressing SpCas9 and dual gRNAs. More importantly, we further corrected a frameshift mutation in human DMD (exon45del) fibroblasts with SpCas9-dual gRNA ribonucleoproteins. The edited DMD fibroblasts were transdifferentiated into myotubes by lentiviral-mediated overexpression of a human MYOD transcription factor. Restoration of DMD expression at both the mRNA and protein levels was confirmed in the induced myotubes. With further development, the combination of SpCas9-dual gRNA-corrected DMD patient fibroblasts and transdifferentiation may provide a valuable therapeutic strategy for DMD.
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Affiliation(s)
- Xi Xiang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Xiaoying Zhao
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Zhanying Dong
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Jiaying Yu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Siyuan Li
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xue Liang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
| | - Jonas Brorson Jensen
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Jean Farup
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Fei Wang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | | | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Huajing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
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Zhang S, Xu H, Tian Y, Liu D, Hou X, Zeng B, Chen B, Liu H, Li R, Li X, Zuo B, Tang R, Tang W. High Genetic Heterogeneity in Chinese Patients With Waardenburg Syndrome Revealed by Next-Generation Sequencing. Front Genet 2021; 12:643546. [PMID: 34149797 PMCID: PMC8212959 DOI: 10.3389/fgene.2021.643546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Objective This study aimed to explore the genetic causes of probands who were diagnosed with Waardenburg syndrome (WS) or congenital sensorineural hearing loss. Methods A detailed physical and audiological examinations were carried out to make an accurate diagnosis of 14 patients from seven unrelated families. We performed whole-exome sequencing in probands to detect the potential genetic causes and further validated them by Sanger sequencing in the probands and their family members. Results The genetic causes for all 14 patients with WS or congenital sensorineural hearing loss were identified. A total of seven heterozygous variants including c.1459C > T, c.123del, and c.959-409_1173+3402del of PAX3 gene (NM_181459.4), c.198_262del and c.529_556del of SOX10 gene (NM_006941.4), and c.731G > A and c.970dup of MITF gene (NM_000248.3) were found for the first time. Of these mutations, we had confirmed two (c.1459C > T and c.970dup) are de novo by Sanger sequencing of variants in the probands and their parents. Conclusion We revealed a total of seven novel mutations in PAX3, SOX10, and MITF, which underlie the pathogenesis of WS. The clinical and genetic characterization of these families with WS elucidated high heterogeneity in Chinese patients with WS. This study expands the database of PAX3, SOX10, and MITF mutations and improves our understanding of the causes of WS.
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Affiliation(s)
- Sen Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongan Tian
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Danhua Liu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinyue Hou
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Beiping Zeng
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Bei Chen
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanfei Liu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Ruijun Li
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xiaohua Li
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bin Zuo
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ryan Tang
- Johns Hopkins University, Maryland, MD, United States
| | - Wenxue Tang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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Shen Y, Shu S, Ren Y, Xia W, Chen J, Dong L, Ge H, Fan S, Shi L, Peng B, Zhang X. Case Report: Two Novel Frameshift Mutations in SLC20A2 and One Novel Splice Donor Mutation in PDGFB Associated With Primary Familial Brain Calcification. Front Genet 2021; 12:643452. [PMID: 34025715 PMCID: PMC8138311 DOI: 10.3389/fgene.2021.643452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Primary familial brain calcification (PFBC, OMIM#213600), also known as Fahr's disease, is characterized by bilateral and symmetric brain calcification in the basal ganglia (globus pallidus, caudate nucleus, and putamen), thalamus, subcortical white matter, and cerebellum. PFBC can be caused by loss-of-function mutations in any of the six known causative genes. The most common clinical manifestations include movement disorders, cognitive impairment, and neuropsychiatric signs that gradually emerge in middle-aged patients. To broaden the PFBC mutation spectrum, we examined nine members of a family with PFBC and two sporadic cases from clinical departments, and sequenced all PFBC-causative genes in the index case. Two novel frameshift mutations in SLC20A2 [NM_001257180.2; c.806delC, p.(Pro269Glnfs*49) and c.1154delG, p.(Ser385Ilefs*70)] and one novel splice donor site mutation (NM_002608.4, c.456+1G>C, r.436_456del) in PDGFB were identified in the patient cohort. c.806delC co-segregated with brain calcification and led to SLC20A2 haploinsufficiency among the affected family members. The c.456+1G>C mutation in PDGFB resulted in aberrant mRNA splicing, thereby forming mature transcripts containing an in-frame 21 base pair (bp) deletion, which might create a stably truncated protein [p.(Val146_Gln152del)] and exert a dominant negative effect on wild-type PDGFB. All three mutations were located in highly conserved regions among multiple species and predicted to be pathogenic, as evaluated by at least eight common genetic variation scoring systems. This study identified three novel mutations in SLC20A2 and PDGFB, which broadened and enriched the PFBC mutation spectrum.
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Affiliation(s)
- Yuqi Shen
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China
| | - Shi Shu
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China.,Department of Neurology, Peking Union Medical College Hospital (PUMCH), CAMS&PUMC, Beijing, China
| | - Yaqiong Ren
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China
| | - Weibo Xia
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, PUMCH, CAMS&PUMC, Beijing, China
| | - Jianhua Chen
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), CAMS&PUMC, Beijing, China
| | - Liling Dong
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), CAMS&PUMC, Beijing, China
| | - Haijun Ge
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China
| | - Shiqi Fan
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China
| | - Lei Shi
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China.,National Health Commission (NHC) and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, China
| | - Bin Peng
- Department of Neurology, Peking Union Medical College Hospital (PUMCH), CAMS&PUMC, Beijing, China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS&PUMC), Beijing, China.,National Health Commission (NHC) and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, China
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Montaser H, Patel KA, Balboa D, Ibrahim H, Lithovius V, Näätänen A, Chandra V, Demir K, Acar S, Ben-Omran T, Colclough K, Locke JM, Wakeling M, Lindahl M, Hattersley AT, Saarimäki-Vire J, Otonkoski T. Loss of MANF Causes Childhood-Onset Syndromic Diabetes Due to Increased Endoplasmic Reticulum Stress. Diabetes 2021; 70:1006-1018. [PMID: 33500254 PMCID: PMC7610619 DOI: 10.2337/db20-1174] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023]
Abstract
Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-resident protein that plays a crucial role in attenuating ER stress responses. Although MANF is indispensable for the survival and function of mouse β-cells, its precise role in human β-cell development and function is unknown. In this study, we show that lack of MANF in humans results in diabetes due to increased ER stress, leading to impaired β-cell function. We identified two patients from different families with childhood diabetes and a neurodevelopmental disorder associated with homozygous loss-of-function mutations in the MANF gene. To study the role of MANF in human β-cell development and function, we knocked out the MANF gene in human embryonic stem cells and differentiated them into pancreatic endocrine cells. Loss of MANF induced mild ER stress and impaired insulin-processing capacity of β-cells in vitro. Upon implantation to immunocompromised mice, the MANF knockout grafts presented elevated ER stress and functional failure, particularly in recipients with diabetes. By describing a new form of monogenic neurodevelopmental diabetes syndrome caused by disturbed ER function, we highlight the importance of adequate ER stress regulation for proper human β-cell function and demonstrate the crucial role of MANF in this process.
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Affiliation(s)
- Hossam Montaser
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, U.K.
| | - Diego Balboa
- Bioinformatics and Genomics Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hazem Ibrahim
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Väinö Lithovius
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Näätänen
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vikash Chandra
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Korcan Demir
- Department of Pediatric Endocrinology, Dokuz Eylül University, Izmir, Turkey
| | - Sezer Acar
- Department of Pediatric Endocrinology, Dokuz Eylül University, Izmir, Turkey
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
- Department of Pediatrics, Weill Cornell Medical College, Doha, Qatar
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar
| | - Kevin Colclough
- Department of Molecular Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, U.K
| | - Jonathan M Locke
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, U.K
| | - Matthew Wakeling
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, U.K
| | - Maria Lindahl
- Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, U.K
| | - Jonna Saarimäki-Vire
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Abstract
Werner syndrome, also called adult progeria, is a heritable autosomal recessive human disorder characterized by the premature onset of numerous age-related diseases including juvenile cataracts, dyslipidemia, diabetes mellitus (DM), osteoporosis, atherosclerosis, and cancer. Werner syndrome is a segmental progeroid syndrome whose presentation resembles accelerated aging. The most common causes of death for WS patients are atherosclerosis and cancer. A 40-year-old female presented with short stature, bird-like facies, canities with alopecia, scleroderma-like skin changes, and non-healing foot ulcers. The patient reported a history of delayed puberty, abortion, hypertriglyceridemia, and juvenile cataracts. A clinical diagnosis of WS was made and subsequently confirmed. We discovered two WRN gene mutations in the patient, Variant 1 was the most common WRN mutation, nonsense mutation (c.1105C>T:p.R369Ter) in exon 9, which caused a premature termination codon (PTC) at position 369. Variant 2 was a frameshift mutation (c.1134delA:p.E379KfsTer5) in exon 9, which caused a PTC at position 383 and has no published reports describing. Patients with WS can show a wide variety of clinical and biological manifestations in endocrine-metabolic systems (DM, thyroid dysfunction, and hyperlipidemia). Doctors must be cognizant of early manifestations of WS and treatment options.
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Affiliation(s)
- Huan Li
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Maoguang Yang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Hong Shen
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Sisi Wang
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Hanqing Cai
- Department of Endocrinology, The Second Hospital of Jilin University, Changchun, Jilin, China
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Zhu Q, Rui X, Li Y, You Y, Sheng XL, Lei B. Identification of Four Novel Variants and Determination of Genotype-Phenotype Correlations for ABCA4 Variants Associated With Inherited Retinal Degenerations. Front Cell Dev Biol 2021; 9:634843. [PMID: 33732702 PMCID: PMC7957020 DOI: 10.3389/fcell.2021.634843] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose The purpose of the study is to describe the genetic and clinical features of 17 patients with ABCA4-related inherited retinal degenerations (IRDs) and define the phenotype–genotype correlations. Methods In this multicenter retrospective study, 17 patients from 16 families were enrolled, and ABCA4 gene variants were detected using targeted next-generation sequencing using a custom designed panel for IRDs. Sanger sequencing and co-segregation analysis of the suspected pathogenic variants were performed with the family members. The pathogenicities of variants were evaluated according to the American College of Medical Genetics and Genomics guidelines (ACMG). Protein structure modifications mediated by the variants were studied using bioinformatic analyses. Results The probands were diagnosed with Stargardt disease 1 (7), cone-rod dystrophy type 3 (8), cone dystrophy (1), and retinitis pigmentosa 19 (1). Onset of symptoms occurred between 5 and 27 years of age (median age = 12.4 years). A total of 30 unique ABCA4 suspicious pathogenic variations were observed, including 18 missense mutations, seven frameshift mutations, two nonsense mutations, one canonical splice site mutation, one small in-frame deletion, and one insertion. Four novel ABCA4 variants were identified. Two novel frameshift variants, c.1290dupC (p.W431fs), and c.2967dupT (G990fs), were determined to be pathogenic. A novel missense variant c.G5761T (p.V1921L) was likely pathogenic, and another novel missense c.C170G (p.P57R) variant was of undetermined significance. All ABCA4 variants tested in this study inordinately changed the physico-chemical parameters and structure of protein based on in silico analysis. Conclusion ABCA4-related IRD is genetically and clinically highly heterogeneous. Four novel ABCA4 variants were identified. This study will expand the spectrum of disease-causing variants in ABCA4, which will further facilitate genetic counseling.
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Affiliation(s)
- Qing Zhu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xue Rui
- Ningxia Clinical Research Center of Blinding Eye Disease, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Yinchuan, China
| | - Ya Li
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute and Henan Eye Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ya You
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute and Henan Eye Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xun-Lun Sheng
- Ningxia Clinical Research Center of Blinding Eye Disease, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Yinchuan, China
| | - Bo Lei
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute and Henan Eye Hospital, Henan Provincial People's Hospital, Zhengzhou, China
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66
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Artero-Castro A, Long K, Bassett A, Ávila-Fernandez A, Cortón M, Vidal-Puig A, Jendelova P, Rodriguez-Jimenez FJ, Clemente E, Ayuso C, Erceg S. Gene Correction Recovers Phagocytosis in Retinal Pigment Epithelium Derived from Retinitis Pigmentosa-Human-Induced Pluripotent Stem Cells. Int J Mol Sci 2021; 22:ijms22042092. [PMID: 33672445 PMCID: PMC7923278 DOI: 10.3390/ijms22042092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022] Open
Abstract
Hereditary retinal dystrophies (HRD) represent a significant cause of blindness, affecting mostly retinal pigment epithelium (RPE) and photoreceptors (PRs), and currently suffer from a lack of effective treatments. Highly specialized RPE and PR cells interact mutually in the functional retina, therefore primary HRD affecting one cell type leading to a secondary HRD in the other cells. Phagocytosis is one of the primary functions of the RPE and studies have discovered that mutations in the phagocytosis-associated gene Mer tyrosine kinase receptor (MERTK) lead to primary RPE dystrophy. Treatment strategies for this rare disease include the replacement of diseased RPE with healthy autologous RPE to prevent PR degeneration. The generation and directed differentiation of patient-derived human-induced pluripotent stem cells (hiPSCs) may provide a means to generate autologous therapeutically-relevant adult cells, including RPE and PR. However, the continued presence of the MERTK gene mutation in patient-derived hiPSCs represents a significant drawback. Recently, we reported the generation of a hiPSC model of MERTK-associated Retinitis Pigmentosa (RP) that recapitulates disease phenotype and the subsequent creation of gene-corrected RP-hiPSCs using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9. In this study, we differentiated gene-corrected RP-hiPSCs into RPE and found that these cells had recovered both wild-type MERTK protein expression and the lost phagocytosis of fluorescently-labeled photoreceptor outer segments observed in uncorrected RP-hiPSC-RPE. These findings provide proof-of-principle for the utility of gene-corrected hiPSCs as an unlimited cell source for personalized cell therapy of rare vision disorders.
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Affiliation(s)
- Ana Artero-Castro
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Centro de Investigación Principe Felipe (CIPF), 46012 Valencia, Spain; (A.A.-C.); (F.J.R.-J.); (E.C.)
| | - Kathleen Long
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; (K.L.); (A.B.)
| | - Andrew Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; (K.L.); (A.B.)
| | - Almudena Ávila-Fernandez
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, (IIS-FJD, UAM), 28040 Madrid, Spain; (A.Á.-F.); (M.C.); (C.A.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Marta Cortón
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, (IIS-FJD, UAM), 28040 Madrid, Spain; (A.Á.-F.); (M.C.); (C.A.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Antonio Vidal-Puig
- Metabolic Research Laboratories, Wellcome Trust MRC Institute of Metabolic Science, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK;
| | - Pavla Jendelova
- Institute of Experimental Medicine, Department of Neuroregeneration, Czech Academy of Science, 14220 Prague, Czech Republic;
| | - Francisco Javier Rodriguez-Jimenez
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Centro de Investigación Principe Felipe (CIPF), 46012 Valencia, Spain; (A.A.-C.); (F.J.R.-J.); (E.C.)
| | - Eleonora Clemente
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Centro de Investigación Principe Felipe (CIPF), 46012 Valencia, Spain; (A.A.-C.); (F.J.R.-J.); (E.C.)
| | - Carmen Ayuso
- Department of Genetics and Genomics, IIS-Fundación Jiménez Díaz, (IIS-FJD, UAM), 28040 Madrid, Spain; (A.Á.-F.); (M.C.); (C.A.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Slaven Erceg
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Centro de Investigación Principe Felipe (CIPF), 46012 Valencia, Spain; (A.A.-C.); (F.J.R.-J.); (E.C.)
- Institute of Experimental Medicine, Department of Neuroregeneration, Czech Academy of Science, 14220 Prague, Czech Republic;
- National Stem Cell Bank-Valencia Node, Proteomics, Genotyping and Cell Line Platform, PRB3, ISCIII, Research Centre Principe Felipe, c/ Eduardo Primo Yúfera 3, 46012 Valencia, Spain
- Correspondence: ; Tel.: +34-963-289-680 (ext. 1102)
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Ahn LY, Coatti GC, Liu J, Gumus E, Schaffer AE, Miranda HC. An epilepsy-associated ACTL6B variant captures neuronal hyperexcitability in a human induced pluripotent stem cell model. J Neurosci Res 2021; 99:110-123. [PMID: 33141462 PMCID: PMC7756336 DOI: 10.1002/jnr.24747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 01/01/2023]
Abstract
ACTL6B is a component of the neuronal BRG1/brm-associated factor (nBAF) complex, which is required for chromatin remodeling in postmitotic neurons. We recently reported biallelic pathogenic variants in ACTL6B in patients diagnosed with early infantile epileptic encephalopathy, subtype 76 (EIEE-76), presenting with severe, global developmental delay, epileptic encephalopathy, cerebral atrophy, and abnormal central nervous system myelination. However, the pathophysiological mechanisms underlying their phenotype is unknown. Here, we investigate the molecular pathogenesis of ACTL6B p.(Val421_Cys425del) using in silico 3D protein modeling predictions and patient-specific induced pluripotent stem cell-derived neurons. We found neurons derived from EIEE-76 patients showed impaired accumulation of ACTL6B compared to unaffected relatives, caused by reduced protein stability. Furthermore, EIEE-76 patient-derived neurons had dysregulated nBAF target gene expression, including genes important for neuronal development and disease. Multielectrode array system analysis unveiled elevated electrophysiological activity of EIEE-76 patients-derived neurons, consistent with the patient phenotype. Taken together, our findings validate a new model for EIEE-76 and reveal how reduced ACTL6B expression affects neuronal function.
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Affiliation(s)
- Lucie Y. Ahn
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA,Medical Scientist Training ProgramCase Western Reserve UniversityClevelandOHUSA
| | - Giuliana C. Coatti
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA
| | - Jingyi Liu
- Department of PathologyCase Western Reserve UniversityClevelandOHUSA
| | - Evren Gumus
- Department of Medical GeneticsFaculty of MedicineMugla Sitki Kocman UniversityMuglaTurkey,Department of Medical GeneticsFaculty of MedicineUniversity of HarranSanliurfaTurkey
| | - Ashleigh E. Schaffer
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA,Center for RNA Science and TherapeuticsCase Western Reserve UniversityClevelandOHUSA
| | - Helen C. Miranda
- Department of Genetics and Genome SciencesCase Western Reserve UniversityClevelandOHUSA,Department of NeurosciencesCase Western Reserve UniversityClevelandOHUSA
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Park PG, Lim SH, Lee H, Ahn YH, Cheong HI, Kang HG. Genotype and Phenotype Analysis in X-Linked Hypophosphatemia. Front Pediatr 2021; 9:699767. [PMID: 34434907 PMCID: PMC8382157 DOI: 10.3389/fped.2021.699767] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/08/2021] [Indexed: 11/13/2022] Open
Abstract
Background: X-linked hypophosphatemia (XLH) is the most frequent form of hypophosphatemic rickets and is caused by mutations in the PHEX gene. We analyzed genotype-phenotype correlations in XLH patients with proven PHEX mutations. Methods: PHEX mutations were detected in 55 out of 81 patients who clinically presented with hypophosphatemic rickets. The patients were grouped into nontruncating (n = 9) and truncating (n = 46) mutation groups; their initial presentation as well as long-term clinical findings were evaluated according to these groups. Results: Initial findings, including presenting symptoms, onset age, height standard deviation scores (SDS), and laboratory tests, including serum phosphate level and tubular resorption of phosphate, were not significantly different between the two groups (onset age: nontruncating mutation group, 2.0 years, truncating mutation group, 2.2 years; height SDS: nontruncating mutation group, -1.9, truncating mutation group, -1.7; serum phosphate: nontruncating mutation group, 2.5 mg/dL, truncating mutation group, 2.6 mg/dL). However, at their last follow-up, the serum phosphate level was significantly lower in patients with truncating mutations (nontruncating mutation group: 3.2 mg/dl, truncating mutation group: 2.3 mg/dl; P = 0.006). Additionally, 62.5% of patients with truncating mutations developed nephrocalcinosis at their last follow-up, while none of the patients with nontruncating mutations developed nephrocalcinosis (P = 0.015). Orthopedic surgery due to bony deformations was performed significantly more often in patients with truncating mutations (52.3 vs. 10.0%, P = 0.019). Conclusion: Although considerable inconsistency exists regarding the correlation of truncating mutations and their disease phenotype in several other studies, we cautiously suggest that there would be genotype-phenotype correlation in some aspects of disease manifestation after long-term follow-up. This information can be used when consulting patients with confirmed XLH regarding their disease prognosis.
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Affiliation(s)
| | - Seon Hee Lim
- Department of Pediatrics, Uijeongbu Eulji Medical Center, Uijeongbu, South Korea
| | - HyunKyung Lee
- Department of Pediatrics, Kangwon National University Hopsital, Chuncheon, South Korea
| | - Yo Han Ahn
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pediatrics, Seoul National University Children's Hospital, Seoul, South Korea.,Kidney Research Institute, Seoul National University Medical Research Center, Seoul, South Korea
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pediatrics, Hallym University Sacred Heart Hospital, Seoul, South Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pediatrics, Seoul National University Children's Hospital, Seoul, South Korea.,Kidney Research Institute, Seoul National University Medical Research Center, Seoul, South Korea.,Wide River Institute of Immunology, Seoul National University, Hongcheon, South Korea
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69
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Molecular Insights into Determinants of Translational Readthrough and Implications for Nonsense Suppression Approaches. Int J Mol Sci 2020; 21:ijms21249449. [PMID: 33322589 PMCID: PMC7764779 DOI: 10.3390/ijms21249449] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/27/2020] [Accepted: 12/05/2020] [Indexed: 02/07/2023] Open
Abstract
The fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense and stop codons. However, premature termination codons (PTCs) arising from mutations may, at low frequency, be misrecognized and result in PTC suppression, named ribosome readthrough, with production of full-length proteins through the insertion of a subset of amino acids. Since some drugs have been identified as readthrough inducers, this fidelity drawback has been explored as a therapeutic approach in several models of human diseases caused by nonsense mutations. Here, we focus on the mechanisms driving translation in normal and aberrant conditions, the potential fates of mRNA in the presence of a PTC, as well as on the results obtained in the research of efficient readthrough-inducing compounds. In particular, we describe the molecular determinants shaping the outcome of readthrough, namely the nucleotide and protein context, with the latter being pivotal to produce functional full-length proteins. Through the interpretation of experimental and mechanistic findings, mainly obtained in lysosomal and coagulation disorders, we also propose a scenario of potential readthrough-favorable features to achieve relevant rescue profiles, representing the main issue for the potential translatability of readthrough as a therapeutic strategy.
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Zardadi S, Razmara E, Asgaritarghi G, Jafarinia E, Bitarafan F, Rayat S, Almadani N, Morovvati S, Garshasbi M. Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss. Mol Genet Genomic Med 2020; 8:e1550. [PMID: 33205915 PMCID: PMC7767568 DOI: 10.1002/mgg3.1550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/22/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Background Hereditary hearing loss (HL) is a heterogeneous and most common sensory neural disorder. At least, 76 genes have been reported in association with autosomal recessive nonsyndromic HL (ARNSHL). Herein, we subjected two patients with bilateral sensorineural HL in two distinct consanguineous Iranian families to figure out the underlying genetic factors. Methods Physical and sensorineural examinations were performed on the patients. Imaging also was applied to unveil any abnormalities in anatomical structures of the middle and inner ear. In order to decipher the possible genetic causes of the verified GJB2‐negative samples, the probands were subjected to whole‐exome sequencing and, subsequently, Sanger sequencing was applied for variant confirmation. Results Clinical examinations showed ARNSHL in the patients. After doing whole exome sequencing, two novel variants were identified that were co‐segregating with HL that were absent in 100 ethnically matched controls. In the first family, a novel homozygous variant, NM_138691.2: c.530T>C; p.(lle177Thr), in TMC1 gene co‐segregated with prelingual ARNSHL. In the second family, NM_022124.6: c.2334G>A; p.(Trp778*) was reported as a nonsense variant causing prelingual ARNSHL. Conclusion These findings can, in turn, endorse how TMC1 and CDH23 screening is critical to detecting HL in Iranian patients. Identifying TMC1 and CDH23 pathogenic variants doubtlessly help in the detailed genotypic characterization of HL.
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Affiliation(s)
- Safoura Zardadi
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Golareh Asgaritarghi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Bitarafan
- Department of Cellular and Molecular Biology, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sima Rayat
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Navid Almadani
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Saeid Morovvati
- Department of Genetics, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Bar C, Kuchenbuch M, Barcia G, Schneider A, Jennesson M, Le Guyader G, Lesca G, Mignot C, Montomoli M, Parrini E, Isnard H, Rolland A, Keren B, Afenjar A, Dorison N, Sadleir LG, Breuillard D, Levy R, Rio M, Dupont S, Negrin S, Danieli A, Scalais E, De Saint Martin A, El Chehadeh S, Chelly J, Poisson A, Lebre A, Nica A, Odent S, Sekhara T, Brankovic V, Goldenberg A, Vrielynck P, Lederer D, Maurey H, Terrone G, Besmond C, Hubert L, Berquin P, Billette de Villemeur T, Isidor B, Freeman JL, Mefford HC, Myers CT, Howell KB, Rodríguez‐Sacristán Cascajo A, Meyer P, Genevieve D, Guët A, Doummar D, Durigneux J, van Dooren MF, de Wit MCY, Gerard M, Marey I, Munnich A, Guerrini R, Scheffer IE, Kabashi E, Nabbout R. Developmental and epilepsy spectrum of
KCNB1
encephalopathy with long‐term outcome. Epilepsia 2020; 61:2461-2473. [DOI: 10.1111/epi.16679] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Claire Bar
- Department of Pediatric Neurology Reference Center for Rare Epilepsies Assistance Publique‐Hôpitaux de Paris (AP‐HP), Necker‐Enfants Malades Hospital Paris France
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
| | - Mathieu Kuchenbuch
- Department of Pediatric Neurology Reference Center for Rare Epilepsies Assistance Publique‐Hôpitaux de Paris (AP‐HP), Necker‐Enfants Malades Hospital Paris France
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
| | - Giulia Barcia
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
- Department of Clinical Genetics AP‐HP, Necker‐Enfants Malades Hospital Paris France
| | - Amy Schneider
- Department of Medicine Epilepsy Research Centre Austin Health University of Melbourne Heidelberg Victoria Australia
| | | | - Gwenaël Le Guyader
- Department of Genetics Poitiers University Hospital CenterPoitiers Cedex France
- EA3808–NEUVACOD Neurovascular and Cognitive Disorders Unit University of Poitiers Poitiers France
| | - Gaetan Lesca
- Department of Genetics Lyon Civil Hospices Lyon France
- NeuroMyoGène Institute National Center for Scientific Research Mixed Unit of Research 5310, National Institute of Health and Medical Research U1217University of LyonClaude Bernard Lyon 1 University Villeurbanne France
| | - Cyril Mignot
- National Institute of Health and Medical Research, U1127 National Center for Scientific Research Mixed Unit of Research 7225 Pierre and Marie Curie University Paris 6 Mixed Unit of Research S1127 Brain and Spine Institute Sorbonne University Paris France
- Department of Genetics Rare Causes of Intellectual Disability Reference Center AP‐HP, Pitié‐Salpêtrière HospitalSorbonne University Paris France
| | - Martino Montomoli
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories Neuroscience Department A. Meyer Children's HospitalUniversity of Florence Florence Italy
| | - Elena Parrini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories Neuroscience Department A. Meyer Children's HospitalUniversity of Florence Florence Italy
| | - Hervé Isnard
- Pediatric Neurologist Medical Office Lyon France
| | - Anne Rolland
- Department of Pediatrics Nantes University Hospital Center Nantes France
| | - Boris Keren
- Department of Genetics Rare Causes of Intellectual Disability Reference Center AP‐HP, Pitié‐Salpêtrière HospitalSorbonne University Paris France
| | - Alexandra Afenjar
- Department of Genetics and Medical Embryology Reference Center for Malformations and Congenital Diseases of the Cerebellum and Rare Causes of Intellectual Disabilities Sorbonne UniversityAP‐HP, Trousseau Hospital Paris France
| | - Nathalie Dorison
- Pediatric Neurosurgery Department Rothschild Foundation Hospital Paris France
- Department of Pediatric Neurology AP‐HP, Armand Trousseau HospitalSorbonne University Paris France
| | - Lynette G. Sadleir
- Department of Pediatrics and Child Health University of Otago Wellington New Zealand
| | - Delphine Breuillard
- Department of Pediatric Neurology Reference Center for Rare Epilepsies Assistance Publique‐Hôpitaux de Paris (AP‐HP), Necker‐Enfants Malades Hospital Paris France
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
| | - Raphael Levy
- Department of Pediatric Radiology Necker‐Enfants Malades Hospital Paris France
| | - Marlène Rio
- Department of Clinical Genetics AP‐HP, Necker‐Enfants Malades Hospital Paris France
- Laboratory of Developmental Brain Disorders National Institute of Health and Medical Research Mixed Unit of Research 1163 Imagine InstituteSorbonne University Paris France
| | - Sophie Dupont
- National Institute of Health and Medical Research, U1127 National Center for Scientific Research Mixed Unit of Research 7225 Pierre and Marie Curie University Paris 6 Mixed Unit of Research S1127 Brain and Spine Institute Sorbonne University Paris France
- Epileptology Unit and Rehabilitation Unit AP‐HP, Pitie‐Salpêtrière‐Charles Foix Hospital Paris France
| | - Susanna Negrin
- Epilepsy and Clinical Neurophysiology Unit Scientific InstituteIRCCS E. Medea Treviso Italy
| | - Alberto Danieli
- Epilepsy and Clinical Neurophysiology Unit Scientific InstituteIRCCS E. Medea Treviso Italy
| | - Emmanuel Scalais
- Pediatric Neurology Unit Luxembourg Hospital Center Luxembourg City Luxembourg
| | - Anne De Saint Martin
- Department of Pediatric Neurology Strasbourg University HospitalHautepierre Hospital Strasbourg France
| | - Salima El Chehadeh
- Department of Medical Genetics Strasbourg University HospitalsHautepierre Hospital Strasbourg France
| | - Jamel Chelly
- Department of Medical Genetics Strasbourg University HospitalsHautepierre Hospital Strasbourg France
| | - Alice Poisson
- GénoPsy Reference Center for Diagnosis and Management of Genetic Psychiatric Disorders le Vinatier Hospital Center and EDR‐Psy Team (National Center for Scientific Research and Lyon 1 Claude Bernard University) Villeurbanne France
| | - Anne‐Sophie Lebre
- Reims University Hospital CenterMaison Blanche HospitalBiology Department Reims France
| | - Anca Nica
- Neurology Department Center for Clinical Research (CIC 1414) Rennes University Hospital Rennes France
- Laboratory of Signal ProcessingNational Institute of Health and Medical Research Mixed Unit of Research 1099 Rennes France
| | - Sylvie Odent
- Reference Center for Rare Developmental Abnormalities CLAD‐Ouest Rennes University Hospital Center Rennes France
- National Center for Scientific Research Mixed Unit of Research 6290, Institute of Genetics and Development of Rennes (IGDR)University of Rennes Rennes France
| | - Tayeb Sekhara
- Department of Pediatric Neurology C.H.I.R.E.C Brussels Belgium
| | | | - Alice Goldenberg
- Reference Center for Developmental Anomalies and Malformation Syndromes Rouen University Hospital Center Rouen France
| | - Pascal Vrielynck
- Reference Center for Refractory Epilepsy, Catholic University of Louvain William Lennox Neurological Hospital Ottignies Belgium
| | | | - Hélène Maurey
- Department of Pediatric Neurology AP‐HP, Bicêtre University Hospital Kremlin Bicêtre France
| | - Gaetano Terrone
- Department of Translational Medical Sciences Section of Pediatrics, Child Neurology Unit Federico II University Naples Italy
| | - Claude Besmond
- Translational Genetics National Institute of Health and Medical Research Mixed Unit of Research 1163Imagine InstituteUniversity of Paris Paris France
| | - Laurence Hubert
- Translational Genetics National Institute of Health and Medical Research Mixed Unit of Research 1163Imagine InstituteUniversity of Paris Paris France
| | - Patrick Berquin
- Department of Pediatric Neurology Amiens‐Picardie University Hospital CenterUniversity of Picardy Jules Verne Amiens France
| | | | - Bertrand Isidor
- Department of Clinical Genetics Nantes University Hospital Center Nantes France
| | - Jeremy L. Freeman
- Departments of Neurology and Paediatrics Royal Children's Hospital University of Melbourne Melbourne Victoria Australia
- Murdoch Children’s Research Institute Melbourne Victoria Australia
| | - Heather C. Mefford
- Department of Pediatrics Division of Genetic Medicine University of Washington Seattle Washington United States
| | - Candace T. Myers
- Department of Pediatrics Division of Genetic Medicine University of Washington Seattle Washington United States
| | - Katherine B. Howell
- Departments of Neurology and Paediatrics Royal Children's Hospital University of Melbourne Melbourne Victoria Australia
- Murdoch Children’s Research Institute Melbourne Victoria Australia
| | - Andrés Rodríguez‐Sacristán Cascajo
- Pediatric Neurology Unit Department of Pediatric Virgen Macarena Hospital Seville Spain
- Department of Pediatrics School of Medicine University of Seville Seville Spain
| | - Pierre Meyer
- Department of Pediatric Neurology Montpellier University Hospital Center Montpellier France
- PhyMedExp National Institute of Health and Medical Research, U1046National Center for Scientific Research Mixed Unit of Research 9214University of Montpellier Montpellier France
| | - David Genevieve
- Department of Medical Genetics, Rare Disease, and Personalized Medicine IRMBUniversity of MontpellierNational Institute of Health and Medical ResearchMontpellier University Hospital Center Montpellier France
| | - Agnès Guët
- Department of Pediatrics Louis‐Mourier Hospital Colombes France
| | - Diane Doummar
- Department of Pediatric Neurology AP‐HP, Armand Trousseau HospitalSorbonne University Paris France
| | - Julien Durigneux
- Departments of Neurology and Paediatrics Royal Children's Hospital University of Melbourne Melbourne Victoria Australia
| | - Marieke F. van Dooren
- Department of Clinical Genetics Erasmus University Medical Center Rotterdam the Netherlands
| | - Marie Claire Y. de Wit
- Department of Pediatric Neurology and ENCORE Expertise Center Erasmus University Medical Center Sophia Children’s Hospital Rotterdam the Netherlands
| | - Marion Gerard
- Clinical Genetics Côte de Nacre University Hospital Center Caen France
| | - Isabelle Marey
- Department of Genetics Rare Causes of Intellectual Disability Reference Center AP‐HP, Pitié‐Salpêtrière HospitalSorbonne University Paris France
| | - Arnold Munnich
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
- Department of Clinical Genetics AP‐HP, Necker‐Enfants Malades Hospital Paris France
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics, and Neurobiology Unit and Laboratories Neuroscience Department A. Meyer Children's HospitalUniversity of Florence Florence Italy
| | - Ingrid E. Scheffer
- Department of Medicine Epilepsy Research Centre Austin Health University of Melbourne Heidelberg Victoria Australia
- Departments of Neurology and Paediatrics Royal Children's Hospital University of Melbourne Melbourne Victoria Australia
- Murdoch Children’s Research Institute Melbourne Victoria Australia
- Florey Institute of Neurosciences and Mental Health Heidelberg Victoria Australia
| | - Edor Kabashi
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
| | - Rima Nabbout
- Department of Pediatric Neurology Reference Center for Rare Epilepsies Assistance Publique‐Hôpitaux de Paris (AP‐HP), Necker‐Enfants Malades Hospital Paris France
- Imagine Institute, Mixed Unit of Research 1163 University of ParisSorbonne University Paris France
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Echols J, Siddiqui A, Dai Y, Havasi V, Sun R, Kaczmarczyk A, Keeling KM. A regulated NMD mouse model supports NMD inhibition as a viable therapeutic option to treat genetic diseases. Dis Model Mech 2020; 13:dmm044891. [PMID: 32737261 PMCID: PMC7473645 DOI: 10.1242/dmm.044891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/17/2020] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) targets mRNAs that contain a premature termination codon (PTC) for degradation, preventing their translation. By altering the expression of PTC-containing mRNAs, NMD modulates the inheritance pattern and severity of genetic diseases. NMD also limits the efficiency of suppressing translation termination at PTCs, an emerging therapeutic approach to treat genetic diseases caused by in-frame PTCs (nonsense mutations). Inhibiting NMD may help rescue partial levels of protein expression. However, it is unclear whether long-term, global NMD attenuation is safe. We hypothesize that a degree of NMD inhibition can be safely tolerated after completion of prenatal development. To test this hypothesis, we generated a novel transgenic mouse that expresses an inducible, dominant-negative form of human UPF1 (dnUPF1) to inhibit NMD in mouse tissues by different degrees, allowing us to examine the effects of global NMD inhibition in vivo A thorough characterization of these mice indicated that expressing dnUPF1 at levels that promote relatively moderate to strong NMD inhibition in most tissues for a 1-month period produced modest immunological and bone alterations. In contrast, 1 month of dnUPF1 expression to promote more modest NMD inhibition in most tissues did not produce any discernable defects, indicating that moderate global NMD attenuation is generally well tolerated in non-neurological somatic tissues. Importantly, a modest level of NMD inhibition that produced no overt abnormalities was able to significantly enhance in vivo PTC suppression. These results suggest that safe levels of NMD attenuation are likely achievable, and this can help rescue protein deficiencies resulting from PTCs.
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Affiliation(s)
- Josh Echols
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Amna Siddiqui
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yanying Dai
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Viktoria Havasi
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Richard Sun
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aneta Kaczmarczyk
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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73
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Terkelsen T, Larsen OH, Vang S, Jensen UB, Wikman F. Deleterious mis-splicing of STK11 caused by a novel single-nucleotide substitution in the 3' polypyrimidine tract of intron five. Mol Genet Genomic Med 2020; 8:e1381. [PMID: 32573125 PMCID: PMC7507455 DOI: 10.1002/mgg3.1381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/28/2020] [Accepted: 05/31/2020] [Indexed: 01/07/2023] Open
Abstract
Background Pathogenic variants in STK11, also designated as LKB1, cause Peutz–Jeghers syndrome, which is a rare autosomal dominant disorder characterized by mucocutaneous pigmentation changes, polyposis, and a high risk of cancer. Methods A male meeting the clinical diagnostic criteria for Peutz–Jeghers syndrome underwent next‐generation sequencing. To validate the predicted splicing impact of a detected STK11 variant, we performed RNA‐Seq on mRNA extracted from patient‐derived Epstein‐Barr virus‐transformed lymphocytes treated with cycloheximide to inhibit nonsense‐mediated decay ex vivo. Results Blood testing identified a novel single‐nucleotide substitution, NM_000455.4:c.735‐10C>A, at the end of the 3′ polypyrimidine tract of intron five in STK11. RNA‐Seq confirmed a predicted eight base pair insertion in the mRNA transcript. Following inhibition of nonsense‐mediated decay, the out‐of‐frame insertion was detected in 50% of all RNA‐Seq reads. This confirmed a strong, deleterious splicing impact of the variant. Conclusion We characterized a novel likely pathogenic germline variant in intron five of STK11 associated with Peutz–Jeghers syndrome. The study highlights RNA‐Seq as a useful supplement in hereditary cancer predisposition testing.
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Affiliation(s)
- Thorkild Terkelsen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Ole H Larsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Vang
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Uffe B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Friedrik Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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74
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Torrico B, Antón-Galindo E, Fernàndez-Castillo N, Rojo-Francàs E, Ghorbani S, Pineda-Cirera L, Hervás A, Rueda I, Moreno E, Fullerton JM, Casadó V, Buitelaar JK, Rommelse N, Franke B, Reif A, Chiocchetti AG, Freitag C, Kleppe R, Haavik J, Toma C, Cormand B. Involvement of the 14-3-3 Gene Family in Autism Spectrum Disorder and Schizophrenia: Genetics, Transcriptomics and Functional Analyses. J Clin Med 2020; 9:E1851. [PMID: 32545830 PMCID: PMC7356291 DOI: 10.3390/jcm9061851] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
The 14-3-3 protein family are molecular chaperones involved in several biological functions and neurological diseases. We previously pinpointed YWHAZ (encoding 14-3-3ζ) as a candidate gene for autism spectrum disorder (ASD) through a whole-exome sequencing study, which identified a frameshift variant within the gene (c.659-660insT, p.L220Ffs*18). Here, we explored the contribution of the seven human 14-3-3 family members in ASD and other psychiatric disorders by investigating the: (i) functional impact of the 14-3-3ζ mutation p.L220Ffs*18 by assessing solubility, target binding and dimerization; (ii) contribution of common risk variants in 14-3-3 genes to ASD and additional psychiatric disorders; (iii) burden of rare variants in ASD and schizophrenia; and iv) 14-3-3 gene expression using ASD and schizophrenia transcriptomic data. We found that the mutant 14-3-3ζ protein had decreased solubility and lost its ability to form heterodimers and bind to its target tyrosine hydroxylase. Gene-based analyses using publicly available datasets revealed that common variants in YWHAE contribute to schizophrenia (p = 6.6 × 10-7), whereas ultra-rare variants were found enriched in ASD across the 14-3-3 genes (p = 0.017) and in schizophrenia for YWHAZ (meta-p = 0.017). Furthermore, expression of 14-3-3 genes was altered in post-mortem brains of ASD and schizophrenia patients. Our study supports a role for the 14-3-3 family in ASD and schizophrenia.
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Affiliation(s)
- Bàrbara Torrico
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Institut de Recerca Sant Joan de Déu (IR-SJD), 08950 Esplugues de Llobregat, Spain
| | - Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Institut de Recerca Sant Joan de Déu (IR-SJD), 08950 Esplugues de Llobregat, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Institut de Recerca Sant Joan de Déu (IR-SJD), 08950 Esplugues de Llobregat, Spain
| | - Eva Rojo-Francàs
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Institut de Recerca Sant Joan de Déu (IR-SJD), 08950 Esplugues de Llobregat, Spain
| | - Sadaf Ghorbani
- Centre for Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, N5009 Bergen, Norway; (S.G.); (R.K.); (J.H.)
| | - Laura Pineda-Cirera
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Institut de Recerca Sant Joan de Déu (IR-SJD), 08950 Esplugues de Llobregat, Spain
| | - Amaia Hervás
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, 08221 Terrassa, Spain; (A.H.); (I.R.)
- IGAIN, Global Institute of Integral Attention to Neurodevelopment, 08007 Barcelona, Spain
| | - Isabel Rueda
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, 08221 Terrassa, Spain; (A.H.); (I.R.)
| | - Estefanía Moreno
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, NSW 2031, Australia;
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Vicent Casadó
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Jan K. Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR Nijmegen, The Netherlands;
- Karakter Child and Adolescent Psychiatry University Centre, 6525 GC Nijmegen, The Netherlands;
| | - Nanda Rommelse
- Karakter Child and Adolescent Psychiatry University Centre, 6525 GC Nijmegen, The Netherlands;
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR Nijmegen, The Netherlands;
| | - Barbara Franke
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR Nijmegen, The Netherlands;
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR Nijmegen, The Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Andreas G. Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence Frankfurt, JW Goethe University, 60323 Frankfurt am Main, Germany; (A.G.C.); (C.F.)
| | - Christine Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence Frankfurt, JW Goethe University, 60323 Frankfurt am Main, Germany; (A.G.C.); (C.F.)
| | - Rune Kleppe
- Centre for Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, N5009 Bergen, Norway; (S.G.); (R.K.); (J.H.)
- Division of Psychiatry, Haukeland University Hospital, 5021 Bergen, Norway
| | - Jan Haavik
- Centre for Neuropsychiatric Disorders, Department of Biomedicine, University of Bergen, N5009 Bergen, Norway; (S.G.); (R.K.); (J.H.)
| | - Claudio Toma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Neuroscience Research Australia, Sydney, NSW 2031, Australia;
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Centro de Biología Molecular “Severo Ochoa”, Universidad Autónoma de Madrid/CSIC, C/Nicolás Cabrera, 1, Campus UAM, 28049 Madrid, Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Prevosti Building, floor 2, Av. Diagonal 643, 08028 Barcelona, Spain; (B.T.); (E.A.-G.); (N.F.-C.); (E.R.-F.); (L.P.-C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain; (E.M.); (V.C.)
- Institut de Recerca Sant Joan de Déu (IR-SJD), 08950 Esplugues de Llobregat, Spain
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Erwood S, Laselva O, Bily TM, Brewer RA, Rutherford AH, Bear CE, Ivakine EA. Allele-Specific Prevention of Nonsense-Mediated Decay in Cystic Fibrosis Using Homology-Independent Genome Editing. Mol Ther Methods Clin Dev 2020; 17:1118-1128. [PMID: 32490033 PMCID: PMC7256445 DOI: 10.1016/j.omtm.2020.05.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated decay (NMD) is a major pathogenic mechanism underlying a diversity of genetic disorders. Nonsense variants tend to lead to more severe disease phenotypes and are often difficult targets for small molecule therapeutic development as a result of insufficient protein production. The treatment of cystic fibrosis (CF), an autosomal recessive disease caused by mutations in the CFTR gene, exemplifies the challenge of therapeutically addressing nonsense mutations in human disease. Therapeutic development in CF has led to multiple, highly successful protein modulatory interventions, yet no targeted therapies have been approved for nonsense mutations. Here, we have designed a CRISPR-Cas9-based strategy for the targeted prevention of NMD of CFTR transcripts containing the second most common nonsense variant listed in CFTR2, W1282X. By introducing a deletion of the downstream genic region following the premature stop codon, we demonstrate significantly increased protein expression of this mutant variant. Notably, in combination with protein modulators, genome editing significantly increases the potentiated channel activity of W1282X-CFTR in human bronchial epithelial cells. Furthermore, we show how the outlined approach can be modified to permit allele-specific editing. The described approach can be extended to other late-occurring nonsense mutations in the CFTR gene or applied as a generalized approach for gene-specific prevention of NMD in disorders where a truncated protein product retains full or partial functionality.
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Affiliation(s)
- Steven Erwood
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Onofrio Laselva
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Teija M.I. Bily
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Reid A. Brewer
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Alexandra H. Rutherford
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Christine E. Bear
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Evgueni A. Ivakine
- Program in Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
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76
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Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics. Cancers (Basel) 2020; 12:cancers12030765. [PMID: 32213869 PMCID: PMC7140085 DOI: 10.3390/cancers12030765] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a surveillance pathway used by cells to control the quality mRNAs and to fine-tune transcript abundance. NMD plays an important role in cell cycle regulation, cell viability, DNA damage response, while also serving as a barrier to virus infection. Disturbance of this control mechanism caused by genetic mutations or dys-regulation of the NMD pathway can lead to pathologies, including neurological disorders, immune diseases and cancers. The role of NMD in cancer development is complex, acting as both a promoter and a barrier to tumour progression. Cancer cells can exploit NMD for the downregulation of key tumour suppressor genes, or tumours adjust NMD activity to adapt to an aggressive immune microenvironment. The latter case might provide an avenue for therapeutic intervention as NMD inhibition has been shown to lead to the production of neoantigens that stimulate an immune system attack on tumours. For this reason, understanding the biology and co-option pathways of NMD is important for the development of novel therapeutic agents. Inhibitors, whose design can make use of the many structures available for NMD study, will play a crucial role in characterizing and providing diverse therapeutic options for this pathway in cancer and other diseases.
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77
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The position of the target site for engineered nucleases improves the aberrant mRNA clearance in in vivo genome editing. Sci Rep 2020; 10:4173. [PMID: 32144373 PMCID: PMC7060192 DOI: 10.1038/s41598-020-61154-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/18/2020] [Indexed: 11/08/2022] Open
Abstract
Engineered nucleases are widely used for creating frameshift or nonsense mutations in the target genes to eliminate gene functions. The resulting mRNAs carrying premature termination codons can be eliminated by nonsense-mediated mRNA decay. However, it is unclear how effective this process would be in vivo. Here, we found that the nonsense-mediated decay was unable to remove the mutant mRNAs in twelve out of sixteen homozygous mutant mice with frameshift mutations generated using engineered nucleases, which is far beyond what we expected. The frameshift mutant proteins translated by a single nucleotide deletion within the coding region were also detected in the p53 mutant mice. Furthermore, we showed that targeting the exons present downstream of the exons with a start codon or distant from ATG is relatively effective for eliminating mutant mRNAs in vivo, whereas the exons with a start codon are targeted to express the mutant mRNAs. Of the sixteen mutant mice generated, only four mutant mice targeting the downstream exons exhibited over 80% clearance of mutant mRNAs. Since the abnormal products, either mutant RNAs or mutant proteins, expressed by the target alleles might obscure the outcome of genome editing, these findings will provide insights in the improved performance of engineered nucleases when they are applied in vivo.
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78
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Daum H, Mor-Shaked H, Ta-Shma A, Shaag A, Silverstein S, Shohat M, Elpeleg O, Meiner V, Harel T. Grandparental genotyping enhances exome variant interpretation. Am J Med Genet A 2020; 182:689-696. [PMID: 32027463 DOI: 10.1002/ajmg.a.61511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/09/2019] [Accepted: 01/03/2020] [Indexed: 12/14/2022]
Abstract
Trio exome sequencing is a powerful tool in the molecular investigation of monogenic disorders and provides an incremental diagnostic yield over proband-only sequencing, mainly due to the rapid identification of de novo disease-causing variants. However, heterozygous variants inherited from unaffected parents may be inadvertently dismissed, although multiple explanations are available for such scenarios including mosaicism in the parent, incomplete penetrance, imprinting, or skewed X-inactivation. We report three probands, in which a pathogenic or likely pathogenic variant was identified upon exome sequencing, yet was inherited from an unaffected parent. Segregation of the variants (in NOTCH1, PHF6, and SOX10) in the grandparent generation revealed that the variant was de novo in each case. Additionally, one proband had skewed X-inactivation. We discuss the possible genetic mechanism in each case, and urge caution in data interpretation of exome sequencing data. We illustrate the utility of expanding segregation studies to the grandparent generation and demonstrate the impact on exome interpretation strategies, by showing that objective genotype data can overcome subjective parental report of lack of symptoms.
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Affiliation(s)
- Hagit Daum
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Hagar Mor-Shaked
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Asaf Ta-Shma
- Department of Pediatric Cardiology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avraham Shaag
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.,Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shira Silverstein
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Mordechai Shohat
- Bioinformatics Unit - Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,The Genetic Institute of Maccabi Health Medicinal Organization, Rehovot, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orly Elpeleg
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.,Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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79
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Chen Y, Liu X, Chen S, Zhang J, Xu C. Targeted Sequencing and RNA Assay Reveal a Noncanonical JAG1 Splicing Variant Causing Alagille Syndrome. Front Genet 2020; 10:1363. [PMID: 32038717 PMCID: PMC6993058 DOI: 10.3389/fgene.2019.01363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/12/2019] [Indexed: 11/13/2022] Open
Abstract
Alagille syndrome (ALGS), as known as congenital arteriohepatic dysplasia, is a rare autosomal dominant multi-systemic disorder. Mutations in JAG1 or more rarely NOTCH2 have been reported as the cause of ALGS. In this study, a 5-year old girl with typical ALGS feature and her pregnant mother came to our reproductive genetics clinic for counseling. We aimed to clarify the genetic diagnosis and provide prenatal genetic diagnosis for the pregnant. Next generation sequencing (NGS)-based multigene panel was used to identify pathogenic variant of the proband. Then the candidate variant was verified by using Sanger sequencing. RNA assay was performed to clarify splicing effect of the candidate variant. Amniocentesis, karyotyping, and Sanger sequencing were performed for prenatal testing. We found a novel de novo noncanonical JAG1 splicing variant (c.2917-8C > A) in the proband. Peripheral blood RNA assay suggested that the mutant transcript might escape nonsense-mediated messenger RNA (mRNA) decay (NMD) and encode a C-terminal truncated protein. Information of the variant has resulted in a successful prenatal diagnosis of the fetus. Our results clarified the genetic diagnosis of an ALGS patient and ensured utility of prenatal genetic testing.
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Affiliation(s)
- Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Xueli Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Junyu Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
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80
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Screening Readthrough Compounds to Suppress Nonsense Mutations: Possible Application to β-Thalassemia. J Clin Med 2020; 9:jcm9020289. [PMID: 31972957 PMCID: PMC7073686 DOI: 10.3390/jcm9020289] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Several types of thalassemia (including β039-thalassemia) are caused by nonsense mutations in genes controlling globin production, leading to premature translation termination and mRNA destabilization mediated by the nonsense mediated mRNA decay. Drugs (for instance, aminoglycosides) can be designed to suppress premature translation termination by inducing readthrough (or nonsense suppression) at the premature termination codon. These findings have introduced new hopes for the development of a pharmacologic approach to cure this genetic disease. In the present review, we first summarize the principle and current status of the chemical relief for the expression of functional proteins from genes otherwise unfruitful for the presence of nonsense mutations. Second, we compare data available on readthrough molecules for β0-thalassemia. The examples reported in the review strongly suggest that ribosomal readthrough should be considered as a therapeutic approach for the treatment of β0-thalassemia caused by nonsense mutations. Concluding, the discovery of molecules, exhibiting the property of inducing β-globin, such as readthrough compounds, is of great interest and represents a hope for several patients, whose survival will depend on the possible use of drugs rendering blood transfusion and chelation therapy unnecessary.
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81
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Branchini A, Pinotti M. A recoded view on the F9 p.Cys178Ter pathogenic mechanism. Thromb Res 2020; 187:88-90. [PMID: 31978811 DOI: 10.1016/j.thromres.2020.01.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/14/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy..
| | - Mirko Pinotti
- Department of Life Sciences and Biotechnology, University of Ferrara, Italy
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82
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Peled A, Samuelov L, Sarig O, Bochner R, Malki L, Pavlovsky M, Pichinuk E, Weil M, Sprecher E. Treatment of hereditary hypotrichosis simplex of the scalp with topical gentamicin. Br J Dermatol 2019; 183:114-120. [DOI: 10.1111/bjd.18718] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2019] [Indexed: 12/11/2022]
Affiliation(s)
- A. Peled
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
- Department of Human Molecular Genetics and Biochemistry Tel Aviv University Tel Aviv Israel
| | - L. Samuelov
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - O. Sarig
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - R. Bochner
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - L. Malki
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
- Department of Human Molecular Genetics and Biochemistry Tel Aviv University Tel Aviv Israel
| | - M. Pavlovsky
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
| | - E. Pichinuk
- Blavatnik Center for Drug Discovery Tel Aviv University Tel Aviv Israel
| | - M. Weil
- Blavatnik Center for Drug Discovery Tel Aviv University Tel Aviv Israel
| | - E. Sprecher
- Division of Dermatology Tel Aviv Sourasky Medical Center Tel Aviv Israel
- Department of Human Molecular Genetics and Biochemistry Tel Aviv University Tel Aviv Israel
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83
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Contribution of a Novel B3GLCT Variant to Peters Plus Syndrome Discovered by a Combination of Next-Generation Sequencing and Automated Text Mining. Int J Mol Sci 2019; 20:ijms20236006. [PMID: 31795264 PMCID: PMC6928627 DOI: 10.3390/ijms20236006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 12/30/2022] Open
Abstract
Anterior segment dysgenesis (ASD) encompasses a spectrum of ocular disorders affecting the structures of the anterior eye chamber. Mutations in several genes, involved in eye development, are implicated in this disorder. ASD is often accompanied by diverse multisystemic symptoms and another genetic cause, such as variants in genes encoding collagen type IV. Thus, a wide spectrum of phenotypes and underlying genetic diversity make fast and proper diagnosis challenging. Here, we used AMELIE, an automatic text mining tool that enriches data with the most up-to-date information from literature, and wANNOVAR, which is based on well-documented databases and incorporates variant filtering strategy to identify genetic variants responsible for severely-manifested ASD in a newborn child. This strategy, applied to trio sequencing data in compliance with ACMG 2015 guidelines, helped us find two compound heterozygous variants of the B3GLCT gene, of which c.660+1G>A (rs80338851) was previously associated with the phenotype of Peters plus syndrome (PPS), while the second, NM_194318.3:c.755delC (p.T252fs), in exon 9 of the same gene was noted for the first time. PPS, a very rare subtype of ASD, is a glycosylation disorder, where the dysfunctional B3GLCT gene product, O-fucose-specific β-1,3-glucosyltransferase, is ineffective in providing a noncanonical quality control system for proper protein folding in cells. Our study expands the mutation spectrum of the B3GLCT gene related to PPS. We suggest that the implementation of automatic text mining tools in combination with careful variant filtering could help translate sequencing results into diagnosis, thus, considerably accelerating the diagnostic process and, thereby, improving patient management.
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84
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Insights into the Effects of Cancer Associated Mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1. Int J Mol Sci 2019; 20:ijms20225644. [PMID: 31718065 PMCID: PMC6888360 DOI: 10.3390/ijms20225644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 12/22/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that recognizes post-transcriptionally abnormal transcripts and mediates their degradation. The master regulator of NMD is UPF1, an enzyme with intrinsic ATPase and helicase activities. The cancer genomic sequencing data has identified frequently mutated residues in the CH-domain and ATP-binding site of UPF1. In silico screening of UPF1 stability change as a function over 41 cancer mutations has identified five variants with significant effects: K164R, R253W, T499M, E637K, and E833K. To explore the effects of these mutations on the associated energy landscape of UPF1, molecular dynamics simulations (MDS) were performed. MDS identified stable H-bonds between residues S152, S203, S205, Q230/R703, and UPF2/AMPPNP, and suggest that phosphorylation of Serine residues may control UPF1-UPF2 binding. Moreover, the alleles K164R and R253W in the CH-domain improved UPF1-UPF2 binding. In addition, E637K and E833K alleles exhibited improved UPF1-AMPPNP binding compared to the T499M variant; the lower binding is predicted from hindrance caused by the side-chain of T499M to the docking of the tri-phosphate moiety (AMPPNP) into the substrate site. The dynamics of wild-type/mutant systems highlights the flexible nature of the ATP-binding region in UPF1. These insights can facilitate the development of drug discovery strategies for manipulating NMD signaling in cell systems using chemical tools.
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85
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Lindeboom RGH, Vermeulen M, Lehner B, Supek F. The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy. Nat Genet 2019; 51:1645-1651. [PMID: 31659324 PMCID: PMC6858879 DOI: 10.1038/s41588-019-0517-5] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022]
Abstract
Premature termination codons (PTCs) can result in the production of truncated proteins or the degradation of messenger RNAs by nonsense-mediated mRNA decay (NMD). Which of these outcomes occurs can alter the effect of a mutation, with the engagement of NMD being dependent on a series of rules. Here, by applying these rules genome-wide to obtain a resource called NMDetective, we explore the impact of NMD on genetic disease and approaches to therapy. First, human genetic diseases differ in whether NMD typically aggravates or alleviates the effects of PTCs. Second, failure to trigger NMD is a cause of ineffective gene inactivation by CRISPR-Cas9 gene editing. Finally, NMD is a determinant of the efficacy of cancer immunotherapy, with only frameshifted transcripts that escape NMD predicting a response. These results demonstrate the importance of incorporating the rules of NMD into clinical decision-making. Moreover, they suggest that inhibiting NMD may be effective in enhancing cancer immunotherapy.
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Affiliation(s)
- Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
| | - Fran Supek
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain. .,Institut de Recerca Biomedica Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
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86
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Bar C, Barcia G, Jennesson M, Le Guyader G, Schneider A, Mignot C, Lesca G, Breuillard D, Montomoli M, Keren B, Doummar D, Billette de Villemeur T, Afenjar A, Marey I, Gerard M, Isnard H, Poisson A, Dupont S, Berquin P, Meyer P, Genevieve D, De Saint Martin A, El Chehadeh S, Chelly J, Guët A, Scalais E, Dorison N, Myers CT, Mefford HC, Howell KB, Marini C, Freeman JL, Nica A, Terrone G, Sekhara T, Lebre A, Odent S, Sadleir LG, Munnich A, Guerrini R, Scheffer IE, Kabashi E, Nabbout R. Expanding the genetic and phenotypic relevance of
KCNB1
variants in developmental and epileptic encephalopathies: 27 new patients and overview of the literature. Hum Mutat 2019; 41:69-80. [DOI: 10.1002/humu.23915] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Claire Bar
- Department of Pediatric Neurology, Reference Centre for Rare EpilepsiesHôpital Necker‐Enfants MaladesParis France
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
| | - Giulia Barcia
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
- Department of genetics, Necker Enfants Malades hospitalAssistance Publique‐Hôpitaux de ParisParis France
| | | | - Gwenaël Le Guyader
- Department of geneticsUniversity hospital PoitiersPoitiers Cedex France
- EA3808‐NEUVACOD Unité Neurovasculaire et Troubles Cognitifs, Pôle Biologie SantéUniversité de PoitiersPoitiers France
| | - Amy Schneider
- Department of Medicine, Epilepsy Research Centre, Austin HealthThe University of MelbourneHeidelberg Victoria Australia
| | - Cyril Mignot
- Institut du Cerveau et de la Moelle épinière, INSERM, U 1127, CNRS UMR 7225Sorbonne Universités UPMC Univ Paris 06 UMR S 1127 Paris France
- Département de Génétique et de Cytogénétique, Centre de Reference Déficience Intellectuelle de Causes Rares, APHP, Hôpital Pitié‐SalpêtrièreGRC UPMC (Déficience Intellectuelle et Autisme)Paris France
| | - Gaetan Lesca
- Department of geneticsHospices Civils de LyonLyon France
- Neurosciences centre of Lyon, INSERM U1028, UMR CNRS 5292Université Claude Bernard Lyon 1Bron Cedex France
| | - Delphine Breuillard
- Department of Pediatric Neurology, Reference Centre for Rare EpilepsiesHôpital Necker‐Enfants MaladesParis France
| | - Martino Montomoli
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A Meyer Children's HospitalUniversity of FlorenceFlorence Italy
| | - Boris Keren
- Département de Génétique et de Cytogénétique, Centre de Reference Déficience Intellectuelle de Causes Rares, APHP, Hôpital Pitié‐SalpêtrièreGRC UPMC (Déficience Intellectuelle et Autisme)Paris France
| | - Diane Doummar
- Department of Pediatric Neurology, Hôpital Armand TrousseauAP‐HPParis France
| | | | - Alexandra Afenjar
- Département de Génétique et Embryologie Médicale, Pathologies Congénitales du Cervelet‐LeucoDystrophies, Centre de Référence déficiences intellectuelles de causes rares, AP‐HP, Hôpital Armand Trousseau, GRC n°19Sorbonne UniversitéParis France
| | - Isabelle Marey
- Département de Génétique et de Cytogénétique, Centre de Reference Déficience Intellectuelle de Causes Rares, APHP, Hôpital Pitié‐SalpêtrièreGRC UPMC (Déficience Intellectuelle et Autisme)Paris France
| | | | | | - Alice Poisson
- Reference Center for Diagnosis and Management of Genetic Psychiatric Disorders, Centre Hospitalier le Vinatier and EDR‐Psy TeamCentre National de la Recherche Scientifique & Lyon 1 Claude Bernard UniversityVilleurbanne France
| | - Sophie Dupont
- Institut du Cerveau et de la Moelle épinière, INSERM, U 1127, CNRS UMR 7225Sorbonne Universités UPMC Univ Paris 06 UMR S 1127 Paris France
- Epileptology and Rehabilitation department, GH Pitie‐Salpêtrière‐Charles FoixAP‐HPParis France
| | - Patrick Berquin
- Department of pediatric neurology Amiens‐Picardie university hospitalUniversité de Picardie Jules VerneAmiens France
| | - Pierre Meyer
- Department of pediatric neurologyMontpellier university hospitalMontpellier France
- PhyMedExp, U1046 INSERMUMR9214 CNRSMontpellier France
| | - David Genevieve
- Service de génétique clinique et du Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Centre de référence maladies rares anomalies du développementCHU MontpellierMontpellier France
| | - Anne De Saint Martin
- Department of Pediatric NeurologyStrasbourg University HospitalStrasbourg France
| | - Salima El Chehadeh
- Department of genetics, Hôpital de HautepierreHôpitaux Universitaires de StrasbourgStrasbourg France
| | - Jamel Chelly
- Department of genetics, Hôpital de HautepierreHôpitaux Universitaires de StrasbourgStrasbourg France
| | - Agnès Guët
- Department of PediatricLouis‐Mourier HospitalColombes France
| | - Emmanuel Scalais
- Department of Pediatric Neurology, Centre Hospitalier de LuxembourgLuxembourg CityLuxembourg City Luxembourg
| | - Nathalie Dorison
- Department of pediatric NeurosurgeryRothschild Foundation HospitalParis France
| | - Candace T. Myers
- Department of PediatricsUniversity of WashingtonSeattle Washington
| | - Heather C. Mefford
- Department of Pediatrics, Division of Genetic MedicineUniversity of WashingtonSeattle Washington
| | - Katherine B. Howell
- Departments of Neurology and Paediatrics, Royal Children's HospitalUniversity of MelbourneMelbourne Victoria Australia
- Murdoch Children's Research InstituteMelbourne Victoria Australia
| | - Carla Marini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A Meyer Children's HospitalUniversity of FlorenceFlorence Italy
| | - Jeremy L. Freeman
- Departments of Neurology and Paediatrics, Royal Children's HospitalUniversity of MelbourneMelbourne Victoria Australia
- Murdoch Children's Research InstituteMelbourne Victoria Australia
| | - Anca Nica
- Department of Neurology, Center for Clinical Research (CIC 1414)Rennes University HospitalRennes France
| | - Gaetano Terrone
- Department of Translational Medical Sciences, Section of Pediatrics‐Child Neurology UnitFederico II UniversityNaples Italy
| | - Tayeb Sekhara
- Department of Pediatric NeurologyC.H.I.R.E.CBrussels Belgium
| | - Anne‐Sophie Lebre
- Department of genetics, Maison Blanche hospitalUniversity hospital, ReimsReims France
| | - Sylvie Odent
- Reference Centre for Rare Developmental AbnormalitiesCLAD‐Ouest, CHU RennesRennes France
- Institute of genetics and developmentCNRS UMR 6290, Rennes universityRennes France
| | - Lynette G. Sadleir
- Department of Paediatrics and Child HealthUniversity of OtagoWellington New Zealand
| | - Arnold Munnich
- Université Paris Descartes‐Sorbonne Paris CitéParis France
- Department of genetics, Necker Enfants Malades hospitalAssistance Publique‐Hôpitaux de ParisParis France
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A Meyer Children's HospitalUniversity of FlorenceFlorence Italy
| | - Ingrid E. Scheffer
- Department of Medicine, Epilepsy Research Centre, Austin HealthThe University of MelbourneHeidelberg Victoria Australia
- Departments of Neurology and Paediatrics, Royal Children's HospitalUniversity of MelbourneMelbourne Victoria Australia
- The Florey Institute of Neurosciences and Mental HealthHeidelberg Victoria Australia
| | - Edor Kabashi
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
| | - Rima Nabbout
- Department of Pediatric Neurology, Reference Centre for Rare EpilepsiesHôpital Necker‐Enfants MaladesParis France
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
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87
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Das RG, Becker D, Jagannathan V, Goldstein O, Santana E, Carlin K, Sudharsan R, Leeb T, Nishizawa Y, Kondo M, Aguirre GD, Miyadera K. Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness. Sci Rep 2019; 9:14166. [PMID: 31578364 PMCID: PMC6775105 DOI: 10.1038/s41598-019-50573-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/05/2019] [Indexed: 01/11/2023] Open
Abstract
Congenital stationary night blindness (CSNB), in the complete form, is caused by dysfunctions in ON-bipolar cells (ON-BCs) which are secondary neurons of the retina. We describe the first disease causative variant associated with CSNB in the dog. A genome-wide association study using 12 cases and 11 controls from a research colony determined a 4.6 Mb locus on canine chromosome 32. Subsequent whole-genome sequencing identified a 1 bp deletion in LRIT3 segregating with CSNB. The canine mutant LRIT3 gives rise to a truncated protein with unaltered subcellular expression in vitro. Genetic variants in LRIT3 have been associated with CSNB in patients although there is limited evidence regarding its apparently critical function in the mGluR6 pathway in ON-BCs. We determine that in the canine CSNB retina, the mutant LRIT3 is correctly localized to the region correlating with the ON-BC dendritic tips, albeit with reduced immunolabelling. The LRIT3-CSNB canine model has direct translational potential enabling studies to help understand the CSNB pathogenesis as well as to develop new therapies targeting the secondary neurons of the retina.
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Affiliation(s)
- Rueben G Das
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Doreen Becker
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America.,Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | | | - Orly Goldstein
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Evelyn Santana
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Kendall Carlin
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Raghavi Sudharsan
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern, Switzerland
| | - Yuji Nishizawa
- Department of Biomedical Sciences, Chubu University, Kasugai, Aichi, Japan
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Gustavo D Aguirre
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America
| | - Keiko Miyadera
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Pennsylvania, United States of America.
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88
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A deep intronic splice mutation of STAT3 underlies hyper IgE syndrome by negative dominance. Proc Natl Acad Sci U S A 2019; 116:16463-16472. [PMID: 31346092 DOI: 10.1073/pnas.1901409116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Heterozygous in-frame mutations in coding regions of human STAT3 underlie the only known autosomal dominant form of hyper IgE syndrome (AD HIES). About 5% of familial cases remain unexplained. The mutant proteins are loss-of-function and dominant-negative when tested following overproduction in recipient cells. However, the production of mutant proteins has not been detected and quantified in the cells of heterozygous patients. We report a deep intronic heterozygous STAT3 mutation, c.1282-89C>T, in 7 relatives with AD HIES. This mutation creates a new exon in the STAT3 complementary DNA, which, when overexpressed, generates a mutant STAT3 protein (D427ins17) that is loss-of-function and dominant-negative in terms of tyrosine phosphorylation, DNA binding, and transcriptional activity. In immortalized B cells from these patients, the D427ins17 protein was 2 kDa larger and 4-fold less abundant than wild-type STAT3, on mass spectrometry. The patients' primary B and T lymphocytes responded poorly to STAT3-dependent cytokines. These findings are reminiscent of the impaired responses of leukocytes from other patients with AD HIES due to typical STAT3 coding mutations, providing further evidence for the dominance of the mutant intronic allele. These findings highlight the importance of sequencing STAT3 introns in patients with HIES without candidate variants in coding regions and essential splice sites. They also show that AD HIES-causing STAT3 mutant alleles can be dominant-negative even if the encoded protein is produced in significantly smaller amounts than wild-type STAT3.
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89
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Han X, Wei Y, Wang H, Wang F, Ju Z, Li T. Nonsense-mediated mRNA decay: a 'nonsense' pathway makes sense in stem cell biology. Nucleic Acids Res 2019; 46:1038-1051. [PMID: 29272451 PMCID: PMC5814811 DOI: 10.1093/nar/gkx1272] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/09/2017] [Indexed: 01/04/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is a highly conserved post-transcriptional regulatory mechanism of gene expression in eukaryotes. Originally, NMD was identified as an RNA surveillance machinery in degrading 'aberrant' mRNA species with premature termination codons. Recent studies indicate that NMD regulates the stability of natural gene transcripts that play significant roles in cell functions. Although components and action modes of the NMD machinery in degrading its RNA targets have been extensively studied with biochemical and structural approaches, the biological roles of NMD remain to be defined. Stem cells are rare cell populations, which play essential roles in tissue homeostasis and hold great promises in regenerative medicine. Stem cells self-renew to maintain the cellular identity and differentiate into somatic lineages with specialized functions to sustain tissue integrity. Transcriptional regulations and epigenetic modulations have been extensively implicated in stem cell biology. However, post-transcriptional regulatory mechanisms, such as NMD, in stem cell regulation are largely unknown. In this paper, we summarize the recent findings on biological roles of NMD factors in embryonic and tissue-specific stem cells. Furthermore, we discuss the possible mechanisms of NMD in regulating stem cell fates.
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Affiliation(s)
- Xin Han
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Yanling Wei
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Hua Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Feilong Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Zhenyu Ju
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
| | - Tangliang Li
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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90
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Balestra D, Branchini A. Molecular Mechanisms and Determinants of Innovative Correction Approaches in Coagulation Factor Deficiencies. Int J Mol Sci 2019; 20:ijms20123036. [PMID: 31234407 PMCID: PMC6627357 DOI: 10.3390/ijms20123036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/07/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular strategies tailored to promote/correct the expression and/or processing of defective coagulation factors would represent innovative therapeutic approaches beyond standard substitutive therapy. Here, we focus on the molecular mechanisms and determinants underlying innovative approaches acting at DNA, mRNA and protein levels in inherited coagulation factor deficiencies, and in particular on: (i) gene editing approaches, which have permitted intervention at the DNA level through the specific recognition, cleavage, repair/correction or activation of target sequences, even in mutated gene contexts; (ii) the rescue of altered pre-mRNA processing through the engineering of key spliceosome components able to promote correct exon recognition and, in turn, the synthesis and secretion of functional factors, as well as the effects on the splicing of missense changes affecting exonic splicing elements; this section includes antisense oligonucleotide- or siRNA-mediated approaches to down-regulate target genes; (iii) the rescue of protein synthesis/function through the induction of ribosome readthrough targeting nonsense variants or the correction of folding defects caused by amino acid substitutions. Overall, these approaches have shown the ability to rescue the expression and/or function of potentially therapeutic levels of coagulation factors in different disease models, thus supporting further studies in the future aimed at evaluating the clinical translatability of these new strategies.
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Affiliation(s)
- Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
| | - Alessio Branchini
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
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91
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Grimholt RM, Fjeld B, Selsås H, Schwettmann L, Klingenberg O. Hb Aalesund ( HBA2: c.400_406delAGCACCG), an Unstable α-Globin Variant Found in a Norwegian Patient Causing Moderate Hemolytic Anemia and Falsely High Hb A 1c Using Ion Exchange High Performance Liquid Chromatography. Hemoglobin 2019; 43:122-125. [PMID: 31145010 DOI: 10.1080/03630269.2019.1614048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A new unstable hemoglobin (Hb) variant, named Hb Aalesund, was detected during Hb A1c measurement in a patient with a nearly compensated hemolytic anemia. Sequencing of the α-globin genes revealed a 7 bp deletion in exon 3 of the HBA2 gene (HBA2: c.400_406delAGCACCG) (NM_000517.4) causing a frameshift and a premature termination codon (PTC) two positions downstream. Apparently, the transcript bypassed nonsense-mediated decay (NMD), and a truncated protein was translated. The unstable Hb variant presumably underwent rapid denaturation, as heterozygosity of Hb Aalesund was associated with mild hemolytic anemia. In addition, the Hb variant interfered with Hb A1c measurement by cation exchange high performance liquid chromatography (HPLC), causing a falsely high Hb A1c result when using the Bio-Rad D10™ Hemoglobin Analyzer fast Hb A1c Program.
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Affiliation(s)
- Runa M Grimholt
- a Department of Medical Biochemistry , Oslo University Hospital, Ullevaal , Oslo , Norway.,b Institute of Clinical Medicine , University of Oslo , Oslo , Norway.,c Department of Life Sciences and Health , OsloMet (Oslo Metropolitan) University , Oslo , Norway
| | - Bente Fjeld
- a Department of Medical Biochemistry , Oslo University Hospital, Ullevaal , Oslo , Norway.,b Institute of Clinical Medicine , University of Oslo , Oslo , Norway
| | - Hilde Selsås
- d Department of Endocrinology , Aalesund Hospital , Aalesund , Norway
| | - Lutz Schwettmann
- e Department of Medical Biochemistry , Aalesund Hospital , Aalesund , Norway.,f Department of Biological Sciences , Norwegian University of Science and Technology , Aalesund , Norway
| | - Olav Klingenberg
- a Department of Medical Biochemistry , Oslo University Hospital, Ullevaal , Oslo , Norway.,b Institute of Clinical Medicine , University of Oslo , Oslo , Norway
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92
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Yabe SG, Nishida J, Fukuda S, Takeda F, Nasiro K, Yasuda K, Iwasaki N, Okochi H. Expression of mutant mRNA and protein in pancreatic cells derived from MODY3- iPS cells. PLoS One 2019; 14:e0217110. [PMID: 31145732 PMCID: PMC6542550 DOI: 10.1371/journal.pone.0217110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Maturity-onset diabetes of the young (MODY) is a heterozygous monogenic diabetes; more than 14 disease genes have been identified. However, the pathogenesis of MODY is not fully understood because the patients' pancreatic beta cells are inaccessible. To elucidate the pathology of MODY, we established MODY3 patient-derived iPS (MODY3-iPS) cells using non-integrating Sendai virus (SeV) vector and examined the mutant mRNA and protein of HNF1A (Hepatocyte Nuclear factor 1A) after pancreatic lineage differentiation. Our patient had a cytosine insertion in the HNF1A gene (P291fsinsC) causing frameshift and making a premature termination codon (PTC). We confirmed these MODY3-iPS cells possessed the characteristics of pluripotent stem cells. After we differentiated them into pancreatic beta cells, transcripts of HNF1A gene were cloned and sequenced. We found that P291fsinsC mutant transcripts were much less frequent than wild ones, but they increased after adding cycloheximide (CHX) to the medium. These results suggested that mutant mRNA was destroyed by nonsense-mediated mRNA decay (NMD). Moreover, we were not able to detect any band of mutant proteins in pancreatic lineage cells which were differentiated from MODY3-iPSCs by western blot (WB) analysis. A scarcity of the truncated form of mutant protein may indicate that MODY3 might be caused by a haplo-insufficiency effect rather than a dominant negative manner.
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Affiliation(s)
- Shigeharu G. Yabe
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Junko Nishida
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Satsuki Fukuda
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Fujie Takeda
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kiyoko Nasiro
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuki Yasuda
- Department of Metabolic Disorders, Diabetes Research Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naoko Iwasaki
- Institute of Geriatrics, Diabetes Center, Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - Hitoshi Okochi
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
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93
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Rodríguez-Contreras FJ, Marbán-Calzón M, Vallespín E, Del Pozo Á, Solís-López M, Lobato-Vidal N, Fernández-Elvira M, Del Valle Rex-Romero M, Heath KE, González-Casado I, Campos-Barros Á. Loss of function BMP4 mutation supports the implication of the BMP/TGF-β pathway in the etiology of combined pituitary hormone deficiency. Am J Med Genet A 2019; 179:1591-1597. [PMID: 31120642 DOI: 10.1002/ajmg.a.61201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/19/2022]
Abstract
Despite BMP4 signaling being critical to Rathke's pouch induction and maintenance during early stages of pituitary development, its implication in the etiology of combined pituitary hormone deficiency (CPHD) and other clinical presentations of congenital hypopituitarism has not yet been definitely demonstrated. We report here the first CPHD patient with a de novo pathogenic loss-of-function variant in BMP4. A 6-year-old boy, with macrocephaly, myopia/astigmatism, mild psychomotor retardation, anterior pituitary hypoplasia and ectopic posterior pituitary, clinically diagnosed with growth hormone deficiency, and central hypothyroidism, was referred for genetic analysis of CPHD. Targeted NGS analysis with a custom panel (n = 310 genes) identified a novel heterozygous de novo nonsense variant, NM_001202.5:c.794G > A, p.(Trp265*) in BMP4, which introduces a premature stop codon in the BMP4 pro-domain, impairing the transcription of the TGF-β mature peptide domain. Additional relevant variants in other genes implicated in pituitary development signaling pathways such as SMAD4 and E2F4 (BMP/TGF-pathway), ALMS1 (NOTCH-pathway), and TSHZ1 (Prokineticin-pathway), were also identified. Our results support the implication of the BMP/TGF-β signaling pathway in the etiology of CPHD and suggest that oligogenic contribution of additional inherited variants may modify the phenotypic expressivity of BMP4 pathogenic variants.
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Affiliation(s)
- Francisco J Rodríguez-Contreras
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Department of Pediatrics, Centro de Salud Galapagar, Madrid, Spain
| | | | - Elena Vallespín
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | - Ángela Del Pozo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario Solís-López
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - Nerea Lobato-Vidal
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - María Fernández-Elvira
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - María Del Valle Rex-Romero
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Ángel Campos-Barros
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autonóma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER; U753), Instituto de Salud Carlos III, Madrid, Spain
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94
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Bell S, Rousseau J, Peng H, Aouabed Z, Priam P, Theroux JF, Jefri M, Tanti A, Wu H, Kolobova I, Silviera H, Manzano-Vargas K, Ehresmann S, Hamdan FF, Hettige N, Zhang X, Antonyan L, Nassif C, Ghaloul-Gonzalez L, Sebastian J, Vockley J, Begtrup AG, Wentzensen IM, Crunk A, Nicholls RD, Herman KC, Deignan JL, Al-Hertani W, Efthymiou S, Salpietro V, Miyake N, Makita Y, Matsumoto N, Østern R, Houge G, Hafström M, Fassi E, Houlden H, Klein Wassink-Ruiter JS, Nelson D, Goldstein A, Dabir T, van Gils J, Bourgeron T, Delorme R, Cooper GM, Martinez JE, Finnila CR, Carmant L, Lortie A, Oegema R, van Gassen K, Mehta SG, Huhle D, Abou Jamra R, Martin S, Brunner HG, Lindhout D, Au M, Graham JM, Coubes C, Turecki G, Gravel S, Mechawar N, Rossignol E, Michaud JL, Lessard J, Ernst C, Campeau PM. Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons. Am J Hum Genet 2019; 104:815-834. [PMID: 31031012 PMCID: PMC6507050 DOI: 10.1016/j.ajhg.2019.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/01/2019] [Indexed: 02/04/2023] Open
Abstract
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Justine Rousseau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Arnaud Tanti
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Ilaria Kolobova
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Heika Silviera
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Karla Manzano-Vargas
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Sophie Ehresmann
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Fadi F Hamdan
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Christina Nassif
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | | | | | - Robert D Nicholls
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Kristin C Herman
- University of California at Davis Medical Center, Section of Medical Genomics, Sacramento, CA 95817, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Walla Al-Hertani
- Departments of Medical Genetics and Paediatrics, Cumming School of Medicine, Alberta Children's Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Rune Østern
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Maria Hafström
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Dominic Nelson
- McGill University, Department of Human Genetics, Montreal, QC H3G 0B1, Canada
| | - Amy Goldstein
- Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, UK
| | - Julien van Gils
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Richard Delorme
- Assistance Publique Hôpitaux de Paris (APHP), Robert Debré Hospital, Child and Adolescent Psychiatry Department, Paris, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Lionel Carmant
- Children's Rehabilitation Service, Mobile, AL 36604, USA
| | - Anne Lortie
- Department of Neurology, University of Montreal, Montreal, QC, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Sarju G Mehta
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Dagmar Huhle
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Sonja Martin
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 GA, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - Dick Lindhout
- Department of Genetics, University Medical Center Utrecht, Utrecht & Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Margaret Au
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - John M Graham
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christine Coubes
- Service de génétique clinique, Département de génétique médicale, Maladies rares et médecine personnalisée, Centre de Référence Anomalies du développement et Syndromes malformatifs du Sud-Ouest Occitanie Réunion, CHU de Montpellier, 34295 Montpellier Cedex 5, France
| | - Gustavo Turecki
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Simon Gravel
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Naguib Mechawar
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Elsa Rossignol
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Jacques L Michaud
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Julie Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Carl Ernst
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada.
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada.
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95
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Harel T, Levy-Lahad E, Daana M, Mechoulam H, Horowitz-Cederboim S, Gur M, Meiner V, Elpeleg O. Homozygous stop-gain variant in LRRC32, encoding a TGFβ receptor, associated with cleft palate, proliferative retinopathy, and developmental delay. Eur J Hum Genet 2019; 27:1315-1319. [PMID: 30976112 DOI: 10.1038/s41431-019-0380-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 03/01/2019] [Accepted: 03/07/2019] [Indexed: 02/03/2023] Open
Abstract
The transforming growth factor-beta (TGFβ) signaling pathway is essential for palatogenesis and retinal development. Glycoprotein A repetitions predominant (GARP), encoded by LRRC32, is a TGFβ cell surface receptor that has been studied primarily in the context of cellular immunity. We identified a homozygous stop-gain variant in LRRC32 (c.1630C>T; p.(Arg544Ter)) in two families with developmental delay, cleft palate, and proliferative retinopathy. Garp-null mice have palate defects and die within 24 h after birth. Our study establishes LRRC32 as a candidate disease-associated gene in humans and lends further support to the role of the TGFβ pathway in palatogenesis and retinal development.
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Affiliation(s)
- Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel.
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Muhannad Daana
- Child Development Centers, Clalit and Maccabi Health Care Services, Jerusalem District, Jerusalem, Israel
| | - Hadas Mechoulam
- Center for Pediatric Ophthalmology, Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Smadar Horowitz-Cederboim
- Medical Genetics Institute, Shaare Zedek Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Gur
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel
| | - Orly Elpeleg
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, 9112001, Jerusalem, Israel.,Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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96
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Ma KM, Thomas ES, Wereszczynski J, Menhart N. Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy. Biochemistry 2019; 58:2061-2076. [PMID: 30896926 DOI: 10.1021/acs.biochem.9b00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a common and devastating genetic disease primarily caused by exon deletions that create a genetic frameshift in dystrophin. Exon skipping therapy seeks to correct this by masking an exon during the mRNA maturation process, restoring dystrophin expression, but creating an edited protein missing both the original defect and the therapeutically skipped region. Crucially, it is possible to correct many defects in alternative ways, by skipping an exon either before or after the patient's defect. This results in alternatively edited, hybrid proteins that might have different properties and therapeutic consequences. We examined three such dystrophin exon-skipped edits, Δe45-53, Δe46-54, and Δe47-55, comprising two pairs of alternative repairs of Δe46-53 and Δe47-54 DMD defects. We found that in both cases, Δe46-54 was the more stable repair as determined by a variety of thermodynamic and biochemical measurements. We also examined the origin of these differences with molecular dynamics simulations, which showed that these stability differences were the result of different types of structural perturbations. For example, in one edit there was partial unfolding at the edit site that caused domain-localized perturbations while in another there was unfolding at the protein domain junctions distal to the edit site that increased molecular flexibility. These results demonstrate that alternative exon skip repairs of the same underlying defect can have very different consequences at the level of protein structure and stability and furthermore that these can arise by different mechanisms, either locally or by more subtle long-range perturbations.
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97
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Posey JE, O'Donnell-Luria AH, Chong JX, Harel T, Jhangiani SN, Coban Akdemir ZH, Buyske S, Pehlivan D, Carvalho CMB, Baxter S, Sobreira N, Liu P, Wu N, Rosenfeld JA, Kumar S, Avramopoulos D, White JJ, Doheny KF, Witmer PD, Boehm C, Sutton VR, Muzny DM, Boerwinkle E, Günel M, Nickerson DA, Mane S, MacArthur DG, Gibbs RA, Hamosh A, Lifton RP, Matise TC, Rehm HL, Gerstein M, Bamshad MJ, Valle D, Lupski JR. Insights into genetics, human biology and disease gleaned from family based genomic studies. Genet Med 2019; 21:798-812. [PMID: 30655598 PMCID: PMC6691975 DOI: 10.1038/s41436-018-0408-7] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Identifying genes and variants contributing to rare disease phenotypes and Mendelian conditions informs biology and medicine, yet potential phenotypic consequences for variation of >75% of the ~20,000 annotated genes in the human genome are lacking. Technical advances to assess rare variation genome-wide, particularly exome sequencing (ES), enabled establishment in the United States of the National Institutes of Health (NIH)-supported Centers for Mendelian Genomics (CMGs) and have facilitated collaborative studies resulting in novel "disease gene" discoveries. Pedigree-based genomic studies and rare variant analyses in families with suspected Mendelian conditions have led to the elucidation of hundreds of novel disease genes and highlighted the impact of de novo mutational events, somatic variation underlying nononcologic traits, incompletely penetrant alleles, phenotypes with high locus heterogeneity, and multilocus pathogenic variation. Herein, we highlight CMG collaborative discoveries that have contributed to understanding both rare and common diseases and discuss opportunities for future discovery in single-locus Mendelian disorder genomics. Phenotypic annotation of all human genes; development of bioinformatic tools and analytic methods; exploration of non-Mendelian modes of inheritance including reduced penetrance, multilocus variation, and oligogenic inheritance; construction of allelic series at a locus; enhanced data sharing worldwide; and integration with clinical genomics are explored. Realizing the full contribution of rare disease research to functional annotation of the human genome, and further illuminating human biology and health, will lay the foundation for the Precision Medicine Initiative.
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Affiliation(s)
- Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Boston Children's Hospital, Boston, MA, USA
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shalini N Jhangiani
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Steven Buyske
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
- Department of Statistics, Rutgers University, Piscataway, NJ, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratory, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sushant Kumar
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Dimitri Avramopoulos
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Janson J White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kimberly F Doheny
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Corinne Boehm
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Eric Boerwinkle
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center, Houston, TX, USA
| | - Murat Günel
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Shrikant Mane
- Yale Center for Genome Analysis, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Richard P Lifton
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Heidi L Rehm
- Analytic and Translational Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University Medical School, New Haven, CT, USA
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA.
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98
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Pharmacologic normalization of pathogenic dosage underlying genetic diseases: an overview of the literature and path forward. Emerg Top Life Sci 2019; 3:53-62. [PMID: 33523192 DOI: 10.1042/etls20180099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 12/17/2022]
Abstract
Most monogenic disorders are caused by a pathologic deficit or excess of a single transcript and/or protein. Given that small molecules, including drugs, can affect levels of mRNA and protein, the pharmacologic normalization of such pathogenic dosage represents a possible therapeutic approach for such conditions. Here, we review the literature exploring pharmacologic modulation of mRNA and/or protein levels for disorders with paralogous modifier genes, for haploinsufficient disorders (insufficient gene-product), as well as toxic gain-of-function disorders (surplus or pathologic gene-product). We also discuss challenges facing the development of rare disease therapy by pharmacologic modulation of mRNA and protein. Finally, we lay out guiding principles for selection of disorders which may be amenable to this approach.
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99
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He WB, Du J, Yang XW, Li W, Tang WL, Dai C, Chen YZ, Zhang YX, Lu GX, Lin G, Gong F, Tan YQ. Novel inactivating mutations in the FSH receptor cause premature ovarian insufficiency with resistant ovary syndrome. Reprod Biomed Online 2019; 38:397-406. [DOI: 10.1016/j.rbmo.2018.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/29/2018] [Accepted: 11/29/2018] [Indexed: 02/05/2023]
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100
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Pedersen HR, Neitz M, Gilson SJ, Landsend ECS, Utheim ØA, Utheim TP, Baraas RC. The Cone Photoreceptor Mosaic in Aniridia: Within-Family Phenotype-Genotype Discordance. Ophthalmol Retina 2019; 3:523-534. [PMID: 31174676 DOI: 10.1016/j.oret.2019.01.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/01/2023]
Abstract
PURPOSE Investigate in vivo cone photoreceptor structure in familial aniridia caused by deletion in the PAX6 gene to elucidate the complexity of between-individual variation in retinal phenotype. DESIGN Descriptive case-control study. PARTICIPANTS Eight persons with congenital aniridia (40-66 yrs) from 1 family and 33 normal control participants (14-69 yrs), including 7 unaffected family members (14-53 yrs). METHODS DNA was isolated from saliva samples and used in polymerase chain reaction analysis to amplify and sequence exons and intron or exon junctions of the PAX6 gene. High-resolution retinal images were acquired with OCT and adaptive optics scanning light ophthalmoscopy. Cone density (CD; in cones per square millimeter) and mosaic regularity were estimated along nasal-temporal meridians within the central 0° to 5° eccentricity. Horizontal spectral-domain OCT line scans were segmented to analyze the severity of foveal hypoplasia (FH) and to measure retinal layer thicknesses. MAIN OUTCOMES AND MEASURES Within-family variability in macular retinal layer thicknesses, cone photoreceptor density, and mosaic regularity in aniridia compared with normal control participants. RESULTS DNA sequencing revealed a known PAX6 mutation (IV2-2delA). Those with aniridia showed variable iris phenotype ranging from almost normal appearance to no iris. Four participants with aniridia demonstrated FH grade 2, 2 demonstrated grade 3 FH, and 1 demonstrated grade 4 FH. Visual acuity ranged from 0.20 to 0.86 logarithm of the minimum angle of resolution. Adaptive optics scanning light ophthalmoscopy images were acquired from 5 family members with aniridia. Foveal CD varied between 19 899 and 55 128 cones/mm2 with overlap between the foveal hypoplasia grades. Cone density was 3 standard deviations (SDs) or more less than the normal mean within 0.5°, 2 SDs less than the normal mean at 0.5° to 4°, and more than 1 SD less than the normal mean at 5° retinal eccentricity. CONCLUSIONS The results showed considerable variability in foveal development within a family carrying the same PAX6 mutation. This, together with the structural and functional variability within each grade of foveal hypoplasia, underlines the importance of advancing knowledge about retinal cellular phenotype in aniridia.
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Affiliation(s)
- Hilde R Pedersen
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | - Maureen Neitz
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - Stuart J Gilson
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway
| | | | | | - Tor Paaske Utheim
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway; Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Rigmor C Baraas
- National Centre for Optics, Vision and Eye Care, Faculty of Health and Social Sciences, University of South-Eastern Norway, Kongsberg, Norway.
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