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Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, Ponder JW, Shen J, Smith RJH, Yang W, Ren P, Schnieders MJ. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. J Chem Phys 2024; 161:012501. [PMID: 38958156 PMCID: PMC11223778 DOI: 10.1063/5.0214652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024] Open
Abstract
Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid-base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.
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Affiliation(s)
- Rose A. Gogal
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Aaron J. Nessler
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Andrew C. Thiel
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Hernan V. Bernabe
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Rae A. Corrigan Grove
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Leah M. Cousineau
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Litman
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jacob M. Miller
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Guowei Qi
- Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
| | - Matthew J. Speranza
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Mallory R. Tollefson
- Roy J. Carver Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
| | - Timothy D. Fenn
- Analytical Development, LEXEO Therapeutics, New York, New York 10010, USA
| | - Jacob J. Michaelson
- Department of Psychiatry, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | - Okimasa Okada
- Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | | | - Jay W. Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA
| | | | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas, Austin, Texas 78712, USA
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Thuma TBT, Procopio RA, Jimenez HJ, Gunton KB, Pulido JS. Hypomorphic variants in inherited retinal and ocular diseases: A review of the literature with clinical cases. Surv Ophthalmol 2024; 69:337-348. [PMID: 38036193 DOI: 10.1016/j.survophthal.2023.11.006] [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: 06/20/2022] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Hypomorphic variants decrease, but do not eliminate, gene function via a reduction in the amount of mRNA or protein product produced by a gene or by production of a gene product with reduced function. Many hypomorphic variants have been implicated in inherited retinal diseases (IRDs) and other genetic ocular conditions; however, there is heterogeneity in the use of the term "hypomorphic" in the scientific literature. We searched for all hypomorphic variants reported to cause IRDs and ocular disorders. We also discuss the presence of hypomorphic variants in the patient population of our ocular genetics department over the past decade. We propose that standardized criteria should be adopted for use of the term "hypomorphic" to describe gene variants to improve genetic counseling and patient care outcomes.
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Affiliation(s)
- Tobin B T Thuma
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | | | - Hiram J Jimenez
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA
| | - Kammi B Gunton
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | - Jose S Pulido
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA; Retina Service, Wills Eye Hospital, Philadelphia, PA, USA.
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3
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Gupta M, Pazour GJ. Intraflagellar transport: A critical player in photoreceptor development and the pathogenesis of retinal degenerative diseases. Cytoskeleton (Hoboken) 2023:10.1002/cm.21823. [PMID: 38140908 PMCID: PMC11193844 DOI: 10.1002/cm.21823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
In vertebrate vision, photons are detected by highly specialized sensory cilia called outer segments. Photoreceptor outer segments form by remodeling the membrane of a primary cilium into a stack of flattened disks. Intraflagellar transport (IFT) is critical to the formation of most types of eukaryotic cilia including the outer segments. This review covers the state of knowledge of the role of IFT in the formation and maintenance of outer segments and the human diseases that result from mutations in genes encoding the IFT complex and associated motors.
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Affiliation(s)
- Mohona Gupta
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Suite 213 Biotech II, 373 Plantation Street, Worcester MA USA 01605
- Morningside Graduate School of Biological Sciences, University of Massachusetts Chan Medical School, 55 Lake Avenue North, Worcester MA USA 01655
| | - Gregory J. Pazour
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Suite 213 Biotech II, 373 Plantation Street, Worcester MA USA 01605
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4
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Li Y, Deng M, Han T, Mo W, Mao H. Thalidomide as an Effective Treatment in Sideroblastic Anemia, Immunodeficiency, Periodic Fevers, and Developmental Delay (SIFD). J Clin Immunol 2023; 43:780-793. [PMID: 36729249 PMCID: PMC9893968 DOI: 10.1007/s10875-023-01441-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/19/2023] [Indexed: 02/03/2023]
Abstract
PURPOSE Sideroblastic anemia, immunodeficiency, periodic fevers, and developmental delay (SIFD) is an autosomal recessive syndrome caused by biallelic loss-of-function variant of tRNA nucleotidyl transferase 1 (TRNT1). Efficacious methods to treat SIFD are lacking. We identified two novel mutations in TRNT1 and an efficacious and novel therapy for SIFD. METHODS We retrospectively summarized the clinical records of two patients with SIFD from different families and reviewed all published cases of SIFD. RESULTS Both patients had periodic fever, developmental delay, rash, microcytic anemia, and B cell lymphopenia with infections. Whole-exome sequencing of patient 1 identified a previously unreported homozygous mutation of TRNT1 (c.706G > A/p.Glu236Lys). He received intravenous immunoglobulin (IVIG) replacement and antibiotics, but died at 1 year of age. Gene testing in patient 2 revealed compound heterozygous mutations (c.907C > G/p.Gln303Glu and c.88A > G/p.Met30Val) in TRNT1, the former of which is a novel mutation. Periodic fever was controlled in the first month after adalimumab therapy and IVIG replacement, but recurred in the second month. Adalimumab was discontinued and replaced with thalidomide, which controlled the periodic fever and normalized inflammatory markers effectively. A retrospective analysis of reported cases revealed 69 patients with SIFD carrying 46 mutations. The male: female ratio was 1: 1, and the mean age of onset was 3.0 months. The most common clinical manifestations in patients with SIFD were microcytic anemia (82.6%), hypogammaglobulinemia/B cell lymphopenia (75.4%), periodic fever (66.7%), and developmental delay (60.0%). In addition to the typical tetralogy, SIFD features several heterogeneous symptoms involving multiple systems. Corticosteroids, immunosuppressants, and anakinra have low efficacy, whereas etanercept suppressed fever and improved anemia in reports. Bone-marrow transplantation can be used to treat severe SIFD, but carries a high risk. In total, 28.2% (20/71) of reported patients died, mainly because of multi-organ failure. Biallelic mutations located in exon1-intron5 lead to more severe phenotypes and higher mortality. Furthermore, 15.5% (11/71) patients survived to adulthood. The symptoms could be resolved spontaneously in five patients. CONCLUSIONS Thalidomide can control the inflammation of SIFD and represents a new treatment for SIFD.
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Affiliation(s)
- Yan Li
- Department of Immunology, Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Mengyue Deng
- Department of Immunology, Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Tongxin Han
- Department of Immunology, Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Wenxiu Mo
- Department of Immunology, Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, No. 56 Nanlishi Road, Beijing, 100045, China
| | - Huawei Mao
- Department of Immunology, Ministry of Education Key Laboratory of Major Diseases in Children, Beijing Children's Hospital, National Center for Children's Health, Capital Medical University, No. 56 Nanlishi Road, Beijing, 100045, China.
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5
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Kwan JT, Ramsey DJ. Multimodal image alignment aids in the evaluation and monitoring of sector retinitis pigmentosa. Ophthalmic Genet 2023; 44:93-102. [PMID: 35769018 DOI: 10.1080/13816810.2022.2092755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
PURPOSE To present a semi-automated method of image alignment to aid in monitoring the progression of inherited retinal degenerations (IRDs). RESULTS A 22-year-old woman presented with nyctalopia and a family history of retinitis pigmentosa (RP), but with no prior genetic testing. Fundus examination showed a sectoral retinal degeneration involving the inferior and nasal retina with rare, pigmented deposits. Goldmann kinetic perimetry demonstrated corresponding superotemporal visual field defects. The best-corrected visual acuity was 20/20 in both eyes. Multimodal imaging delineated geographically restricted peripheral retinal degeneration extending to the inferior edge of the macula. Central visual function remained intact with normal multifocal electroretinography findings. Optical coherence tomography (OCT) through the leading edge of the retinal degeneration confirmed loss of the photoreceptor layer and associated retinal pigment epithelium. In the region of retinal degeneration, loss of vascular flow density was noted on optical coherence tomography angiography (OCTA). Genetic testing identified a pathologic sequence variant in RHO (c.68C>A, p.Pro23His), confirming autosomal dominant sector retinitis pigmentosa (SRP). Image alignment allowed for precise measurement of the progression of SRP over a period of 18 months. CONCLUSION SRP is a rare subtype of RP characterized by focal, typically inferior and nasal, retinal degeneration of the peripheral retina. Although the onset and extent of peripheral retinal degeneration varies, compared with RP, SRP typically progresses more slowly to involve the macula. In this report, we highlight the utility of image registration and alignment to aid in monitoring disease progression in IRDs by means of multimodal imaging.
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Affiliation(s)
- James T Kwan
- Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, USA.,Department of Surgery, Division of Ophthalmology, Lahey Hospital & Medical Center, Burlington, Massachusetts, USA
| | - David J Ramsey
- Department of Ophthalmology, Tufts University School of Medicine, Boston, Massachusetts, USA.,Department of Surgery, Division of Ophthalmology, Lahey Hospital & Medical Center, Burlington, Massachusetts, USA
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Modopathies Caused by Mutations in Genes Encoding for Mitochondrial RNA Modifying Enzymes: Molecular Mechanisms and Yeast Disease Models. Int J Mol Sci 2023; 24:ijms24032178. [PMID: 36768505 PMCID: PMC9917222 DOI: 10.3390/ijms24032178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, mitochondrial RNAs (mt-tRNAs and mt-rRNAs) are subject to specific nucleotide modifications, which are critical for distinct functions linked to the synthesis of mitochondrial proteins encoded by mitochondrial genes, and thus for oxidative phosphorylation. In recent years, mutations in genes encoding for mt-RNAs modifying enzymes have been identified as being causative of primary mitochondrial diseases, which have been called modopathies. These latter pathologies can be caused by mutations in genes involved in the modification either of tRNAs or of rRNAs, resulting in the absence of/decrease in a specific nucleotide modification and thus on the impairment of the efficiency or the accuracy of the mitochondrial protein synthesis. Most of these mutations are sporadic or private, thus it is fundamental that their pathogenicity is confirmed through the use of a model system. This review will focus on the activity of genes that, when mutated, are associated with modopathies, on the molecular mechanisms through which the enzymes introduce the nucleotide modifications, on the pathological phenotypes associated with mutations in these genes and on the contribution of the yeast Saccharomyces cerevisiae to confirming the pathogenicity of novel mutations and, in some cases, for defining the molecular defects.
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Maccora I, Ramanan AV, Wiseman D, Marrani E, Mastrolia MV, Simonini G. Clinical and Therapeutic Aspects of Sideroblastic Anaemia with B-Cell Immunodeficiency, Periodic Fever and Developmental Delay (SIFD) Syndrome: a Systematic Review. J Clin Immunol 2023; 43:1-30. [PMID: 35984545 PMCID: PMC9840570 DOI: 10.1007/s10875-022-01343-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/01/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND PURPOSE Sideroblastic anaemia with B-cell immunodeficiency, periodic fever and developmental delay (SIFD) syndrome is a novel rare autoinflammatory multisystem disorder. We performed a systematic review of the available clinical and therapeutics aspects of the SIFD syndrome. METHODS A systematic review according to PRISMA approach, including all articles published before the 30th of July 2021 in Pubmed and EMBASE database, was performed. RESULTS The search identified 29 publications describing 58 unique patients. To date, 41 unique mutations have been reported. Onset of disease is very early with a median age of 4 months (range 0-252 months). The most frequent manifestations are haematologic such as microcytic anaemia or sideroblastic anaemia (55/58), recurrent fever (52/58), neurologic abnormalities (48/58), immunologic abnormalities in particular a humoral immunodeficiency (48/58), gastrointestinal signs and symptoms (38/58), eye diseases as cataract and retinitis pigmentosa (27/58), failure to thrive (26/58), mucocutaneous involvement (29/58), sensorineural deafness (19/58) and others. To date, 19 patients (35.85%) died because of disease course (16) and complications of hematopoietic cell stems transplantation (3). The use of anti-TNFα and hematopoietic cell stems transplantation (HCST) is dramatically changing the natural history of this disease. CONCLUSIONS SIFD syndrome is a novel entity to consider in a child presenting with recurrent fever, anaemia, B-cell immunodeficiency and neurodevelopmental delay. To date, therapeutic guidelines are lacking but anti-TNFα treatment and/or HCST are attractive and might modify the clinical course of this syndrome.
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Affiliation(s)
- Ilaria Maccora
- Rheumatology Unit, Meyer Children's University Hospital, Viale Pieraccini 24, 50139, Florence, Italy.
- NeuroFARBA Department, University of Florence, Viale Pieraccini 24, 50139, Florence, Italy.
| | - Athimalaipet V Ramanan
- Bristol Royal Hospital for Children and Translational Health Sciences, University of Bristol, Bristol, UK
| | - Daniel Wiseman
- Department of Haematology, Royal Manchester Children's Hospital, Manchester, UK
| | - Edoardo Marrani
- Rheumatology Unit, Meyer Children's University Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Maria V Mastrolia
- Rheumatology Unit, Meyer Children's University Hospital, Viale Pieraccini 24, 50139, Florence, Italy
| | - Gabriele Simonini
- Rheumatology Unit, Meyer Children's University Hospital, Viale Pieraccini 24, 50139, Florence, Italy
- NeuroFARBA Department, University of Florence, Viale Pieraccini 24, 50139, Florence, Italy
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8
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Chen X, Fu F, Mo X, Cheng S, Zeng H. Case report: Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay: Three cases and a literature review. Front Pediatr 2023; 11:1001222. [PMID: 36937953 PMCID: PMC10017860 DOI: 10.3389/fped.2023.1001222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/20/2023] [Indexed: 03/06/2023] Open
Abstract
Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) is a serious autosomal recessive syndrome caused by biallelic mutations in cytosine-cytosine-adenosine tRNA nucleotidyltransferase 1 (TRNT1). The main clinical features of SIFD are periodic fevers, developmental delay, sideroblastic or microcytic anemia, and immunodeficiency. Herein, we report three cases of SIFD with compound heterozygous variants of TRNT1. Patients 1 and 2 were siblings; they presented with periodic fevers, arthritis, low immunoglobulin A, bilateral cataracts, anemia, and neurodevelopmental and developmental delay. Patient 3 had severed clinical features with recurrent fever and infections. She was treated with infliximab and symptomatic treatments but without therapeutic effect. She received a stem cell transplantation of umbilical cord blood but died of posttransplant infection and posttransplant graft-vs.-host disease 17 days after transplantation. Finally, a literature review revealed that TRNT1 variants differed among SIFD patients. Our cases and literature review further expand existing knowledge on the phenotype and TRNT1 variations of SIFD and suggest that the early genomic diagnosis of TRNT1 is valuable to promptly assess bone marrow transplantation and tumor necrosis factor inhibitor treatments, which might be effective for the immunodeficiency and inflammation caused by SIFD.
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Affiliation(s)
- Xiangyuan Chen
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Fang Fu
- Department Institute of Birth Health and Perinatal Medicine, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Xiaolan Mo
- Department of Pharmacy, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Suyun Cheng
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
| | - Huasong Zeng
- Department of Allergy, Immunology and Rheumatology, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, China
- Correspondence: Huasong Zeng
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9
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Bhardwaj A, Yadav A, Yadav M, Tanwar M. Genetic dissection of non-syndromic retinitis pigmentosa. Indian J Ophthalmol 2022; 70:2355-2385. [PMID: 35791117 PMCID: PMC9426071 DOI: 10.4103/ijo.ijo_46_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Retinitis pigmentosa (RP) belongs to a group of pigmentary retinopathies. It is the most common form of inherited retinal dystrophy, characterized by progressive degradation of photoreceptors that leads to nyctalopia, and ultimately, complete vision loss. RP is distinguished by the continuous retinal degeneration that progresses from the mid-periphery to the central and peripheral retina. RP was first described and named by Franciscus Cornelius Donders in the year 1857. It is one of the leading causes of bilateral blindness in adults, with an incidence of 1 in 3000 people worldwide. In this review, we are going to focus on the genetic heterogeneity of this disease, which is provided by various inheritance patterns, numerosity of variations and inter-/intra-familial variations based upon penetrance and expressivity. Although over 90 genes have been identified in RP patients, the genetic cause of approximately 50% of RP cases remains unknown. Heterogeneity of RP makes it an extremely complicated ocular impairment. It is so complicated that it is known as “fever of unknown origin”. For prognosis and proper management of the disease, it is necessary to understand its genetic heterogeneity so that each phenotype related to the various genetic variations could be treated.
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Affiliation(s)
- Aarti Bhardwaj
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Anshu Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Manoj Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Mukesh Tanwar
- Department of Genetics, M. D. University, Rohtak, Haryana, India
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10
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Bravo García-Morato M, Padilla-Merlano B, Matas Pérez E, Shephard JLV, Marhuenda ÁR, Santos Simarro F, López-Granados E, Pena RR. Hypomorphic Variant in TRNT1 Induces a Milder Autoinflammatory Disease with Congenital Cataracts and Impaired Sexual Development. Rheumatology (Oxford) 2021; 61:e114-e116. [PMID: 34864912 DOI: 10.1093/rheumatology/keab903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 11/05/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- María Bravo García-Morato
- Department of Clinical Immunology, La Paz University Hospital, Madrid, Spain.,Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, IdiPAZ.,Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
| | | | | | | | - Ángel Robles Marhuenda
- Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain.,Department of Internal Medicine, La Paz University Hospital, Madrid, Spain
| | - Fernando Santos Simarro
- Clinical Genetics Section, Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, La Paz Institute of Biomedical Research, IdiPAZ, Madrid, Spain
| | - Eduardo López-Granados
- Department of Clinical Immunology, La Paz University Hospital, Madrid, Spain.,Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, IdiPAZ.,Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
| | - Rebeca Rodríguez Pena
- Department of Clinical Immunology, La Paz University Hospital, Madrid, Spain.,Lymphocyte Pathophysiology Group, La Paz Institute of Biomedical Research, IdiPAZ.,Center for Biomedical Network Research on Rare Diseases (CIBERER U767), Madrid, Spain
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11
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Zhou J, Flores-Bellver M, Pan J, Benito-Martin A, Shi C, Onwumere O, Mighty J, Qian J, Zhong X, Hogue T, Amponsah-Antwi B, Einbond L, Gharbaran R, Wu H, Chen BJ, Zheng Z, Tchaikovskaya T, Zhang X, Peinado H, Canto-Soler MV, Redenti S. Human retinal organoids release extracellular vesicles that regulate gene expression in target human retinal progenitor cells. Sci Rep 2021; 11:21128. [PMID: 34702879 PMCID: PMC8548301 DOI: 10.1038/s41598-021-00542-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/07/2021] [Indexed: 01/23/2023] Open
Abstract
The mechanisms underlying retinal development have not been completely elucidated. Extracellular vesicles (EVs) are novel essential mediators of cell-to-cell communication with emerging roles in developmental processes. Nevertheless, the identification of EVs in human retinal tissue, characterization of their cargo, and analysis of their potential role in retina development has not been accomplished. Three-dimensional retinal tissue derived from human induced pluripotent stem cells (hiPSC) provide an ideal developmental system to achieve this goal. Here we report that hiPSC-derived retinal organoids release exosomes and microvesicles with small noncoding RNA cargo. EV miRNA cargo-predicted targetome correlates with Gene Ontology (GO) pathways involved in mechanisms of retinogenesis relevant to specific developmental stages corresponding to hallmarks of native human retina development. Furthermore, uptake of EVs by human retinal progenitor cells leads to changes in gene expression correlated with EV miRNA cargo predicted gene targets, and mechanisms involved in retinal development, ganglion cell and photoreceptor differentiation and function.
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Affiliation(s)
- Jing Zhou
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Miguel Flores-Bellver
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, 12800 East 19th Avenue, Aurora, CO, 80045, USA
| | - Jianbo Pan
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Alberto Benito-Martin
- Departments of Pediatrics, Hematology/Oncology Division, Weill Medical College of Cornell University, 413 E. 69th St., New York, NY, 10021, USA
| | - Cui Shi
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Jason Mighty
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Xiufeng Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tasmim Hogue
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Linda Einbond
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | | | - Hao Wu
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Bo-Juen Chen
- New York Genome Center, New York, NY, 10013, USA
| | - Zhiliang Zheng
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | - Tatyana Tchaikovskaya
- Department of Medicine, Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xusheng Zhang
- Department of Medicine, Computational Genomics Core in Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hector Peinado
- Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Maria Valeria Canto-Soler
- CellSight Ocular Stem Cell and Regeneration Program, Department of Ophthalmology, Sue Anschutz- Rodgers Eye Center, University of Colorado, 12800 East 19th Avenue, Aurora, CO, 80045, USA.
| | - Stephen Redenti
- Lehman College, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA.
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
- Biochemistry Doctoral Program, The Graduate School, City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.
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12
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Tucker BA, Burnight ER, Cranston CM, Ulferts MJ, Luse MA, Westfall T, Scott CA, Marsden A, Gibson-Corley K, Wiley LA, Han IC, Slusarski DC, Mullins RF, Stone EM. Development and biological characterization of a clinical gene transfer vector for the treatment of MAK-associated retinitis pigmentosa. Gene Ther 2021; 29:259-288. [PMID: 34518651 PMCID: PMC9159943 DOI: 10.1038/s41434-021-00291-5] [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: 05/18/2021] [Revised: 08/02/2021] [Accepted: 08/26/2021] [Indexed: 12/31/2022]
Abstract
By combining next generation whole exome sequencing and induced pluripotent stem cell (iPSC) technology we found that an Alu repeat inserted in exon 9 of the MAK gene results in a loss of normal MAK transcript and development of human autosomal recessive retinitis pigmentosa (RP). Although a relatively rare cause of disease in the general population, the MAK variant is enriched in individuals of Jewish ancestry. In this population, 1 in 55 individuals are carriers and one third of all cases of recessive RP is caused by this gene. The purpose of this study was to determine if a viral gene augmentation strategy could be used to safely restore functional MAK protein as a step toward a treatment for early stage MAK-associated RP. Patient iPSC-derived photoreceptor precursor cells were generated and transduced with viral vectors containing the MAK transcript. One week after transduction, transcript and protein could be detected via rt-PCR and western blotting respectively. Using patient-derived fibroblast cells and mak knockdown zebra fish we demonstrate that over-expression of the retinal MAK transgene restored the cells ability to regulate primary cilia length. In addition, the visual defect in mak knockdown zebrafish was mitigated via treatment with the retinal MAK transgene. There was no evidence of local or systemic toxicity at 1-month or 3-months following subretinal delivery of clinical grade vector into wild type rats. The findings reported here will help pave the way for initiation of a phase 1 clinical trial for the treatment of patients with MAK-associated RP.
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Affiliation(s)
- Budd A Tucker
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA. .,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| | - Erin R Burnight
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Cathryn M Cranston
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mallory J Ulferts
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Meagan A Luse
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Trudi Westfall
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
| | - C Anthony Scott
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
| | - Autumn Marsden
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
| | - Katherine Gibson-Corley
- Department of Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luke A Wiley
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ian C Han
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Diane C Slusarski
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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13
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Maccora I, Marrani E, Mastrolia MV, Abu-Rumeileh S, Maniscalco V, Fusco E, Barbati F, Pagnini I, Simonini G. Ocular involvement in monogenic autoinflammatory disease. Autoimmun Rev 2021; 20:102944. [PMID: 34509650 DOI: 10.1016/j.autrev.2021.102944] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Monogenic Autoinflammatory diseases (AIDs) are a broad spectrum of rare hereditary diseases whose ocular involvement has not been well characterized yet. This systematic review aims to provide an overview of the current knowledge about ocular findings in AIDs. METHODS A systematic literature review was conducted using 2 electronic databases, according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. A combination of AIDs and ophthalmology-related search terms were used. All articles were screened by 2 independent reviewers for title, abstract and full text level. We included solely studies that investigated ocular findings in AIDs. RESULTS 198 papers of 4268 records were retained. Data about 1353 patients with a diagnosis of autoinflammatory disease and ocular involvement were collected (680 CAPS, 211 FMF, 138 TRAPS, 238 Blau, 32 MKD, 21 SIFD, 7 Aicardi Goutières, 3 CANDLE, 8 DADA2, 9 HA20, 6 APLAID). Conjunctivitis was significantly more frequent in CAPS (p < 0.00001), uveitis in Blau, MKD, HA20 and CANDLE (p < 0.00001), papillitis/papilledema in CAPS (p < 0.00001), optic neuritis in Aicardi and DADA2 (p < 0.008), retinal vasculitis in FMF (p < 0.00001), progressive reduction in choroidal thickness in FMF and DADA2 (p < 0.00001), periorbital oedema in TRAPS (p < 0.00001) and retinitis in SIFD (p < 0.00001). Among AIDs with uveitis, granulomatous inflammation was more common in Blau syndrome (p < 0.00001). CONCLUSION This systematic literature review characterized the ocular involvement of several AIDs, and the present data may encourage to consider a timely ophthalmological screening program for these rare diseases.
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Affiliation(s)
- Ilaria Maccora
- Rheumatology Unit, Meyer Children's University Hospital, NEUROFARBA Department, University of Florence, Florence, Italy.
| | - Edoardo Marrani
- Rheumatology Unit, Meyer Children's University Hospital, Florence, Italy
| | - Maria Vincenza Mastrolia
- Rheumatology Unit, Meyer Children's University Hospital, NEUROFARBA Department, University of Florence, Florence, Italy.
| | - Sarah Abu-Rumeileh
- Pediatric Rheumatology Unit, Meyer Children's University Hospital, School of Human Health Science, Florence, Italy
| | - Valerio Maniscalco
- Pediatric Rheumatology Unit, Meyer Children's University Hospital, School of Human Health Science, Florence, Italy
| | - Eleonora Fusco
- Pediatric Rheumatology Unit, Meyer Children's University Hospital, School of Human Health Science, Florence, Italy
| | - Federica Barbati
- Pediatric Rheumatology Unit, Meyer Children's University Hospital, School of Human Health Science, Florence, Italy
| | - Ilaria Pagnini
- Rheumatology Unit, Meyer Children's University Hospital, Florence, Italy.
| | - Gabriele Simonini
- Rheumatology Unit, Meyer Children's University Hospital, NEUROFARBA Department, University of Florence, Florence, Italy.
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14
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Maccora I, Ramanan AV, Vergnano S, Roderick MR. Sideroblastic anaemia, immunodeficiency, periodic fevers and developmental delay (SIFD) presenting as systemic inflammation with arthritis. Rheumatology (Oxford) 2021; 60:e234-e236. [PMID: 33493307 DOI: 10.1093/rheumatology/keab010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/24/2020] [Accepted: 12/19/2020] [Indexed: 01/28/2023] Open
Affiliation(s)
- I Maccora
- Paediatric Rheumatology Unit, Anna Meyer Children's University Hospital, School of Human Health Science, Florence, Italy
| | - A V Ramanan
- Bristol Royal Hospital for Children, Translational Health Sciences, University of Bristol, Bristol, UK
| | - S Vergnano
- Paediatric Immunology and Infectious Diseases Service, Bristol Royal Hospital for Children & Bristol Children's Vaccine Centre, Schools of Cellular and Molecular Medicine Population Health Sciences, University of Bristol, Bristol, UK
| | - M R Roderick
- Paediatric Immunology and Infectious Diseases Service, Bristol Royal Hospital for Children & Bristol Children's Vaccine Centre, Schools of Cellular and Molecular Medicine Population Health Sciences, University of Bristol, Bristol, UK
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15
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Wang J, Deng Q, He X, Chen D, Hang S, Gao Y, Chen Y. Two cases of sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) syndrome in Chinese Han children caused by novel compound heterozygous variants of the TRNT1 gene. Clin Chim Acta 2021; 521:244-250. [PMID: 34310935 DOI: 10.1016/j.cca.2021.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/18/2021] [Accepted: 07/18/2021] [Indexed: 01/03/2023]
Abstract
Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) syndrome is a serious autosomal recessive genetic disease. So far, <40 cases have been reported worldwide, and only one case has been reported in China. The main clinical features of SIFD are sideroblastic or microcytic anemia, immune deficiency, and recurrent episodes of inflammation. Here, we describe two unrelated cases of SIFD from China with different clinical manifestations and mild symptoms. Patient 1 was hospitalized at the age of 3.5 years due to persistent joint swelling with imaging of multiple joint effusions. Patient 2 was hospitalized at the age of 12 years due to repeated rashes on both lower limbs and oral ulcers. SIFD was detected using gene testing, which revealed the following compound heterozygous variants in TRNT1 in cases 1 and 2, respectively: c.88A > G/c.363G > T and c.302 T > C/c.1234cC > T. Searches of the HGMD databases revealed that these variants were all novel. Molecular dynamics simulations revealed that the missense variants c.363G > T and c.302 T > C would cause changes in protein structure and thus affect protein function. Finally, through literature reviewing, we found that the mortality in cases of SIFD was approximately 44% (14/32), and about 79% of individuals who died carried the hot-spot mutation c.668 T > C. Moreover, variants in the non-coding region were significantly more common among patients who died than among survivors. Our cases further expand the existing knowledge of the phenotype and variation spectrums of SIFD and suggest that genomic diagnosis is valuable for the hierarchical clinical management of this disease.
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Affiliation(s)
- Juanjuan Wang
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China
| | - Qian Deng
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China
| | - Xiaoliang He
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China
| | - Denghuan Chen
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China
| | - Shouwei Hang
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China
| | - Yutong Gao
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China
| | - Yuqing Chen
- Department of Rheumatology and Immunology, Anhui Provincial Children's Hospital, China.
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16
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Mullin NK, Voigt AP, Cooke JA, Bohrer LR, Burnight ER, Stone EM, Mullins RF, Tucker BA. Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease. Prog Retin Eye Res 2021; 83:100918. [PMID: 33130253 PMCID: PMC8559964 DOI: 10.1016/j.preteyeres.2020.100918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of inherited retinal disease has benefited immensely from molecular genetic analysis over the past several decades. New technologies that allow for increasingly detailed examination of a patient's DNA have expanded the catalog of genes and specific variants that cause retinal disease. In turn, the identification of pathogenic variants has allowed the development of gene therapies and low-cost, clinically focused genetic testing. Despite this progress, a relatively large fraction (at least 20%) of patients with clinical features suggestive of an inherited retinal disease still do not have a molecular diagnosis today. Variants that are not obviously disruptive to the codon sequence of exons can be difficult to distinguish from the background of benign human genetic variations. Some of these variants exert their pathogenic effect not by altering the primary amino acid sequence, but by modulating gene expression, isoform splicing, or other transcript-level mechanisms. While not discoverable by DNA sequencing methods alone, these variants are excellent targets for studies of the retinal transcriptome. In this review, we present an overview of the current state of pathogenic variant discovery in retinal disease and identify some of the remaining barriers. We also explore the utility of new technologies, specifically patient-derived induced pluripotent stem cell (iPSC)-based modeling, in further expanding the catalog of disease-causing variants using transcriptome-focused methods. Finally, we outline bioinformatic analysis techniques that will allow this new method of variant discovery in retinal disease. As the knowledge gleaned from previous technologies is informing targets for therapies today, we believe that integrating new technologies, such as iPSC-based modeling, into the molecular diagnosis pipeline will enable a new wave of variant discovery and expanded treatment of inherited retinal disease.
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Affiliation(s)
- Nathaniel K Mullin
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Andrew P Voigt
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jessica A Cooke
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Laura R Bohrer
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Erin R Burnight
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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17
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Aksentijevich I, Schnappauf O. Molecular mechanisms of phenotypic variability in monogenic autoinflammatory diseases. Nat Rev Rheumatol 2021; 17:405-425. [PMID: 34035534 DOI: 10.1038/s41584-021-00614-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2021] [Indexed: 02/08/2023]
Abstract
Monogenic autoinflammatory diseases are a group of rheumatologic disorders caused by dysregulation in the innate immune system. The molecular mechanisms of these disorders are linked to defects in inflammasome-mediated, NF-κB-mediated or interferon-mediated inflammatory signalling pathways, cytokine receptors, the actin cytoskeleton, proteasome complexes and various enzymes. As with other human disorders, disease-causing variants in a single gene can present with variable expressivity and incomplete penetrance. In some cases, pathogenic variants in the same gene can be inherited either in a recessive or dominant manner and can cause distinct and seemingly unrelated phenotypes, although they have a unifying biochemical mechanism. With an enhanced understanding of protein structure and functionality of protein domains, genotype-phenotype correlations are beginning to be unravelled. Many of the mutated proteins are primarily expressed in haematopoietic cells, and their malfunction leads to systemic inflammation. Disease presentation is also defined by a specific effect of the mutant protein in a particular cell type and, therefore, the resulting phenotype might be more deleterious in one tissue than in another. Many patients present with the expanded immunological disease continuum that includes autoinflammation, immunodeficiency, autoimmunity and atopy, which necessitate genetic testing.
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Affiliation(s)
- Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Oskar Schnappauf
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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18
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Etanercept as a successful therapy in autoinflammatory syndrome related to TRNT1 mutations: a case-based review. Clin Rheumatol 2021; 40:4341-4348. [PMID: 33646446 DOI: 10.1007/s10067-021-05653-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 01/31/2021] [Accepted: 02/14/2021] [Indexed: 10/22/2022]
Abstract
Mutations in the gene encoding tRNA nucleotidyltransferase 1 (TRNT1) are associated with heterogeneous phenotypes and multisystem involvement of variable severity and progression. Immunodeficiency and inflammation are recurrent-associated features. The use of cytokine inhibitors in suppressing the inflammatory phenotype has been recently reported, with a 3-year follow-up for patients treated with Etanercept. We report on two unrelated patients sharing the same clinical condition, who had been referred to our Pediatric Rheumatology Unit because of recurrent fever associated with cutaneous lesions and increased levels of inflammatory markers since their first months of life. Whole exome sequencing allowed to identify compound heterozygosity for functionally relevant variants in TRNT1 as the only molecular event shared by the two patients. Both patients have been treated with Etanercept during 11 years, documenting normalization of inflammatory indexes and resolution of recurrent fever and associated symptoms. This is the longest follow-up assessment of Etanercept treatment in patients with TRNT1 mutations. Our findings confirm efficacy and safety of the treatment. Key Points • Mutations in TRNT1 have been associated with phenotypic heterogeneity. • We report on two patients with early-onset autoinflammatory syndrome. • Whole exome sequencing led to reveal compound heterozygosity for two variants in TRNT1 in both patients. • The patients were successfully treated with Etanercept for more than 10 years, the longest follow-up described in literature.
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19
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Yang XR, Benson MD, MacDonald IM, Innes AM. A diagnostic approach to syndromic retinal dystrophies with intellectual disability. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:538-570. [PMID: 32918368 DOI: 10.1002/ajmg.c.31834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Inherited retinal dystrophies are a group of monogenic disorders that, as a whole, contribute significantly to the burden of ocular disease in both pediatric and adult patients. In their syndromic forms, retinal dystrophies can be observed in association with intellectual disability, frequently alongside other systemic manifestations. There are now over 80 genes implicated in syndromic retinal dystrophies with intellectual disability. Identifying and accurately characterizing these disorders allows the clinician to narrow the differential diagnosis, evaluate for relevant associated features, arrive at a timely and accurate diagnosis, and address both sight-threatening ocular manifestations and morbidity-causing systemic manifestations. The co-occurrence of retinal dystrophy and intellectual disability in an individual can be challenging to investigate, diagnose, and counsel given the considerable phenotypic and genotypic heterogeneity that exists within this broad group of disorders. We performed a review of the current literature and propose an algorithm to facilitate the evaluation, and clinical and mechanistic classification, of these individuals.
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Affiliation(s)
- Xiao-Ru Yang
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Matthew D Benson
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada
| | - Ian M MacDonald
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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20
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Slade A, Kattini R, Campbell C, Holcik M. Diseases Associated with Defects in tRNA CCA Addition. Int J Mol Sci 2020; 21:E3780. [PMID: 32471101 PMCID: PMC7312816 DOI: 10.3390/ijms21113780] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023] Open
Abstract
tRNA nucleotidyl transferase 1 (TRNT1) is an essential enzyme catalyzing the addition of terminal cytosine-cytosine-adenosine (CCA) trinucleotides to all mature tRNAs, which is necessary for aminoacylation. It was recently discovered that partial loss-of-function mutations in TRNT1 are associated with various, seemingly unrelated human diseases including sideroblastic anemia with B-cell immunodeficiency, periodic fevers and developmental delay (SIFD), retinitis pigmentosa with erythrocyte microcytosis, and progressive B-cell immunodeficiency. In addition, even within the same disease, the severity and range of the symptoms vary greatly, suggesting a broad, pleiotropic impact of imparting TRNT1 function on diverse cellular systems. Here, we describe the current state of knowledge of the TRNT1 function and the phenotypes associated with mutations in TRNT1.
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Affiliation(s)
| | | | | | - Martin Holcik
- Department of Health Sciences, Carleton University, Ottawa, ON K1S 5B6, Canada; (A.S.); (R.K.); (C.C.)
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21
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Gorbatyuk MS, Starr CR, Gorbatyuk OS. Endoplasmic reticulum stress: New insights into the pathogenesis and treatment of retinal degenerative diseases. Prog Retin Eye Res 2020; 79:100860. [PMID: 32272207 DOI: 10.1016/j.preteyeres.2020.100860] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/08/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
Abstract
Physiological equilibrium in the retina depends on coordinated work between rod and cone photoreceptors and can be compromised by the expression of mutant proteins leading to inherited retinal degeneration (IRD). IRD is a diverse group of retinal dystrophies with multifaceted molecular mechanisms that are not fully understood. In this review, we focus on the contribution of chronically activated unfolded protein response (UPR) to inherited retinal pathogenesis, placing special emphasis on studies employing genetically modified animal models. As constitutively active UPR in degenerating retinas may activate pro-apoptotic programs associated with oxidative stress, pro-inflammatory signaling, dysfunctional autophagy, free cytosolic Ca2+ overload, and altered protein synthesis rate in the retina, we focus on the regulatory mechanisms of translational attenuation and approaches to overcoming translational attenuation in degenerating retinas. We also discuss current research on the role of the UPR mediator PERK and its downstream targets in degenerating retinas and highlight the therapeutic benefits of reprogramming PERK signaling in preclinical animal models of IRD. Finally, we describe pharmacological approaches targeting UPR in ocular diseases and consider their potential applications to IRD.
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Affiliation(s)
- Marina S Gorbatyuk
- The University of Alabama at Birmingham, Department of Optometry and Vision Science, School of Optometry, USA.
| | - Christopher R Starr
- The University of Alabama at Birmingham, Department of Optometry and Vision Science, School of Optometry, USA
| | - Oleg S Gorbatyuk
- The University of Alabama at Birmingham, Department of Optometry and Vision Science, School of Optometry, USA
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22
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Yang L, Xue X, Zeng T, Chen X, Zhao Q, Tang X, Yang J, An Y, Zhao X. Novel biallelic TRNT1 mutations lead to atypical SIFD and multiple immune defects. Genes Dis 2020; 7:128-137. [PMID: 32181284 PMCID: PMC7063413 DOI: 10.1016/j.gendis.2020.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/07/2020] [Indexed: 01/26/2023] Open
Abstract
Mutations in the gene encoding transfer RNA (tRNA) nucleotidyltransferase, CCA-adding 1 (TRNT1), an enzyme essential for the synthesis of the 3'-terminal CCA sequence in tRNA molecules, are associated with a rare syndrome of congenital sideroblastic anemia, B cell immunodeficiency, periodic fevers, and developmental delay (SIFD). Clinical manifestations and immunological phenotypes were assessed in a Chinese patient with novel compound heterozygous mutations in TRNT1. The patient required multiple hospitalizations starting at the age of 2 years for recurrent fevers without an infective cause. During the febrile episode, the patient was found to have microcytic hypochromic anemia, B cell lymphopenia, and hypogammaglobulinemia. Targeted gene sequencing identified novel compound heterozygous mutations in the TRNT1 gene (c.525delT, p.Leu176X; c.938T>C, p.Leu313Ser). Immunophenotyping revealed increased CD8+ T cells, CD4+ terminally differentiated effector memory helper T lymphocytes (CD4 TEMRA), and CD4+ effector memory lymphocytes (CD4 EM). Analysis of CD4+ T subsets identified decreased T follicular helper cells (Tfh) with a biased phenotype to Th2-like cells. The patient also showed a lower percentage of switched memory B (smB) cells. Additionally, defects in the cytotoxicity of the patient's NK and γδT cells were shown by CD107alpha expression. In conclusion, T RNT1 mutations may lead to multiple immune abnormality especially humoral and cytotoxicity defects, which indicate that SIFD is not only suffered 'Predominantly antibody deficiencies' in IUIS classification system, and further studies are needed to understand the pathogenesis of immunodeficiency in these patients.
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Affiliation(s)
- Lu Yang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Xiuhong Xue
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Xi'an Children's Hospital, Shanxi, PR China
| | - Ting Zeng
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Xuemei Chen
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Qin Zhao
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Xuemei Tang
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Jun Yang
- Department of Rheumatology and Immunology, Shenzhen Children's Hospital, Shenzhen, Guangdong, PR China
| | - Yunfei An
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
| | - Xiaodong Zhao
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, PR China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, PR China.,Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University, Chongqing, PR China
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23
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Kuo ME, Antonellis A. Ubiquitously Expressed Proteins and Restricted Phenotypes: Exploring Cell-Specific Sensitivities to Impaired tRNA Charging. Trends Genet 2019; 36:105-117. [PMID: 31839378 DOI: 10.1016/j.tig.2019.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/17/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Aminoacyl-tRNA synthetases (ARS) are ubiquitously expressed, essential enzymes that charge tRNA with cognate amino acids. Variants in genes encoding ARS enzymes lead to myriad human inherited diseases. First, missense alleles cause dominant peripheral neuropathy. Second, missense, nonsense, and frameshift alleles cause recessive multisystem disorders that differentially affect tissues depending on which ARS is mutated. A preponderance of evidence has shown that both phenotypic classes are associated with loss-of-function alleles, suggesting that tRNA charging plays a central role in disease pathogenesis. However, it is currently unclear how perturbation in the function of these ubiquitously expressed enzymes leads to tissue-specific or tissue-predominant phenotypes. Here, we review our current understanding of ARS-associated disease phenotypes and discuss potential explanations for the observed tissue specificity.
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Affiliation(s)
- Molly E Kuo
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; Department of Neurology, University of Michigan, Ann Arbor, MI, USA.
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24
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Blond F, Léveillard T. Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. Int J Mol Sci 2019; 20:E4922. [PMID: 31590277 PMCID: PMC6801968 DOI: 10.3390/ijms20194922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
The retina is the light sensitive part of the eye and nervous tissue that have been used extensively to characterize the function of the central nervous system. The retina has a central position both in fundamental biology and in the physiopathology of neurodegenerative diseases. We address the contribution of functional genomics to the understanding of retinal biology by reviewing key events in their historical perspective as an introduction to major findings that were obtained through the study of the retina using genomics, transcriptomics and proteomics. We illustrate our purpose by showing that most of the genes of interest for retinal development and those involved in inherited retinal degenerations have a restricted expression to the retina and most particularly to photoreceptors cells. We show that the exponential growth of data generated by functional genomics is a future challenge not only in terms of storage but also in terms of accessibility to the scientific community of retinal biologists in the future. Finally, we emphasize on novel perspectives that emerge from the development of redox-proteomics, the new frontier in retinal biology.
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Affiliation(s)
- Frédéric Blond
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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25
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Wellner K, Pöhler MT, Betat H, Mörl M. Dual expression of CCA-adding enzyme and RNase T in Escherichia coli generates a distinct cca growth phenotype with diverse applications. Nucleic Acids Res 2019; 47:3631-3639. [PMID: 30828718 PMCID: PMC6468291 DOI: 10.1093/nar/gkz133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022] Open
Abstract
Correct synthesis and maintenance of functional tRNA 3′-CCA-ends is a crucial prerequisite for aminoacylation and must be achieved by the phylogenetically diverse group of tRNA nucleotidyltransferases. While numerous reports on the in vitro characterization exist, robust analysis under in vivo conditions is lacking. Here, we utilize Escherichia coli RNase T, a tRNA-processing enzyme responsible for the tRNA-CCA-end turnover, to generate an in vivo system for the evaluation of A-adding activity. Expression of RNase T results in a prominent growth phenotype that renders the presence of a CCA- or A-adding enzyme essential for cell survival in an E. coli Δcca background. The distinct growth fitness allows for both complementation and selection of enzyme variants in a natural environment. We demonstrate the potential of our system via detection of altered catalytic efficiency and temperature sensitivity. Furthermore, we select functional enzyme variants out of a sequence pool carrying a randomized codon for a highly conserved position essential for catalysis. The presented E. coli-based approach opens up a wide field of future studies including the investigation of tRNA nucleotidyltransferases from all domains of life and the biological relevance of in vitro data concerning their functionality and mode of operation.
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Affiliation(s)
- Karolin Wellner
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Marie-Theres Pöhler
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
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26
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A High-Throughput Assay for Congenital and Age-Related Eye Diseases in Zebrafish. Biomedicines 2019; 7:biomedicines7020028. [PMID: 30979021 PMCID: PMC6631034 DOI: 10.3390/biomedicines7020028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 01/19/2023] Open
Abstract
Debilitating visual impairment caused by cataracts or microphthalmia is estimated to affect roughly 20 million people in the United States alone. According to the National Eye Institute, by 2050 that number is expected to more than double to roughly 50 million. The identification of candidate disease-causing alleles for cataracts and microphthalmia has been accelerated with advanced sequencing technologies creating a need for verification of the pathophysiology of these genes. Zebrafish pose many advantages as a high-throughput model for human eye disease. By 5 days post-fertilization, zebrafish have quantifiable behavioral responses to visual stimuli. Their small size, many progeny, and external fertilization allows for rapid screening for vision defects. We have adapted the OptoMotor Response to assay visual impairment in zebrafish models of cataracts and microphthalmia. This research demonstrates an inexpensive, high-throughput method for analyzing candidate genes involved in visual impairment.
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27
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Leibovitch M, Reid NE, Victoria J, Hanic-Joyce PJ, Joyce PBM. Analysis of the pathogenic I326T variant of human tRNA nucleotidyltransferase reveals reduced catalytic activity and thermal stability in vitro linked to a conformational change. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:616-626. [PMID: 30959222 DOI: 10.1016/j.bbapap.2019.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/22/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The I326T mutation in the TRNT1 gene encoding human tRNA nucleotidyltransferase (tRNA-NT) is linked to a relatively mild form of SIFD. Previous work indicated that the I326T variant was unable to incorporate AMP into tRNAs in vitro, however, expression of the mutant allele from a strong heterologous promoter supported in vivo CCA addition to both cytosolic and mitochondrial tRNAs in a yeast strain lacking tRNA-NT. To address this discrepancy, we determined the biochemical and biophysical characteristics of the I326T variant enzyme and the related variant, I326A. Our in vitro analysis revealed that the I326T substitution decreases the thermal stability of the enzyme and causes a ten-fold reduction in enzyme activity. We propose that the structural changes in the I326T variant that lead to these altered parameters result from a rearrangement of helices within the body domain of the protein which can be probed by the inability of the monomeric enzyme to form a covalent dimer in vitro mediated by C373. In addition, we confirm that the effects of the I326T or I326A substitutions are relatively mild in vivo by demonstrating that the mutant alleles support both mitochondrial and cytosolic CCA-addition in yeast.
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Affiliation(s)
- M Leibovitch
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - N E Reid
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - J Victoria
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P J Hanic-Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P B M Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada.
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28
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Fujiwara T, Harigae H. Molecular pathophysiology and genetic mutations in congenital sideroblastic anemia. Free Radic Biol Med 2019; 133:179-185. [PMID: 30098397 DOI: 10.1016/j.freeradbiomed.2018.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/04/2018] [Indexed: 01/19/2023]
Abstract
Sideroblastic anemia is a heterogeneous congenital and acquired disorder characterized by anemia and the presence of ring sideroblasts in the bone marrow. Congenital sideroblastic anemia (CSA) is a rare disease caused by mutations in genes involved in the heme biosynthesis, iron-sulfur [Fe-S] cluster biosynthesis, and mitochondrial protein synthesis. The most prevalent form of CSA is X-linked sideroblastic anemia, caused by mutations in the erythroid-specific δ-aminolevulinate synthase (ALAS2), which is the first enzyme of the heme biosynthesis pathway in erythroid cells. To date, a remarkable number of genetically undefined CSA cases remain, but a recent application of the next-generation sequencing technology has recognized novel causative genes for CSA. However, in most instances, the detailed molecular mechanisms of how defects of each gene result in the abnormal mitochondrial iron accumulation remain unclear. This review aims to cover the current understanding of the molecular pathophysiology of CSA.
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Affiliation(s)
- Tohru Fujiwara
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-cho, Aoba-ku, Sendai 980-8575, Japan.
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29
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Kumaki E, Tanaka K, Imai K, Aoki-Nogami Y, Ishiguro A, Okada S, Kanegane H, Ishikawa F, Morio T. Atypical SIFD with novel TRNT1 mutations: a case study on the pathogenesis of B-cell deficiency. Int J Hematol 2019; 109:382-389. [PMID: 30758723 DOI: 10.1007/s12185-019-02614-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/14/2022]
Abstract
Mutation in the gene encoding tRNA nucleotidyl transferase, CCA-adding 1 (TRNT1), an enzyme essential for the synthesis of the 3'-terminal CCA sequence in tRNA molecules, results in a disorder that features sideroblastic anemia, B-cell immunodeficiency, periodic fever, and developmental delay. Mutations in TRNT1 are also linked to phenotypes including retinitis pigmentosa, cataracts, and cardiomyopathy. To date, it has remained unclear how defective TRNT1 is linked to B-cell deficiency. Here we report the case of a 12-year-old boy without sideroblastic anemia who harbors novel compound heterozygous mutations in TRNT1. Immunophenotypic analysis revealed severely decreased levels of B cells and follicular helper T cells. In the bone marrow, B-cell maturation stopped at the CD19+CD10+CD20+/- pre-B-cell stage. Severe combined immunodeficiency mice transplanted with bone marrow hematopoietic stem cells from the patient showed largely normal B-cell engraftment and differentiation in the bone marrow and periphery at 24 weeks post-transplantation, comparable to those in mouse transplanted with healthy hematopoietic stem cells. Biochemical analysis revealed augmented endoplasmic reticulum (ER) stress response in activated T cells. Peripheral B-cell deficiency of TRNT1 deficiency may be associated with augmented ER stress in immature B cells in the bone marrow.
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Affiliation(s)
- Eri Kumaki
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Keisuke Tanaka
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kohsuke Imai
- Department of Community Pediatrics, Perinatal and Maternal Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuki Aoki-Nogami
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.,Laboratory for Human Disease Models, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Akira Ishiguro
- Center for Postgraduate Education and Training, National Center for Child Health and Development, Tokyo, Japan
| | - Satoshi Okada
- Department of Pediatrics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Fumihiko Ishikawa
- Laboratory for Human Disease Models, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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30
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Beck DB, Aksentijevich I. Biochemistry of Autoinflammatory Diseases: Catalyzing Monogenic Disease. Front Immunol 2019; 10:101. [PMID: 30766537 PMCID: PMC6365650 DOI: 10.3389/fimmu.2019.00101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
Monogenic autoinflammatory disorders are a group of conditions defined by systemic or localized inflammation without identifiable causes, such as infection. In contrast to classical primary immunodeficiencies that manifest with impaired immune responses, these disorders are due to defects in genes that regulate innate immunity leading to constitutive activation of pro-inflammatory signaling. Through studying patients with rare autoinflammatory conditions, novel mechanisms of inflammation have been identified that bare on our understanding not only of basic signaling in inflammatory cells, but also of the pathogenesis of more common inflammatory diseases and have guided treatment modalities. Autoinflammation has further been implicated as an important component of cardiovascular, neurodegenerative, and metabolic syndromes. In this review, we will focus on a subset of inherited enzymatic deficiencies that lead to constitutive inflammation, and how these rare diseases have provided insights into diverse areas of cell biology not restricted to immune cells. In this way, Mendelian disorders of the innate immune system, and in particular loss of catalytic activity of enzymes in distinct pathways, have expanded our understanding of the interplay between many seemingly disparate cellular processes. We also explore the overlap between autoinflammation, autoimmunity, and immunodeficiency, which has been increasingly recognized in patients with dysregulated immune responses.
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Affiliation(s)
- David B Beck
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ivona Aksentijevich
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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31
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Ducamp S, Fleming MD. The molecular genetics of sideroblastic anemia. Blood 2019; 133:59-69. [PMID: 30401706 PMCID: PMC6318428 DOI: 10.1182/blood-2018-08-815951] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/21/2018] [Indexed: 01/19/2023] Open
Abstract
The sideroblastic anemias (SAs) are a group of inherited and acquired bone marrow disorders defined by pathological iron accumulation in the mitochondria of erythroid precursors. Like most hematological diseases, the molecular genetic basis of the SAs has ridden the wave of technology advancement. Within the last 30 years, with the advent of positional cloning, the human genome project, solid-state genotyping technologies, and next-generation sequencing have evolved to the point where more than two-thirds of congenital SA cases, and an even greater proportion of cases of acquired clonal disease, can be attributed to mutations in a specific gene or genes. This review focuses on an analysis of the genetics of these diseases and how understanding these defects may contribute to the design and implementation of rational therapies.
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Affiliation(s)
- Sarah Ducamp
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA
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32
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Wang J, Zhao L, Wang X, Chen Y, Xu M, Soens ZT, Ge Z, Wang PR, Wang F, Chen R. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. Genome Biol 2018; 19:203. [PMID: 30477545 PMCID: PMC6258408 DOI: 10.1186/s13059-018-1579-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/02/2018] [Indexed: 11/10/2022] Open
Abstract
Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity.
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Affiliation(s)
- Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Li Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030 USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Miraca Genetics Laboratories, Houston, TX 77030 USA
| | - Yong Chen
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zachry T. Soens
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zhongqi Ge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Peter Ronghan Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030 USA
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33
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Mitochondrial DNA transcription and translation: clinical syndromes. Essays Biochem 2018; 62:321-340. [PMID: 29980628 PMCID: PMC6056718 DOI: 10.1042/ebc20170103] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/17/2018] [Accepted: 05/21/2018] [Indexed: 01/15/2023]
Abstract
Diagnosing primary mitochondrial diseases is challenging in clinical practice. Although, defective oxidative phosphorylation (OXPHOS) is the common final pathway, it is unknown why different mtDNA or nuclear mutations result in largely heterogeneous and often tissue -specific clinical presentations. Mitochondrial tRNA (mt-tRNA) mutations are frequent causes of mitochondrial diseases both in children and adults. However numerous nuclear mutations involved in mitochondrial protein synthesis affecting ubiquitously expressed genes have been reported in association with very tissue specific clinical manifestations suggesting that there are so far unknown factors determining the tissue specificity in mitochondrial translation. Most of these gene defects result in histological abnormalities and multiple respiratory chain defects in the affected organs. The clinical phenotypes are usually early-onset, severe, and often fatal, implying the importance of mitochondrial translation from birth. However, some rare, reversible infantile mitochondrial diseases are caused by very specific defects of mitochondrial translation. An unbiased genetic approach (whole exome sequencing, RNA sequencing) combined with proteomics and functional studies revealed novel factors involved in mitochondrial translation which contribute to the clinical manifestation and recovery in these rare reversible mitochondrial conditions.
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34
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Starr CR, Pitale PM, Gorbatyuk M. Translational attenuation and retinal degeneration in mice with an active integrated stress response. Cell Death Dis 2018; 9:484. [PMID: 29706649 PMCID: PMC5924758 DOI: 10.1038/s41419-018-0513-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/19/2018] [Accepted: 03/22/2018] [Indexed: 12/12/2022]
Abstract
An integrated stress response (ISR), identified in several different animal models of inherited retinal degeneration (IRD), is activated following various cellular stresses. The ISR results in the phosphorylation of eIF2α (p-eIF2α) and a consequent halt in protein synthesis. Although generally protective, persistent elevations in p-eIF2α could lead to cell demise. Therefore, we aimed to determine whether ISR activation is associated with diminished translation rates in mice with IRD. Retinal protein extracts from rd16 mice at different time points were analyzed and the retinal levels of protein synthesis were assessed using the SUnSET method. We found that rd16 mice experience persistent ISR activation: p-eIF2α, ATF4, and CHOP were significantly upregulated at P15 and P20. In agreement with ISR activation, we found that rd16 mice experience translational attenuation at P15. Similar to rd16, other IRD models, T17M RHO, and rd10 also demonstrated a decline in protein synthesis, correlating with p-eIF2α elevation. We then assessed the role of PERK and eIF2α in translational attenuation in rd16 using a PERK inhibitor, GSK2606414. We found that while the treatment significantly reduced p-eIF2α, it did not cause a complete recovery in translation. This suggests that eIF2α is not the only or even the primary point of translational control in IRD, and a second node of translational regulation comprising AKT and mTOR should be evaluated. Surprisingly, we found that AKT-mTOR signaling was diminished in rd16 and rd10 retinas, suggesting a potential link between AKT-mTOR and translational inhibition. Therefore, for the first time, this study shows translation attenuation in IRD models, and highlights the potential roles of eIF2α kinases and AKT-mTOR signaling that could grant valuable insight into the potential treatments for IRD.
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Affiliation(s)
- Christopher R Starr
- Department of Optometry and Vision Science, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Priyamvada M Pitale
- Department of Optometry and Vision Science, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marina Gorbatyuk
- Department of Optometry and Vision Science, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, USA.
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35
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Verbakel SK, van Huet RAC, Boon CJF, den Hollander AI, Collin RWJ, Klaver CCW, Hoyng CB, Roepman R, Klevering BJ. Non-syndromic retinitis pigmentosa. Prog Retin Eye Res 2018; 66:157-186. [PMID: 29597005 DOI: 10.1016/j.preteyeres.2018.03.005] [Citation(s) in RCA: 501] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 12/23/2022]
Abstract
Retinitis pigmentosa (RP) encompasses a group of inherited retinal dystrophies characterized by the primary degeneration of rod and cone photoreceptors. RP is a leading cause of visual disability, with a worldwide prevalence of 1:4000. Although the majority of RP cases are non-syndromic, 20-30% of patients with RP also have an associated non-ocular condition. RP typically manifests with night blindness in adolescence, followed by concentric visual field loss, reflecting the principal dysfunction of rod photoreceptors; central vision loss occurs later in life due to cone dysfunction. Photoreceptor function measured with an electroretinogram is markedly reduced or even absent. Optical coherence tomography (OCT) and fundus autofluorescence (FAF) imaging show a progressive loss of outer retinal layers and altered lipofuscin distribution in a characteristic pattern. Over the past three decades, a vast number of disease-causing variants in more than 80 genes have been associated with non-syndromic RP. The wide heterogeneity of RP makes it challenging to describe the clinical findings and pathogenesis. In this review, we provide a comprehensive overview of the clinical characteristics of RP specific to genetically defined patient subsets. We supply a unique atlas with color fundus photographs of most RP subtypes, and we discuss the relevant considerations with respect to differential diagnoses. In addition, we discuss the genes involved in the pathogenesis of RP, as well as the retinal processes that are affected by pathogenic mutations in these genes. Finally, we review management strategies for patients with RP, including counseling, visual rehabilitation, and current and emerging therapeutic options.
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Affiliation(s)
- Sanne K Verbakel
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ramon A C van Huet
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands; Department of Ophthalmology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - B Jeroen Klevering
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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Wiley LA, Burnight ER, Kaalberg EE, Jiao C, Riker MJ, Halder JA, Luse MA, Han IC, Russell SR, Sohn EH, Stone EM, Tucker BA, Mullins RF. Assessment of Adeno-Associated Virus Serotype Tropism in Human Retinal Explants. Hum Gene Ther 2018; 29:424-436. [PMID: 29160116 DOI: 10.1089/hum.2017.179] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Advances in the discovery of the causes of monogenic retinal disorders, combined with technologies for the delivery of DNA to the retina, offer enormous opportunities for the treatment of previously untreatable blinding diseases. However, for gene augmentation to be most effective, vectors that have the correct cell-type specificity are needed. While animal models are very useful, they often exhibit differences in retinal cell surface receptors compared to the human retina. This study evaluated the use of an ex vivo organotypic explant system to test the transduction efficiency and tropism of seven different adeno-associated virus type 2 (AAV2) serotypes in the human retina and retinal pigment epithelium-choroid-AAV2/1, AAV2/2, AAV2/4, AAV2/5, AAV2/6, AAV2/8, and AAV2/9-all driving expression of GFP under control of the cytomegalovirus promoter. After 7 days in culture, it was found that AAV2/4 and AAV2/5 were particularly efficient at transducing photoreceptor cells and that AAV2/5 was highly specific to the outer nuclear layer, whereas AAV2/8 displayed consistently low transduction of photoreceptors. To validate the authenticity of the organotypic culture system, the transduction of the same set of AAVs was also compared in a pig model, in which sub-retinal injections in vivo were compared to cultured and transduced organotypic cultures ex vivo. This study shows how different AAV serotypes behave in the human retina and provides insight for further investigation of each of these serotypes for gene augmentation-based treatment of inherited retinal degeneration.
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Affiliation(s)
- Luke A Wiley
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Erin R Burnight
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Emily E Kaalberg
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Chunhua Jiao
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Megan J Riker
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Jennifer A Halder
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Meagan A Luse
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Ian C Han
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Stephen R Russell
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Elliott H Sohn
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Edwin M Stone
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Budd A Tucker
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
| | - Robert F Mullins
- 1 Stephen A. Wynn Institute for Vision Research, University of Iowa , Iowa City, Iowa.,2 Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa , Iowa City, Iowa
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Leibovitch M, Hanic-Joyce PJ, Joyce PBM. In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:527-540. [PMID: 29454993 DOI: 10.1016/j.bbapap.2018.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/09/2018] [Accepted: 02/14/2018] [Indexed: 11/15/2022]
Abstract
Mutations in the human TRNT1 gene encoding tRNA nucleotidyltransferase (tRNA-NT), an essential enzyme responsible for addition of the CCA (cytidine-cytidine-adenosine) sequence to the 3'-termini of tRNAs, have been linked to disease phenotypes including congenital sideroblastic anemia with B-cell immunodeficiency, periodic fevers and developmental delay (SIFD) or retinitis pigmentosa with erythrocyte microcytosis. The effects of these disease-linked mutations on the structure and function of tRNA-NT have not been explored. Here we use biochemical and biophysical approaches to study how five SIFD-linked amino acid substitutions (T154I, M158V, L166S, R190I and I223T), residing in the N-terminal head and neck domains of the enzyme, affect the structure and activity of human tRNA-NT in vitro. Our data suggest that the SIFD phenotype is linked to poor stability of the T154I and L166S variant proteins, and to a combination of reduced stability and altered catalytic efficiency in the M158 V, R190I and I223T variants.
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Affiliation(s)
- M Leibovitch
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P J Hanic-Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada
| | - P B M Joyce
- Department of Chemistry and Biochemistry and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke St. W., Montréal H4B 1R6, Québec, Canada.
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Zelinger L, Swaroop A. RNA Biology in Retinal Development and Disease. Trends Genet 2018; 34:341-351. [PMID: 29395379 DOI: 10.1016/j.tig.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023]
Abstract
For decades, RNA has served in a supporting role between the genetic carrier (DNA) and the functional molecules (proteins). It is finally time for RNA to take center stage in all aspects of biology. The retina provides a unique opportunity to dissect the molecular underpinnings of neuronal diversity and disease. Transcriptome profiles of the retina and its resident cell types have unraveled unique features of the RNA landscape. The discovery of distinct RNA molecules and the recognition that RNA processing is a major cause of retinal neurodegeneration have prompted the design of biomarkers and novel therapeutic paradigms. We review here RNA biology as it pertains to the retina, emphasizing new avenues for investigations in development and disease.
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Affiliation(s)
- Lina Zelinger
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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A tRNA's fate is decided at its 3' end: Collaborative actions of CCA-adding enzyme and RNases involved in tRNA processing and degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:433-441. [PMID: 29374586 DOI: 10.1016/j.bbagrm.2018.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 02/07/2023]
Abstract
tRNAs are key players in translation and are additionally involved in a wide range of distinct cellular processes. The vital importance of tRNAs becomes evident in numerous diseases that are linked to defective tRNA molecules. It is therefore not surprising that the structural intactness of tRNAs is continuously scrutinized and defective tRNAs are eliminated. In this process, erroneous tRNAs are tagged with single-stranded RNA sequences that are recognized by degrading exonucleases. Recent discoveries have revealed that the CCA-adding enzyme - actually responsible for the de novo synthesis of the 3'-CCA end - plays an indispensable role in tRNA quality control by incorporating a second CCA triplet that is recognized as a degradation tag. In this review, we give an update on the latest findings regarding tRNA quality control that turns out to represent an interplay of the CCA-adding enzyme and RNases involved in tRNA degradation and maturation. In particular, the RNase-induced turnover of the CCA end is now recognized as a trigger for the CCA-adding enzyme to repeatedly scrutinize the structural intactness of a tRNA. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
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Giannelou A, Wang H, Zhou Q, Park YH, Abu-Asab MS, Ylaya K, Stone DL, Sediva A, Sleiman R, Sramkova L, Bhatla D, Serti E, Tsai WL, Yang D, Bishop K, Carrington B, Pei W, Deuitch N, Brooks S, Edwan JH, Joshi S, Prader S, Kaiser D, Owen WC, Sonbul AA, Zhang Y, Niemela JE, Burgess SM, Boehm M, Rehermann B, Chae J, Quezado MM, Ombrello AK, Buckley RH, Grom AA, Remmers EF, Pachlopnik JM, Su HC, Gutierrez-Cruz G, Hewitt SM, Sood R, Risma K, Calvo KR, Rosenzweig SD, Gadina M, Hafner M, Sun HW, Kastner DL, Aksentijevich I. Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors. Ann Rheum Dis 2018; 77:612-619. [PMID: 29358286 PMCID: PMC5890629 DOI: 10.1136/annrheumdis-2017-212401] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 12/15/2017] [Accepted: 12/30/2017] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To characterise the clinical features, immune manifestations and molecular mechanisms in a recently described autoinflammatory disease caused by mutations in TRNT1, a tRNA processing enzyme, and to explore the use of cytokine inhibitors in suppressing the inflammatory phenotype. METHODS We studied nine patients with biallelic mutations in TRNT1 and the syndrome of congenital sideroblastic anaemia with immunodeficiency, fevers and developmental delay (SIFD). Genetic studies included whole exome sequencing (WES) and candidate gene screening. Patients' primary cells were used for deep RNA and tRNA sequencing, cytokine profiling, immunophenotyping, immunoblotting and electron microscopy (EM). RESULTS We identified eight mutations in these nine patients, three of which have not been previously associated with SIFD. Three patients died in early childhood. Inflammatory cytokines, mainly interleukin (IL)-6, interferon gamma (IFN-γ) and IFN-induced cytokines were elevated in the serum, whereas tumour necrosis factor (TNF) and IL-1β were present in tissue biopsies of patients with active inflammatory disease. Deep tRNA sequencing of patients' fibroblasts showed significant deficiency of mature cytosolic tRNAs. EM of bone marrow and skin biopsy samples revealed striking abnormalities across all cell types and a mix of necrotic and normal-appearing cells. By immunoprecipitation, we found evidence for dysregulation in protein clearance pathways. In 4/4 patients, treatment with a TNF inhibitor suppressed inflammation, reduced the need for blood transfusions and improved growth. CONCLUSIONS Mutations of TRNT1 lead to a severe and often fatal syndrome, linking protein homeostasis and autoinflammation. Molecular diagnosis in early life will be crucial for initiating anti-TNF therapy, which might prevent some of the severe disease consequences.
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Affiliation(s)
- Angeliki Giannelou
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA.,Rheumatology Fellowship and Training Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Hongying Wang
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Qing Zhou
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Yong Hwan Park
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Mones S Abu-Asab
- Section of Histopathology, National Eye Institute, Bethesda, Maryland, USA
| | - Kris Ylaya
- Experimental Pathology Laboratory, National Cancer Institute, Bethesda, Maryland, USA
| | - Deborah L Stone
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Anna Sediva
- Department of Immunology Charles, University and University Hospital Motol, Prague, Czech Republic
| | - Rola Sleiman
- Dr. Sulaiman Al Habib Al Rayan Hospital, Riyadh, Saudi Arabia
| | - Lucie Sramkova
- Department of Pediatric Hematology and Oncology, University Hospital Motol, Prague, Czech Republic
| | - Deepika Bhatla
- SSM Health Cardinal Glennon Children's Hospital, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Elisavet Serti
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Wanxia Li Tsai
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Dan Yang
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA
| | - Kevin Bishop
- Zebrafish Core, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Blake Carrington
- Zebrafish Core, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Wuhong Pei
- Zebrafish Core, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Natalie Deuitch
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Stephen Brooks
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Jehad H Edwan
- Pediatric Translational Research Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Sarita Joshi
- Department of Pathology, The Cleveland Clinic, Cleveland, Ohio, USA
| | - Seraina Prader
- Department of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Daniela Kaiser
- Department of Pediatric Rheumatology, Children's Hospital, Lucerne, Switzerland
| | - William C Owen
- Children's Cancer and Blood Disorders Center, Children's Hospital of the King's Daughters, Norfolk, Virginia, USA
| | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Julie E Niemela
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Shawn M Burgess
- Zebrafish Core, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Manfred Boehm
- Laboratory of Cardiovascular Regenerative Medicine, National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA
| | - Barbara Rehermann
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - JaeJin Chae
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Martha M Quezado
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA
| | - Amanda K Ombrello
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Rebecca H Buckley
- Departments of Pediatrics and Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Alexi A Grom
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Elaine F Remmers
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Jana M Pachlopnik
- Department of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Gustavo Gutierrez-Cruz
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, National Cancer Institute, Bethesda, Maryland, USA
| | - Raman Sood
- Zebrafish Core, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Kimberly Risma
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Katherine R Calvo
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Massimo Gadina
- Translational Immunology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Markus Hafner
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Daniel L Kastner
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, Maryland, USA
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Perez-Lanzon M, Kroemer G, Maiuri MC. Organoids for Modeling Genetic Diseases. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 337:49-81. [DOI: 10.1016/bs.ircmb.2017.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Abstract
BACKGROUND Approximately 1% of normal tension glaucoma (NTG) cases are caused by TANK-binding kinase 1 (TBK1) gene duplications and triplications. However, the precise borders and orientation of these TBK1 gene copy number variations (CNVs) on chromosome 12 are unknown. METHODS We determined the exact borders of TBK1 CNVs and the orientation of duplicated or triplicated DNA segments in 5 NTG patients with different TBK1 mutations using whole-genome sequencing. RESULTS Tandemly duplicated chromosome segments spanning the TBK1 gene were detected in 4 NTG patients, each with unique borders. Four of 5 CNVs had borders located within interspersed repetitive DNA sequences (Alu and long interspersed nuclear element-L1 elements), suggesting that mismatched homologous recombinations likely generated these CNVs. A fifth NTG patient had a complex rearrangement including triplication of a chromosome segment spanning the TBK1 gene. CONCLUSIONS No specific mutation hotspots for TBK1 CNVs were detected, however, interspersed repetitive sequences (ie, Alu elements) were identified at the borders of TBK1 CNVs, which suggest that mismatch of these elements during meiosis may be the mechanism that generated TBK1 gene dosage mutations.
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Kapur M, Monaghan CE, Ackerman SL. Regulation of mRNA Translation in Neurons-A Matter of Life and Death. Neuron 2017; 96:616-637. [PMID: 29096076 DOI: 10.1016/j.neuron.2017.09.057] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 12/14/2022]
Abstract
Dynamic regulation of mRNA translation initiation and elongation is essential for the survival and function of neural cells. Global reductions in translation initiation resulting from mutations in the translational machinery or inappropriate activation of the integrated stress response may contribute to pathogenesis in a subset of neurodegenerative disorders. Aberrant proteins generated by non-canonical translation initiation may be a factor in the neuron death observed in the nucleotide repeat expansion diseases. Dysfunction of central components of the elongation machinery, such as the tRNAs and their associated enzymes, can cause translational infidelity and ribosome stalling, resulting in neurodegeneration. Taken together, dysregulation of mRNA translation is emerging as a unifying mechanism underlying the pathogenesis of many neurodegenerative disorders.
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Affiliation(s)
- Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Caitlin E Monaghan
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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No shortcuts: new findings reinforce why nuance is the rule in genetic autoinflammatory syndromes. Curr Opin Rheumatol 2017; 29:506-515. [PMID: 28604422 DOI: 10.1097/bor.0000000000000422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
PURPOSE OF REVIEW Practitioners dazed by the evolving concept of autoinflammation are in good company. Despite the clinical challenges autoinflammatory patients present, their study has been fundamental to our understanding of basic human inflammation. This review will focus on the ways in which recent discoveries in genetically mediated autoinflammation broaden and refine the concept. RECENT FINDINGS Major developments in pyrin inflammasome biology, defective ubiquitination, and the hyperferritinemic syndromes will be highlighted. SUMMARY We offer a brief discussion of discordance, convergence, genotype, and phenotype in autoinflammation. Additionally, we introduce the concepts of mutation dose effect and hybrid nomenclature. Overall, we hope to provide an update on developments in the field of autoinflammation, some conceptual tools to help navigate the rising tide of discovery, and some encouragement that keeping up with developments in autoinflammation is both exciting and necessary.
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45
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Sharma TP, Wiley LA, Whitmore SS, Anfinson KR, Cranston CM, Oppedal DJ, Daggett HT, Mullins RF, Tucker BA, Stone EM. Patient-specific induced pluripotent stem cells to evaluate the pathophysiology of TRNT1-associated Retinitis pigmentosa. Stem Cell Res 2017; 21:58-70. [PMID: 28390992 DOI: 10.1016/j.scr.2017.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 02/20/2017] [Accepted: 03/10/2017] [Indexed: 12/18/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of monogenic disorders characterized by progressive death of the light-sensing photoreceptor cells of the outer neural retina. We recently identified novel hypomorphic mutations in the tRNA Nucleotidyl Transferase, CCA-Adding 1 (TRNT1) gene that cause early-onset RP. To model this disease in vitro, we generated patient-specific iPSCs and iPSC-derived retinal organoids from dermal fibroblasts of patients with molecularly confirmed TRNT1-associated RP. Pluripotency was confirmed using rt-PCR, immunocytochemistry, and a TaqMan Scorecard Assay. Mutations in TRNT1 caused reduced levels of full-length TRNT1 protein and expression of a truncated smaller protein in both patient-specific iPSCs and iPSC-derived retinal organoids. Patient-specific iPSCs and iPSC-derived retinal organoids exhibited a deficit in autophagy, as evidenced by aberrant accumulation of LC3-II and elevated levels of oxidative stress. Autologous stem cell-based disease modeling will provide a platform for testing multiple avenues of treatment in patients suffering from TRNT1-associated RP.
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Affiliation(s)
- Tasneem P Sharma
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Luke A Wiley
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - S Scott Whitmore
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Kristin R Anfinson
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Cathryn M Cranston
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Douglas J Oppedal
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Heather T Daggett
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Robert F Mullins
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Budd A Tucker
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Edwin M Stone
- Stephen A Wynn Institute for Vision Research, Department of Ophthalmology and Visual Science, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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Blanco-Sánchez B, Clément A, Phillips JB, Westerfield M. Zebrafish models of human eye and inner ear diseases. Methods Cell Biol 2016; 138:415-467. [PMID: 28129854 DOI: 10.1016/bs.mcb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eye and inner ear diseases are the most common sensory impairments that greatly impact quality of life. Zebrafish have been intensively employed to understand the fundamental mechanisms underlying eye and inner ear development. The zebrafish visual and vestibulo-acoustic systems are very similar to these in humans, and although not yet mature, they are functional by 5days post-fertilization (dpf). In this chapter, we show how the zebrafish has significantly contributed to the field of biomedical research and how researchers, by establishing disease models and meticulously characterizing their phenotypes, have taken the first steps toward therapies. We review here models for (1) eye diseases, (2) ear diseases, and (3) syndromes affecting eye and/or ear. The use of new genome editing technologies and high-throughput screening systems should increase considerably the speed at which knowledge from zebrafish disease models is acquired, opening avenues for better diagnostics, treatments, and therapies.
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Affiliation(s)
| | - A Clément
- University of Oregon, Eugene, OR, United States
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48
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Frans G, Moens L, Schaballie H, Wuyts G, Liston A, Poesen K, Janssens A, Rice GI, Crow YJ, Meyts I, Bossuyt X. Homozygous N-terminal missense mutation in TRNT1 leads to progressive B-cell immunodeficiency in adulthood. J Allergy Clin Immunol 2016; 139:360-363.e6. [PMID: 27531075 DOI: 10.1016/j.jaci.2016.06.050] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 06/04/2016] [Accepted: 06/20/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Glynis Frans
- Department of Microbiology and Immunology, Experimental Laboratory Immunology, KU Leuven, Leuven, Belgium
| | - Leen Moens
- Department of Microbiology and Immunology, Experimental Laboratory Immunology, KU Leuven, Leuven, Belgium
| | - Heidi Schaballie
- Department of Microbiology and Immunology, Childhood Immunology, KU Leuven, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Greet Wuyts
- Department of Microbiology and Immunology, Experimental Laboratory Immunology, KU Leuven, Leuven, Belgium
| | - Adrian Liston
- Department of Microbiology and Immunology, Autoimmune Genetics, KU Leuven and VIB, Leuven, Belgium
| | - Koen Poesen
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Ann Janssens
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Gillian I Rice
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Centre, Manchester, United Kingdom
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Centre, Manchester, United Kingdom; INSERM UMR 1163, Laboratory of Neurogenetics and Neuroinflammation, Paris, France; Paris Descartes, Sorbonne Paris Cité University, Institute Imagine, Paris, France
| | - Isabelle Meyts
- Department of Microbiology and Immunology, Childhood Immunology, KU Leuven, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Xavier Bossuyt
- Department of Microbiology and Immunology, Experimental Laboratory Immunology, KU Leuven, Leuven, Belgium; Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium.
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Wedatilake Y, Niazi R, Fassone E, Powell CA, Pearce S, Plagnol V, Saldanha JW, Kleta R, Chong WK, Footitt E, Mills PB, Taanman JW, Minczuk M, Clayton PT, Rahman S. TRNT1 deficiency: clinical, biochemical and molecular genetic features. Orphanet J Rare Dis 2016; 11:90. [PMID: 27370603 PMCID: PMC4930608 DOI: 10.1186/s13023-016-0477-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background TRNT1 (CCA-adding transfer RNA nucleotidyl transferase) enzyme deficiency is a new metabolic disease caused by defective post-transcriptional modification of mitochondrial and cytosolic transfer RNAs (tRNAs). Results We investigated four patients from two families with infantile-onset cyclical, aseptic febrile episodes with vomiting and diarrhoea, global electrolyte imbalance during these episodes, sideroblastic anaemia, B lymphocyte immunodeficiency, retinitis pigmentosa, hepatosplenomegaly, exocrine pancreatic insufficiency and renal tubulopathy. Other clinical features found in children include sensorineural deafness, cerebellar atrophy, brittle hair, partial villous atrophy and nephrocalcinosis. Whole exome sequencing and bioinformatic filtering were utilised to identify recessive compound heterozygous TRNT1 mutations (missense mutation c.668T>C, p.Ile223Thr and a novel splice mutation c.342+5G>T) segregating with disease in the first family. The second family was found to have a homozygous TRNT1 mutation (c.569G>T), p.Arg190Ile, (previously published). We found normal mitochondrial translation products using passage matched controls and functional perturbation of 3’ CCA addition to mitochondrial tRNAs (tRNACys, tRNALeuUUR and tRNAHis) in fibroblasts from two patients, demonstrating a pathomechanism affecting the CCA addition to mt-tRNAs. Acute management of these patients included transfusion for anaemia, fluid and electrolyte replacement and immunoglobulin therapy. We also describe three-year follow-up findings after treatment by bone marrow transplantation in one patient, with resolution of fever and reversal of the abnormal metabolic profile. Conclusions Our report highlights that TRNT1 mutations cause a spectrum of disease ranging from a childhood-onset complex disease with manifestations in most organs to an adult-onset isolated retinitis pigmentosa presentation. Systematic review of all TRNT1 cases and mutations reported to date revealed a distinctive phenotypic spectrum and metabolic and other investigative findings, which will facilitate rapid clinical recognition of future cases.
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Affiliation(s)
- Yehani Wedatilake
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Rojeen Niazi
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Elisa Fassone
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | | | | | | | - José W Saldanha
- Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, UK
| | - Robert Kleta
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK.,UCL Genetics Institute, London, UK.,Division of Medicine, UCL, London, UK
| | - W Kling Chong
- Radiology Department, Great Ormond Street Hospital, London, UK
| | - Emma Footitt
- Metabolic medicine department, Great Ormond Street Hospital, London, UK
| | - Philippa B Mills
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Jan-Willem Taanman
- Department of Clinical Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Peter T Clayton
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Shamima Rahman
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK. .,Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, 30, Guilford Street, London, WC1N 1EH, UK.
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50
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Liwak-Muir U, Mamady H, Naas T, Wylie Q, McBride S, Lines M, Michaud J, Baird SD, Chakraborty PK, Holcik M. Impaired activity of CCA-adding enzyme TRNT1 impacts OXPHOS complexes and cellular respiration in SIFD patient-derived fibroblasts. Orphanet J Rare Dis 2016; 11:79. [PMID: 27317422 PMCID: PMC4912790 DOI: 10.1186/s13023-016-0466-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/10/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND SIFD (Sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay) is a novel form of congenital sideroblastic anemia associated with B-cell immunodeficiency, periodic fevers, and developmental delay caused by mutations in the CCA-adding enzyme TRNT1, but the precise molecular pathophysiology is not known. RESULTS We show that the disease causing mutations in patient-derived fibroblasts do not affect subcellular localization of TRNT1 and show no gross morphological differences when compared to control cells. Analysis of cellular respiration and oxidative phosphorylation (OXPHOS) complexes demonstrates that both basal and maximal respiration rates are decreased in patient cells, which may be attributed to an observed decrease in the abundance of select proteins of the OXPHOS complexes. CONCLUSIONS Our data provides further insight into cellular pathophysiology of SIFD.
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Affiliation(s)
- Urszula Liwak-Muir
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Hapsatou Mamady
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Turaya Naas
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Quinlan Wylie
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Skye McBride
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Matthew Lines
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Jean Michaud
- Department of Pathology and Laboratory Medicine, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, Ontario, Canada
| | - Stephen D Baird
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Pranesh K Chakraborty
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada.
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada.
| | - Martin Holcik
- Molecular Biomedicine Program, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
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