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Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome wide association study and genomic risk prediction of age related macular degeneration in Israel. Sci Rep 2024; 14:13034. [PMID: 38844476 PMCID: PMC11156861 DOI: 10.1038/s41598-024-63065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
The risk of developing age-related macular degeneration (AMD) is influenced by genetic background. In 2016, the International AMD Genomics Consortium (IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score (PRS) from these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish (AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study (GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Our discovery set recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary-statistics excluding our study and developed PRSs via clumping/thresholding or LDpred2. In our discovery set, 31/34 loci reported by IAMDGC were AMD-associated (P < 0.05). Of those, all effects were directionally consistent with IAMDGC and 11 loci had a P-value under Bonferroni-corrected threshold (0.05/34 = 0.0015). At a 5 × 10-5 threshold, we discovered four suggestive associations in FAM189A1, IGDCC4, C7orf50, and CNTNAP4. Only the FAM189A1 variant was AMD-associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS + covariates had an AUC of 0.82 (95% CI 0.79-0.85) and performed better than covariates-only model (P = 5.1 × 10-9). Therefore, previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
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Affiliation(s)
- Michelle Grunin
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Daria Triffon
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel
| | - Gala Beykin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Elior Rahmani
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Regev Schweiger
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Genetics, University of Cambridge, CB21TN, Cambridge, UK
| | - Liran Tiosano
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Shira Hagbi-Levi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Batya Rinsky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Refael Munitz
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel
| | - Thomas W Winkler
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Eran Halperin
- Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
- Department of Anesthesiology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, POB 12271, 9112102, Jerusalem, Israel.
| | - Itay Chowers
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, POB 12000, 91120, Jerusalem, Israel.
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Gazeteci Tekin H, Edem P. DHDDS-related disease; biallelic missense novel variant causing major severity with an early-onset epilepsy and hyperkinetic movement disorder. Int J Neurosci 2024:1-5. [PMID: 38451541 DOI: 10.1080/00207454.2024.2327405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Dehydrodolichyl diphosphate synthase complex is encoded by DHDDS. De novo mutations in this gene are associated with epilepsy, movement disorders, intellectual and motor disabilities. The clinical picture is commonly identified in children and shows variations in terms of age of onset, severity, seizure types, and types of dyskinesia. CASE we present a case with a infantile- onset epilepsy and severe global developmental delay, caused by a novel, de novo homozygous variant (c.425C > T, p.Thr142Met) in DHDDS. Clinical improvement was achieved with valproate and tetrabenazine treatments in the 2-year-old male patient with drug-resistant epilepsy, hyperkinetic movement disorder and myoclonus. CONCLUSION Despite being rare, DHDDS-related diseases should be considered in patients with movement disorders, seizures and global developmental delay in infancy in differential diagnosis of patients resembling neuronal ceroid lipofuscinosis or progressive myoclonic epilepsies.
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Affiliation(s)
- Hande Gazeteci Tekin
- Faculty of Medicine Pediatric Neurology Clinic, İzmir Bakircay University, İzmir, Turkey
| | - Pınar Edem
- Pediatric Neurology, Çiğli Training Hospital, izmir, Türkiye
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3
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Monson E, Cideciyan AV, Roman AJ, Sumaroka A, Swider M, Wu V, Viarbitskaya I, Jacobson SG, Fliesler SJ, Pittler SJ. Inherited Retinal Degeneration Caused by Dehydrodolichyl Diphosphate Synthase Mutation-Effect of an ALG6 Modifier Variant. Int J Mol Sci 2024; 25:1004. [PMID: 38256083 PMCID: PMC10816542 DOI: 10.3390/ijms25021004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Modern advances in disease genetics have uncovered numerous modifier genes that play a role in the severity of disease expression. One such class of genetic conditions is known as inherited retinal degenerations (IRDs), a collection of retinal degenerative disorders caused by mutations in over 300 genes. A single missense mutation (K42E) in the gene encoding the enzyme dehydrodolichyl diphosphate synthase (DHDDS), which is required for protein N-glycosylation in all cells and tissues, causes DHDDS-IRD (retinitis pigmentosa type 59 (RP59; OMIM #613861)). Apart from a retinal phenotype, however, DHDDS-IRD is surprisingly non-syndromic (i.e., without any systemic manifestations). To explore disease pathology, we selected five glycosylation-related genes for analysis that are suggested to have disease modifier variants. These genes encode glycosyltransferases (ALG6, ALG8), an ER resident protein (DDOST), a high-mannose oligosaccharyl transferase (MPDU1), and a protein N-glycosylation regulatory protein (TNKS). DNA samples from 11 confirmed DHDDS (K42E)-IRD patients were sequenced at the site of each candidate genetic modifier. Quantitative measures of retinal structure and function were performed across five decades of life by evaluating foveal photoreceptor thickness, visual acuity, foveal sensitivity, macular and extramacular rod sensitivity, and kinetic visual field extent. The ALG6 variant, (F304S), was correlated with greater macular cone disease severity and less peripheral rod disease severity. Thus, modifier gene polymorphisms may account for a significant portion of phenotypic variation observed in human genetic disease. However, the consequences of the polymorphisms may be counterintuitively complex in terms of rod and cone populations affected in different regions of the retina.
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Affiliation(s)
- Elisha Monson
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Artur V. Cideciyan
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Alejandro J. Roman
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Alexander Sumaroka
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Malgorzata Swider
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Vivian Wu
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Iryna Viarbitskaya
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Samuel G. Jacobson
- Center for Hereditary Retinal Degenerations, Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.J.R.); (A.S.); (M.S.); (V.W.); (I.V.)
| | - Steven J. Fliesler
- Departments of Ophthalmology and Biochemistry, and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York—University at Buffalo, Buffalo, NY 14203, USA;
- Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA
| | - Steven J. Pittler
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
- Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Williams LJ, Waller S, Qiu J, Innes E, Elserafy N, Procopis P, Sampaio H, Mahant N, Tchan MC, Mohammad SS, Morales‐Briceño H, Fung VS. DHDDS and NUS1: A Converging Pathway and Common Phenotype. Mov Disord Clin Pract 2024; 11:76-85. [PMID: 38291835 PMCID: PMC10828623 DOI: 10.1002/mdc3.13920] [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: 03/06/2023] [Revised: 08/11/2023] [Accepted: 10/23/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Variants in dehydrodolichol diphosphate synthetase (DHDDS) and nuclear undecaprenyl pyrophosphate synthase 1 (NUS1) cause a neurodevelopmental disorder, classically with prominent epilepsy. Recent reports suggest a complex movement disorder and an overlapping phenotype has been postulated due to their combined role in dolichol synthesis. CASES We describe three patients with heterozygous variants in DHDDS and five with variants affecting NUS1. They bear a remarkably similar phenotype of a movement disorder dominated by multifocal myoclonus. Diagnostic clues include myoclonus exacerbated by action and facial involvement, and slowly progressive or stable, gait ataxia with disproportionately impaired tandem gait. Myoclonus is confirmed with neurophysiology, including EMG of facial muscles. LITERATURE REVIEW Ninety-eight reports of heterozygous variants in DHDDS, NUS1 and chromosome 6q22.1 structural alterations spanning NUS1, confirm the convergent phenotype of hypotonia at birth, developmental delay, multifocal myoclonus, ataxia, dystonia and later parkinsonism with or without generalized epilepsy. Other features include periodic exacerbations, stereotypies, anxiety, and dysmorphisms. Although their gene products contribute to dolichol biosynthesis, a key step in N-glycosylation, transferrin isoform profiles are typically normal. Imaging is normal or non-specific. CONCLUSIONS Recognition of their shared phenotype may expedite diagnosis through chromosomal microarray and by including DHDDS/NUS1 in movement disorder gene panels.
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Affiliation(s)
- Laura J. Williams
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Sophie Waller
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Jessica Qiu
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Emily Innes
- TY Nelson Department of Neurology and NeurosurgeryThe Children's Hospital at WestmeadWestmeadNew South WalesAustralia
- School of Medicine SydneyThe University of Notre DameSydneyNew South WalesAustralia
| | - Noha Elserafy
- Department of Genomic MedicineWestmead HospitalWestmeadNew South WalesAustralia
| | - Peter Procopis
- TY Nelson Department of Neurology and NeurosurgeryThe Children's Hospital at WestmeadWestmeadNew South WalesAustralia
- The Children's Hospital at Westmead Clinical School, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Hugo Sampaio
- Department of NeurologySydney Children's HospitalRandwickNew South WalesAustralia
- School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Neil Mahant
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Michel C. Tchan
- Department of Genomic MedicineWestmead HospitalWestmeadNew South WalesAustralia
- Specialty of Genomic Medicine, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
| | - Shekeeb S. Mohammad
- TY Nelson Department of Neurology and NeurosurgeryThe Children's Hospital at WestmeadWestmeadNew South WalesAustralia
- Kids Neuroscience CentreThe Children's Hospital at WestmeadWestmeadNew South WalesAustralia
- Sydney Medical School, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Hugo Morales‐Briceño
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
| | - Victor S.C. Fung
- Movement Disorder Unit, Department of NeurologyWestmead HospitalWestmeadNew South WalesAustralia
- Sydney Medical School, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
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Liu J, Liang P. Complexation and evolution of cis-prenyltransferase homologues in Cinnamomum kanehirae deduced from kinetic and functional characterizations. Protein Sci 2023; 32:e4828. [PMID: 37916302 PMCID: PMC10661081 DOI: 10.1002/pro.4828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Eukaryotic dehydrodolichyl diphosphate synthases (DHDDSs), cis-prenyltransferases (cis-PTs) synthesizing precursors of dolichols to mediate glycoprotein biosynthesis require partners, for eample Nus1 in yeast and NgBR in animals, which are cis-PTs homologues without activity but to boost the DHDDSs activity. Unlike animals, plants have multiple cis-PT homologues to pair or stand alone to produce various chain-length products with less known physiological roles. We chose Cinnamomum kanehirae, a tree that contains two DHDDS-like and three NgBR-like proteins from genome analysis, and found that one DHDDS-like protein acted as a homodimeric cis-PT to make a medium-chain C55 product, while the other formed heterodimeric complexes with either one of two NgBR homologues to produce longer-chain products. Both complexes were functional to complement the growth defect of the yeast rer2 deficient strain at a higher temperature. From the roles for the polyprenol and dolichol biosynthesis and sequence motifs, their homologues in various species were compared to reveal their possible evolutionary paths.
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Affiliation(s)
- Jia‐Jin Liu
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Po‐Huang Liang
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
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6
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Singh AK, Chaube B, Citrin KM, Fowler JW, Lee S, Catarino J, Knight J, Lowery S, Shree S, Boutagy N, Ruz-Maldonado I, Harry K, Shanabrough M, Ross TT, Malaker S, Suárez Y, Fernández-Hernando C, Grabinska K, Sessa WC. Loss of cis-PTase function in the liver promotes a highly penetrant form of fatty liver disease that rapidly transitions to hepatocellular carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566870. [PMID: 38014178 PMCID: PMC10680637 DOI: 10.1101/2023.11.13.566870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Obesity-linked fatty liver is a significant risk factor for hepatocellular carcinoma (HCC) 1,2 ; however, the molecular mechanisms underlying the transition from non-alcoholic fatty liver disease (NAFLD) to HCC remains unclear. The present study explores the role of the endoplasmic reticulum (ER)-associated protein NgBR, an essential component of the cis-prenyltransferases (cis-PTase) enzyme 3 , in chronic liver disease. Here we show that genetic depletion of NgBR in hepatocytes of mice (N-LKO) intensifies triacylglycerol (TAG) accumulation, inflammatory responses, ER/oxidative stress, and liver fibrosis, ultimately resulting in HCC development with 100% penetrance after four months on a high-fat diet. Comprehensive genomic and single cell transcriptomic atlas from affected livers provides a detailed molecular analysis of the transition from liver pathophysiology to HCC development. Importantly, pharmacological inhibition of diacylglycerol acyltransferase-2 (DGAT2), a key enzyme in hepatic TAG synthesis, abrogates diet-induced liver damage and HCC burden in N-LKO mice. Overall, our findings establish NgBR/cis-PTase as a critical suppressor of NAFLD-HCC conversion and suggests that DGAT2 inhibition may serve as a promising therapeutic approach to delay HCC formation in patients with advanced non-alcoholic steatohepatitis (NASH).
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Dong Y, Zhang Y, Sheng Y, Wang F, Liu L, Fan LL. Case report: Identification of a recurrent pathogenic DHDDS mutation in Chinese family with epilepsy, intellectual disability and myoclonus. Front Genet 2023; 14:1208540. [PMID: 37881805 PMCID: PMC10597645 DOI: 10.3389/fgene.2023.1208540] [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: 04/19/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
Background: Heterozygous mutations in the dehydrodolichol diphosphate synthase (DHDDS) gene are one of the causes generating developmental and epileptic encephalopathies. So far, only eleven mutations in the DHDDS gene have been identified. The mutation spectrum of the DHDDS gene in the Chinese population remains unclear. Methods: In this study, we enrolled a Chinese family with myoclonus and/or epilepsy and intellectual disability. The epilepsy and myoclonic tremor were improved after deep brain stimulation (DBS) of the subthalamic nucleus (STN) treatment. Whole exome sequencing and Sanger sequencing were employed to explore the genetic variations of the family. Results: Subsequent to data filtering, we identified a recurrent pathogenic mutation (NM_001243564.1, c.113G>A/p.R38H) in the DHDDS gene in the proband. Sanger sequencing further validated that the presence of the mutation in his affected mother but absent in the health family members. Further bioinformatics analysis revealed that this mutation (p.R38H), located in an evolutionarily conserved region of DHDDS, was predicted to be deleterious. Discussion: In this report, we present the first case of intractable epilepsy and/or myoclonus caused by p.R38H mutation of the DHDDS gene in the Chinese population. Furthermore, this study represents the third report of autosomal dominant familial inheritance of DHDDS mutation worldwide.
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Affiliation(s)
- Yi Dong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yi Zhang
- Medical Psychological Center, Medical Psychological Institute of Central South University, National Clinical Research Center for Mental Disorders, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yue Sheng
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Fang Wang
- Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lv Liu
- Department of Respiratory Medicine, Clinical Center for Gene Diagnosis and Therapy, Diagnosis and Treatment Center of Respiratory Disease, Diagnosis and Treatment Center of Respiratory Disease, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Liang-Liang Fan
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
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8
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Grunin M, Triffon D, Beykin G, Rahmani E, Schweiger R, Tiosano L, Khateb S, Hagbi-Levi S, Rinsky B, Munitz R, Winkler TW, Heid IM, Halperin E, Carmi S, Chowers I. Genome-wide association study and genomic risk prediction of age-related macular degeneration in Israel. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.06.23295126. [PMID: 37732190 PMCID: PMC10508791 DOI: 10.1101/2023.09.06.23295126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Purpose The risk of developing age-related macular degeneration(AMD) is influenced by genetic background. In 2016, International AMD Genomics Consortium(IAMDGC) identified 52 risk variants in 34 loci, and a polygenic risk score(PRS) based on these variants was associated with AMD. The Israeli population has a unique genetic composition: Ashkenazi Jewish(AJ), Jewish non-Ashkenazi, and Arab sub-populations. We aimed to perform a genome-wide association study(GWAS) for AMD in Israel, and to evaluate PRSs for AMD. Methods For our discovery set, we recruited 403 AMD patients and 256 controls at Hadassah Medical Center. We genotyped all individuals via custom exome chip. We imputed non-typed variants using cosmopolitan and AJ reference panels. We recruited additional 155 cases and 69 controls for validation. To evaluate predictive power of PRSs for AMD, we used IAMDGC summary statistics excluding our study and developed PRSs via either clumping/thresholding or LDpred2. Results In our discovery set, 31/34 loci previously reported by the IAMDGC were AMD associated with P<0.05. Of those, all effects were directionally consistent with the IAMDGC and 11 loci had a p-value under Bonferroni-corrected threshold(0.05/34=0.0015). At a threshold of 5x10 -5 , we discovered four suggestive associations in FAM189A1 , IGDCC4 , C7orf50 , and CNTNAP4 . However, only the FAM189A1 variant was AMD associated in the replication cohort after Bonferroni-correction. A prediction model including LDpred2-based PRS and other covariates had an AUC of 0.82(95%CI:0.79-0.85) and performed better than a covariates-only model(P=5.1x10 -9 ). Conclusions Previously reported AMD-associated loci were nominally associated with AMD in Israel. A PRS developed based on a large international study is predictive in Israeli populations.
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Nguyen MN, Chakraborty D, Rao SR, Onysk A, Radkiewicz M, Surmacz L, Swiezewska E, Soubeyrand E, Akhtar TA, Kraft TW, Sherry DM, Fliesler SJ, Pittler SJ. A Dhdds K42E knock-in RP59 mouse model shows inner retina pathology and defective synaptic transmission. Cell Death Dis 2023; 14:420. [PMID: 37443173 PMCID: PMC10345138 DOI: 10.1038/s41419-023-05936-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 06/07/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023]
Abstract
Retinitis pigmentosa (RP) defines a group of hereditary progressive rod-cone degenerations that exhibit a common phenotype caused by variants in over 70 genes. While most variants in the dehydrodolichyl diphosphate synthase (DHDDS) gene result in syndromic abnormalities, some variants cause non-syndromic RP (RP59). DHDDS encodes one subunit of the enzyme cis-prenyltransferase (CPT), which is required for the synthesis of dolichol (Dol), that is a necessary protein glycosylation cofactor. We previously reported the creation and initial characterization of a knock-in (KI) mouse model harboring the most prevalent RP59-associated DHDDS variant (K42E) to understand how defects in DHDDS lead to retina-specific pathology. This model exhibited no profound retinal degeneration, nor protein N-glycosylation defects. Here, we report that the Dol isoprenylogue species in retina, liver, and brain of the K42E mouse model are statistically shorter than in the corresponding tissues of age-matched controls, as reported in blood and urine of RP59 patients. Retinal transcriptome analysis demonstrated elevation of many genes encoding proteins involved in synaptogenesis and synaptic function. Quantitative retinal cell layer thickness measurements demonstrated a significant reduction in the inner nuclear layer (INL) and total retinal thickness (TRT) beginning at postnatal (PN) ∼2 months, progressively increasing to PN 18-mo. Histological analysis revealed cell loss in the INL, outer plexiform layer (OPL) disruption, and ectopic localization of outer nuclear layer (ONL) nuclei into the OPL of K42E mutant retinas, relative to controls. Electroretinograms (ERGs) of mutant mice exhibited reduced b-wave amplitudes beginning at PN 1-mo, progressively declining through PN 18-mo, without appreciable a-wave attenuation, relative to controls. Our results suggest that the underlying cause of DHDDS K42E variant driven RP59 retinal pathology is defective synaptic transmission from outer to inner retina.
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Affiliation(s)
- Mai N Nguyen
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Dibyendu Chakraborty
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Sriganesh Ramachandra Rao
- Research Service, VA Western New York Healthcare System, Buffalo, NY, 14215, USA
- Departments of Ophthalmology and Biochemistry and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, The State University of New York, University at Buffalo, Buffalo, NY, 14203, USA
| | - Agnieszka Onysk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02106, Poland
| | - Mariusz Radkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02106, Poland
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02106, Poland
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02106, Poland
| | - Eric Soubeyrand
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Tariq A Akhtar
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Timothy W Kraft
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - David M Sherry
- Departments of Cell Biology, Neurosurgery, and Pharmaceutical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Steven J Fliesler
- Research Service, VA Western New York Healthcare System, Buffalo, NY, 14215, USA
- Departments of Ophthalmology and Biochemistry and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, The State University of New York, University at Buffalo, Buffalo, NY, 14203, USA
| | - Steven J Pittler
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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10
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Lv T, Fu JX, Liu XY, Tang R, Yang GL. Case analysis of epilepsy, neurodevelopmental disorder, and motor disorders associated with mutations in the dehydrodolichyl diphosphate synthase gene. Seizure 2023; 110:126-135. [PMID: 37356182 DOI: 10.1016/j.seizure.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023] Open
Abstract
The objective of this study is to analyze the role of dehydrodolichyl diphosphate synthase (DHDDS), a crucial enzyme in the mevalonate pathway, and its encoded mutations in the onset of developmental delay and seizures, with or without movement abnormalities. Its genotype-phenotype characteristics are still inconclusive. We analyzed the clinical characteristics of epilepsy, and neurodevelopmental and motor disorders related to DHDDS gene mutations and report the genotype-phenotype characteristics of a child with epilepsy caused by DHDDS gene mutation, providing a summary and a statistical analysis of epilepsy cases associated with DHDDS gene mutation up until February 2022. METHODS Using "DHDDS; epilepsy; neurodevelopmental disorder" as the keywords, the literature relevant to DHDDS gene mutations up until February 2022 was reviewed. A total of 25 cases were retrieved, among which 21 cases with complete data were included in the chi-squared test. The clinical characteristics of DHDDS gene-related cases were summarized and analyzed. RESULTS The onset of epilepsy caused by mutations of the DHDDS gene typically occurs during infancy. Predominantly, the mutation occurs in the locus of c.632G>A p.R211Q. Myoclonus is frequently the initial manifestation of epilepsy; it frequently coexists with neurodevelopmental disorder and intellectual disability, and patients have no specific type of motor disorder. Cranial magnetic resonance imaging (MRI) reveals no abnormalities, whereas electroencephalogram (EEG) frequently exhibits abnormalities. Valproic acid (VPA) yields good curative effects. CONCLUSION Mutations in the DHDDS gene are associated with congenital glycosylation disorder, autosomal recessive retinitis pigmentosa, and epilepsy. According to statistical analysis using the chi-squared test, for pediatric patients with mutations in this gene locus, most of the epilepsy types are myoclonic epilepsies with intellectual disability and neurodevelopmental disorders. They have normal brain MRIs and abnormal EEGs. VPA produces beneficial therapeutic results and the differences are all statistically significant. The current diagnosis still relies on next-generation sequencing or whole-exome sequencing.
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Affiliation(s)
- Ting Lv
- Department of Pediatrics, The Affiliated Hospital of Inner Mongolia Medical University, No. 1 North Channel Road, Inner Mongolia, Hohhot 010050, China
| | - Jun-Xian Fu
- Department of Pediatrics, The Affiliated Hospital of Inner Mongolia Medical University, No. 1 North Channel Road, Inner Mongolia, Hohhot 010050, China
| | - Xiao-Yang Liu
- Department of Pediatrics, The Affiliated Hospital of Inner Mongolia Medical University, No. 1 North Channel Road, Inner Mongolia, Hohhot 010050, China
| | - Rong Tang
- Department of Pediatrics, The Affiliated Hospital of Inner Mongolia Medical University, No. 1 North Channel Road, Inner Mongolia, Hohhot 010050, China
| | - Guang-Lu Yang
- Department of Pediatrics, The Affiliated Hospital of Inner Mongolia Medical University, No. 1 North Channel Road, Inner Mongolia, Hohhot 010050, China; Inner Mongolia Science and Technology Department, Inner Mongolia Autonomous Region nervous system disease clinical medical research center, No. 1 North Road, Huimin District, Hohhot 010050, China.
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11
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Rao SR, Pittler SJ, Fliesler SJ. Perspectives on Retinal Dolichol Metabolism, and Visual Deficits in Dolichol Metabolism-Associated Inherited Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:449-456. [PMID: 37440071 DOI: 10.1007/978-3-031-27681-1_66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
De novo synthesis of dolichol (Dol) and dolichyl phosphate (Dol-P) is essential for protein glycosylation. Herein, we provide a brief overview of Dol and Dol-P synthesis and the maintenance of their cellular content. Retinal Dol metabolism and the requirement of Dol-linked oligosaccharide synthesis in the neural retina also are discussed. There are recently discovered and an emerging class of rare congenital disorders that affect Dol metabolism, involving the genes DHDDS, NUS1, SRD5A3, and DOLK. Further understanding of these congenital disorders is evolving, based upon studies utilizing yeast and murine models, as well as clinical reports of these rare disorders. We summarize the known visual deficits associated with Dol metabolism disorders, and identify the need for generation and characterization of suitable animal models of these disorders to elucidate the underlying molecular and cellular mechanisms of the associated retinopathies.
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Affiliation(s)
- Sriganesh Ramachandra Rao
- Departments of Ophthalmology and Biochemistry, and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, USA
- Research Service, VA Western NY Healthcare System, Buffalo, NY, USA
| | - Steven J Pittler
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Steven J Fliesler
- Departments of Ophthalmology and Biochemistry, and Neuroscience Graduate Program, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, NY, USA.
- Research Service, VA Western NY Healthcare System, Buffalo, NY, USA.
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12
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Fliesler SJ, Ramachandra Rao S, Nguyen MN, KhalafAllah MT, Pittler SJ. Vertebrate Animal Models of RP59: Current Status and Future Prospects. Int J Mol Sci 2022; 23:13324. [PMID: 36362109 PMCID: PMC9657489 DOI: 10.3390/ijms232113324] [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: 09/14/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 09/20/2023] Open
Abstract
Retinitis pigmentosa-59 (RP59) is a rare, recessive form of RP, caused by mutations in the gene encoding DHDDS (dehydrodolichyl diphosphate synthase). DHDDS forms a heterotetrameric complex with Nogo-B receptor (NgBR; gene NUS1) to form a cis-prenyltransferase (CPT) enzyme complex, which is required for the synthesis of dolichol, which in turn is required for protein N-glycosylation as well as other glycosylation reactions in eukaryotic cells. Herein, we review the published phenotypic characteristics of RP59 models extant, with an emphasis on their ocular phenotypes, based primarily upon knock-in of known RP59-associated DHDDS mutations as well as cell type- and tissue-specific knockout of DHDDS alleles in mice. We also briefly review findings in RP59 patients with retinal disease and other patients with DHDDS mutations causing epilepsy and other neurologic disease. We discuss these findings in the context of addressing "knowledge gaps" in our current understanding of the underlying pathobiology mechanism of RP59, as well as their potential utility for developing therapeutic interventions to block the onset or to dampen the severity or progression of RP59.
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Affiliation(s)
- Steven J. Fliesler
- Departments of Ophthalmology and Biochemistry, Neuroscience Graduate Program, Jacobs School of Medicine, State University of New York—University at Buffalo, Buffalo, NY 14203, USA
- Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA
| | - Sriganesh Ramachandra Rao
- Departments of Ophthalmology and Biochemistry, Neuroscience Graduate Program, Jacobs School of Medicine, State University of New York—University at Buffalo, Buffalo, NY 14203, USA
- Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA
| | - Mai N. Nguyen
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mahmoud Tawfik KhalafAllah
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Steven J. Pittler
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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13
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Mousa J, Veres L, Mohamed A, De Graef D, Morava E. Acetazolamide treatment in late onset CDG type 1 due to biallelic pathogenic DHDDS variants. Mol Genet Metab Rep 2022; 32:100901. [PMID: 36046393 PMCID: PMC9421445 DOI: 10.1016/j.ymgmr.2022.100901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/29/2022] Open
Abstract
Pathogenic variants in DHDDS have been associated with either autosomal recessive retinitis pigmentosa or DHDDS-CDG. Heterozygous variants in DHDDS have been described in patients with a progressive neurodegenerative disease. Here we report on an individual presenting with a multisystem CDG phenotype who was diagnosed with known homozygous pathogenic DHDDS variants, previously associated with isolated retinitis pigmentosa. An adult Ashkenazi Jewish female developed multiple symptoms of late onset type 1 CDG including seizures, ataxia, protein losing enteropathy, tremor, and titubation in association with elevated mono-oligo/di-oligo transferrin ratio in blood, and classic retinitis pigmentosa. She was diagnosed by whole exome sequencing with the common Ashkenazi Jewish, homozygous p.K42E variants in DHDDS. She was started on Acetazolamide and responded well to the treatment which improved her titubation, tremor, and generalized edema. Reviewing the literature, families with DHDDS variants and multisystem presentation were different from our patient's presentation in terms of clinical manifestations, severity, genetic defect, and mode of inheritance. In previously reported patients with neurologic symptoms including seizures, movement abnormalities, and global development delay, the phenotype was caused by heterozygous pathogenic variants in DHDDS. The infant who was reported with a multisystem phenotype and fatal type 1 CDG had compound heterozygosity for a nonsense and a splice site variant in DHDDS, resulting in DHDDS-CDG. The discovery of the novel phenotype associated with the common p.K42E pathogenic variant in DHDDS expands the spectrum of CDG and further enhances our understanding on the role of DHDDS in glycosylation beyond the retina. We report on the first individual carrying homozygous p.K42E variants in DHDDS associated with protein losing enteropathy, seizures, and ataxia. We observed familial variability in association with p.K42E and progressive ataxia in siblings with in DHDDS-CDG. The novel DHDDS-CDG patient phenotype broadens the current spectrum of CDG. Acetazolamide was successful in treating titubation and recurrent edema in our DHDDS-CDG patient of Ashkenazi Jewish descent.
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Affiliation(s)
- Jehan Mousa
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Larissa Veres
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Anab Mohamed
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Corresponding author at: Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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14
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Giladi M, Lisnyansky Bar-El M, Vaňková P, Ferofontov A, Melvin E, Alkaderi S, Kavan D, Redko B, Haimov E, Wiener R, Man P, Haitin Y. Structural basis for long-chain isoprenoid synthesis by cis-prenyltransferases. SCIENCE ADVANCES 2022; 8:eabn1171. [PMID: 35584224 PMCID: PMC9116609 DOI: 10.1126/sciadv.abn1171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Isoprenoids are synthesized by the prenyltransferase superfamily, which is subdivided according to the product stereoisomerism and length. In short- and medium-chain isoprenoids, product length correlates with active site volume. However, enzymes synthesizing long-chain products and rubber synthases fail to conform to this paradigm, because of an unexpectedly small active site. Here, we focused on the human cis-prenyltransferase complex (hcis-PT), residing at the endoplasmic reticulum membrane and playing a crucial role in protein glycosylation. Crystallographic investigation of hcis-PT along the reaction cycle revealed an outlet for the elongating product. Hydrogen-deuterium exchange mass spectrometry analysis showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Last, using a fluorescence substrate analog, we show that product elongation and membrane association are closely correlated. Together, our results support direct membrane insertion of the elongating isoprenoid during catalysis, uncoupling active site volume from product length.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Michal Lisnyansky Bar-El
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Pavla Vaňková
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Alisa Ferofontov
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Emelia Melvin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Suha Alkaderi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Boris Redko
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elvira Haimov
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, IMRIC, Hadassah Medical School, The Hebrew University, Jerusalem 9112001, Israel
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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15
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Applying Protein–Protein Interactions and Complex Networks to Identify Novel Genes in Retinitis Pigmentosa Pathogenesis. Int J Mol Sci 2022; 23:ijms23073962. [PMID: 35409321 PMCID: PMC8999418 DOI: 10.3390/ijms23073962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/29/2022] [Accepted: 03/29/2022] [Indexed: 12/10/2022] Open
Abstract
Retinitis Pigmentosa (RP) is a hereditary retinal disorder that causes the atrophy of photoreceptor rod cells. Since individual defective genes converge on the same disease, we hypothesized that all causal genes of RP belong in a complex network. To explore this hypothesis, we conducted a gene connection analysis using 161 genes attributed to RP, compiled from the Retinal Information Network, RetNet. We then examined the protein interaction network (PIN) of these genes. In line with our hypothesis, using STRING, we directly connected 149 genes out of the recognized 159 genes. To uncover the association between the PIN and the ten unrecalled genes, we developed an algorithm to pinpoint the best candidate genes to connect the uncalled genes to the PIN and identified ten such genes. We propose that mutations within these ten genes may also cause RP; this notion is supported by analyzing and categorizing the known causal genes based on cellular locations and related functions. The successful establishment of the PIN among all documented genes and the discovery of novel genes for RP strongly suggest an interconnectedness that causes the disease on the molecular level. In addition, our computational gene search protocol can help identify the genes and loci responsible for genetic diseases, not limited to RP.
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16
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Galosi S, Edani BH, Martinelli S, Hansikova H, Eklund EA, Caputi C, Masuelli L, Corsten-Janssen N, Srour M, Oegema R, Bosch DGM, Ellis CA, Amlie-Wolf L, Accogli A, Atallah I, Averdunk L, Barañano KW, Bei R, Bagnasco I, Brusco A, Demarest S, Alaix AS, Di Bonaventura C, Distelmaier F, Elmslie F, Gan-Or Z, Good JM, Gripp K, Kamsteeg EJ, Macnamara E, Marcelis C, Mercier N, Peeden J, Pizzi S, Pannone L, Shinawi M, Toro C, Verbeek NE, Venkateswaran S, Wheeler PG, Zdrazilova L, Zhang R, Zorzi G, Guerrini R, Sessa WC, Lefeber DJ, Tartaglia M, Hamdan FF, Grabińska KA, Leuzzi V. De novo DHDDS variants cause a neurodevelopmental and neurodegenerative disorder with myoclonus. Brain 2022; 145:208-223. [PMID: 34382076 PMCID: PMC8967098 DOI: 10.1093/brain/awab299] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/03/2021] [Accepted: 07/16/2021] [Indexed: 11/12/2022] Open
Abstract
Subcellular membrane systems are highly enriched in dolichol, whose role in organelle homeostasis and endosomal-lysosomal pathway remains largely unclear besides being involved in protein glycosylation. DHDDS encodes for the catalytic subunit (DHDDS) of the enzyme cis-prenyltransferase (cis-PTase), involved in dolichol biosynthesis and dolichol-dependent protein glycosylation in the endoplasmic reticulum. An autosomal recessive form of retinitis pigmentosa (retinitis pigmentosa 59) has been associated with a recurrent DHDDS variant. Moreover, two recurring de novo substitutions were detected in a few cases presenting with neurodevelopmental disorder, epilepsy and movement disorder. We evaluated a large cohort of patients (n = 25) with de novo pathogenic variants in DHDDS and provided the first systematic description of the clinical features and long-term outcome of this new neurodevelopmental and neurodegenerative disorder. The functional impact of the identified variants was explored by yeast complementation system and enzymatic assay. Patients presented during infancy or childhood with a variable association of neurodevelopmental disorder, generalized epilepsy, action myoclonus/cortical tremor and ataxia. Later in the disease course, they experienced a slow neurological decline with the emergence of hyperkinetic and/or hypokinetic movement disorder, cognitive deterioration and psychiatric disturbances. Storage of lipidic material and altered lysosomes were detected in myelinated fibres and fibroblasts, suggesting a dysfunction of the lysosomal enzymatic scavenger machinery. Serum glycoprotein hypoglycosylation was not detected and, in contrast to retinitis pigmentosa and other congenital disorders of glycosylation involving dolichol metabolism, the urinary dolichol D18/D19 ratio was normal. Mapping the disease-causing variants into the protein structure revealed that most of them clustered around the active site of the DHDDS subunit. Functional studies using yeast complementation assay and in vitro activity measurements confirmed that these changes affected the catalytic activity of the cis-PTase and showed growth defect in yeast complementation system as compared with the wild-type enzyme and retinitis pigmentosa-associated protein. In conclusion, we characterized a distinctive neurodegenerative disorder due to de novo DHDDS variants, which clinically belongs to the spectrum of genetic progressive encephalopathies with myoclonus. Clinical and biochemical data from this cohort depicted a condition at the intersection of congenital disorders of glycosylation and inherited storage diseases with several features akin to of progressive myoclonus epilepsy such as neuronal ceroid lipofuscinosis and other lysosomal disorders.
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Affiliation(s)
- Serena Galosi
- Department of Human Neuroscience, Sapienza University, Rome 00185, Italy
| | - Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome 00161, Italy
| | - Hana Hansikova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Erik A Eklund
- Section for Pediatrics, Department of Clinical Sciences, Lund University, Lund 22184, Sweden
| | - Caterina Caputi
- Department of Human Neuroscience, Sapienza University, Rome 00185, Italy
| | - Laura Masuelli
- Department of Experimental Medicine, Sapienza University, Rome 00161, Italy
| | - Nicole Corsten-Janssen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700, The Netherlands
| | - Myriam Srour
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Daniëlle G M Bosch
- Department of Genetics, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Nemours/A I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Andrea Accogli
- Department of Pediatrics, McGill University, Montreal, QC H4A 3J1, Canada.,Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Canada
| | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Luisa Averdunk
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf 40225, Germany
| | - Kristin W Barañano
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Irene Bagnasco
- Division of Neuropsychiatry, Epilepsy Center for Children, Martini Hospital, Turin 10128, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino & Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin 10126, Italy
| | - Scott Demarest
- Children's Hospital Colorado, Aurora, CO 80045, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Anne-Sophie Alaix
- Hopital Universitaire Necker Enfants Malades APHP, Paris 75015, France
| | | | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf 40225, Germany
| | - Frances Elmslie
- South West Thames Regional Genetics Service, St. George's Healthcare NHS Trust, London SW17 0QT, UK
| | - Ziv Gan-Or
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC H4A 3J1, Canada.,Montréal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada.,Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne 1011, Switzerland
| | - Karen Gripp
- Division of Medical Genetics, Nemours/A I duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen 6525, The Netherlands
| | - Ellen Macnamara
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Carlo Marcelis
- Department of Clinical Genetics, Radboud University Medical Centre, Nijmegen 6525, The Netherlands
| | - Noëlle Mercier
- Service d'Epileptologie et Médecine du handicap, Hôpital Neurologique, Institution de Lavigny, Lavigny 1175, Switzerland
| | - Joseph Peeden
- East Tennessee Children's Hospital, University of Tennessee Department of Medicine, Knoxville, TN 37916, USA
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Luca Pannone
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Institutes of Health, Bethesda, MD 20892-2152, USA
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Sunita Venkateswaran
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa ON K1H 8L1, Canada
| | | | - Lucie Zdrazilova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague 12808, Czech Republic
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Giovanna Zorzi
- Department of Pediatric Neurology, IRCCS Foundation Carlo Besta Neurological Institute, Milan 20133, Italy
| | - Renzo Guerrini
- AOU Meyer, Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children's Hospital, University of Florence, Florence 50139, Italy
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Dirk J Lefeber
- Department of Neurology, Translational Metabolic Laboratory, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Nijmegen 6525 AJ, The Netherlands
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome 00146, Italy
| | - Fadi F Hamdan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC H3T1C5, Canada
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Sapienza University, Rome 00185, Italy
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17
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Sompiyachoke K, Nagasaka A, Ito T, Hemmi H. Identification and biochemical characterization of a heteromeric cis-prenyltransferase from the thermophilic archaeon Archaeoglobus fulgidus. J Biochem 2022; 171:641-651. [PMID: 35195245 DOI: 10.1093/jb/mvac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/19/2022] [Indexed: 11/15/2022] Open
Abstract
cis-Prenyltransferases (cPTs) form linear polyprenyl pyrophosphates, the precursors of polyprenyl or dolichyl phosphates that are essential for cell function in all living organisms. Polyprenyl phosphate serves as a sugar-carrier for pesptidoglycan cell wall synthesis in bacteria, a role which dolichyl phosphate performs analogously for protein glycosylation in eukaryotes and archaea. Bacterial cPTs are characterized by their homodimeric structure, while cPTs from eukaryotes usually require two distantly homologous subunits for enzymatic activity. This study identifies the subunits of heteromeric cPT, Af1219 and Af0707, from a thermophilic sulfur-reducing archaeon, Archaeoglobus fulgidus. Both subunits are indispensable for cPT activity, and their protein-protein interactions were demonstrated by a pulldown assay. Gel filtration chromatography and chemical cross-linking experiments suggest that Af1219 and Af0707 likely form a heterotetramer complex. Although this expected subunit composition agrees with a reported heterotetrameric structure of human hCIT/NgBR cPT complex, the similarity of the quaternary structures is likely a result of convergent evolution.
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Affiliation(s)
- Kitty Sompiyachoke
- School of Agricultural Sciences and Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Arisa Nagasaka
- School of Agricultural Sciences and Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Tomokazu Ito
- School of Agricultural Sciences and Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Hisashi Hemmi
- School of Agricultural Sciences and Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
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18
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Jiao X, Xue Y, Yang S, Gong P, Niu Y, Wang Q, Yang H, Xiong H, Zhang Y, Yang Z. Phenotype of heterozygous variants of dehydrodolichol diphosphate synthase. Dev Med Child Neurol 2022; 64:125-134. [PMID: 34275143 DOI: 10.1111/dmcn.14976] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
AIM To further identify and broaden the phenotypic characteristics and genotype spectrum of the dehydrodolichol diphosphate synthase (DHDDS) gene. METHOD Pathogenic variants of DHDDS were identified by whole-exome sequencing; clinical data of 10 patients (six males, four females; age range 2-14y; mean age 5y 9mo, SD 3y 3mo) were collected and analysed. RESULTS All patients had seizures, and myoclonic seizures could be seen in eight patients, with myoclonic status epilepticus in three. The interictal electroencephalogram (EEG) in four patients at seizure onset showed generalized slow waves, slow wave mixed spikes, and spike and waves. Tremor, ataxia, and hypertonia was observed in six, five, and three patients respectively. The results of short-latency somatosensory evoked potential in two patients were normal, and the symptom of tremor was captured on EEG without time-locked discharges in one patient, suggesting that the tremor in both patients was a motor impairment rather than myoclonic seizures. Global developmental delay occurred in all patients, among whom nine showed severe intellectual disability and one moderate. Five DHDDS variants were identified, three of which have not been reported previously. INTERPRETATION Myoclonic seizure is the most common seizure type in heterozygous DHDDS variants, while myoclonic status epilepticus can also occur. The pattern of interictal EEG discharges is characterized by slow waves rather than spike and waves, and generalized discharges was prominent.
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Affiliation(s)
- Xianru Jiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yinan Xue
- Department of Pediatrics, Brain Hospital of Hunan Province, Changsha, China
| | - Sai Yang
- Department of Neurology, Hunan Children's Hospital, Changsha, China
| | - Pan Gong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yue Niu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Qi Wang
- Department of Pediatrics, Brain Hospital of Hunan Province, Changsha, China
| | - Hui Yang
- Department of Pediatrics, Brain Hospital of Hunan Province, Changsha, China
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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19
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Lewandowski D, Sander CL, Tworak A, Gao F, Xu Q, Skowronska-Krawczyk D. Dynamic lipid turnover in photoreceptors and retinal pigment epithelium throughout life. Prog Retin Eye Res 2021; 89:101037. [PMID: 34971765 PMCID: PMC10361839 DOI: 10.1016/j.preteyeres.2021.101037] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/13/2022]
Abstract
The retinal pigment epithelium-photoreceptor interphase is renewed each day in a stunning display of cellular interdependence. While photoreceptors use photosensitive pigments to convert light into electrical signals, the RPE supports photoreceptors in their function by phagocytizing shed photoreceptor tips, regulating the blood retina barrier, and modulating inflammatory responses, as well as regenerating the 11-cis-retinal chromophore via the classical visual cycle. These processes involve multiple protein complexes, tightly regulated ligand-receptors interactions, and a plethora of lipids and protein-lipids interactions. The role of lipids in maintaining a healthy interplay between the RPE and photoreceptors has not been fully delineated. In recent years, novel technologies have resulted in major advancements in understanding several facets of this interplay, including the involvement of lipids in phagocytosis and phagolysosome function, nutrient recycling, and the metabolic dependence between the two cell types. In this review, we aim to integrate the complex role of lipids in photoreceptor and RPE function, emphasizing the dynamic exchange between the cells as well as discuss how these processes are affected in aging and retinal diseases.
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Affiliation(s)
- Dominik Lewandowski
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Christopher L Sander
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Fangyuan Gao
- Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Qianlan Xu
- Department of Physiology and Biophysics, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA; Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, UC Irvine, Irvine, CA, USA.
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20
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Kamarus Jaman N, Rehsi P, Henderson RH, Löbel U, Mankad K, Grunewald S. SRD5A3-CDG: Emerging Phenotypic Features of an Ultrarare CDG Subtype. Front Genet 2021; 12:737094. [PMID: 34925443 PMCID: PMC8671882 DOI: 10.3389/fgene.2021.737094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Background: SRD5A3-CDG is a rare N-glycosylation defect caused by steroid 5 alpha reductase type 3 deficiency. Its key feature is an early severe visual impairment with variable ocular anomalies often leading to diagnosis. Additional symptoms are still poorly defined. In this case study, we discuss 11 genetically confirmed cases, and report on emerging features involving other systems in addition to the eye phenotype. Methods: In total, 11 SRD5A3-CDG patients in five sets of sibships were included in the study. Data on 9 of 11 patients are as of yet unpublished. Patients’ results on biochemical and genetic investigations and on in-depth phenotyping are presented. Results: Key diagnostic features of SRD5A3-CDG are ophthalmological abnormalities with early-onset retinal dystrophy and optic nerve hypoplasia. SRD5A3-CDG is also characterized by variable neurological symptoms including intellectual disability, ataxia, and hypotonia. Furthermore, ichthyosiform skin lesions, joint laxity, and scoliosis have been observed in our cohort. We also report additional findings including dystonia, anxiety disorder, gastrointestinal symptoms, and MRI findings of small basal ganglia and mal-rotated hippocampus, whereas previous publications described dysmorphic features as a common finding in SRD5A3, which could not be confirmed in our patient cohort. Conclusion: The detailed description of the phenotype of this large cohort of patients with SRD5A3-CDG highlights that the key clinical diagnostic features of SRD5A3-CDG are an early onset form of ophthalmological problems in patients with a multisystem disorder with variable symptoms evolving over time. This should aid earlier diagnosis and confirms the need for long-time follow-up of patients.
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Affiliation(s)
- Nazreen Kamarus Jaman
- Metabolic Department, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Preeya Rehsi
- Metabolic Department, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Robert H Henderson
- Ophthalmology Department, Great Ormond Street Hospital, London, United Kingdom.,Ophthalmology Department, Moorfields Eye Hospital, London, United Kingdom
| | - Ulrike Löbel
- Department of Radiology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Kshitij Mankad
- Department of Radiology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Stephanie Grunewald
- Metabolic Department, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom.,Institute for Child Health, NIHR Biomedical Research Center (BRC), University College London, London, United Kingdom
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21
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Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations. The study was performed to identify the underlying cause of inherited retinal degeneration (IRD) in 409 individuals from 108 families. Primarily, these families were recruited from three different geographic regions: Mexico, Pakistan and European Americans from the United States. Blood samples were collected from all individuals for genome analysis. This analysis detected causative variants in 61 out of the 108 pedigrees. A total of 93 gene variants were found in the 61 families. Among these, 54 were previously reported as causative variants and the remaining 39 have not been reported in IRD pedigrees. Interestingly, 54% of these novel variants were not listed in gnomAD. In addition to these findings, complex causative genotypes were observed in 20% of pedigrees. Overall, causative variants were detected in 63% Mexican, 60% Pakistani and 45% European American pedigrees. This study revealed the distribution of IRD causative variants in pedigrees with diverse ethnic and geographic backgrounds.
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Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
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22
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The evolving genetic landscape of congenital disorders of glycosylation. Biochim Biophys Acta Gen Subj 2021; 1865:129976. [PMID: 34358634 DOI: 10.1016/j.bbagen.2021.129976] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023]
Abstract
Congenital Disorders of Glycosylation (CDG) are an expanding and complex group of rare genetic disorders caused by defects in the glycosylation of proteins and lipids. The genetic spectrum of CDG is extremely broad with mutations in over 140 genes leading to a wide variety of symptoms ranging from mild to severe and life-threatening. There has been an expansion in the genetic complexity of CDG in recent years. More specifically several examples of alternate phenotypes in recessive forms of CDG and new types of CDG following an autosomal dominant inheritance pattern have been identified. In addition, novel genetic mechanisms such as expansion repeats have been reported and several already known disorders have been classified as CDG as their pathophysiology was better elucidated. Furthermore, we consider the future and outlook of CDG genetics, with a focus on exploration of the non-coding genome using whole genome sequencing, RNA-seq and multi-omics technology.
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23
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Brandwine T, Ifrah R, Bialistoky T, Zaguri R, Rhodes-Mordov E, Mizrahi-Meissonnier L, Sharon D, Katanaev VL, Gerlitz O, Minke B. Knockdown of Dehydrodolichyl Diphosphate Synthase in the Drosophila Retina Leads to a Unique Pattern of Retinal Degeneration. Front Mol Neurosci 2021; 14:693967. [PMID: 34290587 PMCID: PMC8287061 DOI: 10.3389/fnmol.2021.693967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/14/2021] [Indexed: 01/30/2023] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) is a ubiquitously expressed enzyme that catalyzes cis-prenyl chain elongation to produce the poly-prenyl backbone of dolichol. It appears in all tissues including the nervous system and it is a highly conserved enzyme that can be found in all animal species. Individuals who have biallelic missense mutations in the DHDDS gene are presented with non-syndromic retinitis pigmentosa with unknown underlying mechanism. We have used the Drosophila model to compromise DHDDS ortholog gene (CG10778) in order to look for cellular and molecular mechanisms that, when defective, might be responsible for this retinal disease. The Gal4/UAS system was used to suppress the expression of CG10778 via RNAi-mediated-knockdown in various tissues. The resulting phenotypes were assessed using q-RT-PCR, transmission-electron-microscopy (TEM), electroretinogram, antibody staining and Western blot analysis. Targeted knockdown of CG10778-mRNA in the early embryo using the actin promoter or in the developing wings using the nub promoter resulted in lethality, or wings loss, respectively. Targeted expression of CG10778-RNAi using the glass multiple reporter (GMR)-Gal4 driver (GMR-DHDDS-RNAi) in the larva eye disc and pupal retina resulted in a complex phenotype: (a) TEM retinal sections revealed a unique pattern of retinal-degeneration, where photoreceptors R2 and R5 exhibited a nearly normal structure of their signaling-compartment (rhabdomere), but only at the region of the nucleus, while all other photoreceptors showed retinal degeneration at all regions. (b) Western blot analysis revealed a drastic reduction in rhodopsin levels in GMR-DHDDS-RNAi-flies and TEM sections showed an abnormal accumulation of endoplasmic reticulum (ER). To conclude, compromising DHDDS in the developing retina, while allowing formation of the retina, resulted in a unique pattern of retinal degeneration, characterized by a dramatic reduction in rhodopsin protein level and an abnormal accumulation of ER membranes in the photoreceptors cells, thus indicating that DHDDS is essential for normal retinal formation.
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Affiliation(s)
- Tal Brandwine
- Department of Medical Neurobiology, Faculty of Medicine and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reut Ifrah
- Department of Medical Neurobiology, Faculty of Medicine and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tzofia Bialistoky
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rachel Zaguri
- Department of Medical Neurobiology, Faculty of Medicine and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Elisheva Rhodes-Mordov
- Department of Medical Neurobiology, Faculty of Medicine and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liliana Mizrahi-Meissonnier
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Translational Research Centre in Oncohaematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Offer Gerlitz
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Baruch Minke
- Department of Medical Neurobiology, Faculty of Medicine and The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
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24
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De Giorgi M, Jarrett KE, Burton JC, Doerfler AM, Hurley A, Li A, Hsu RH, Furgurson M, Patel KR, Han J, Borchers CH, Lagor WR. Depletion of essential isoprenoids and ER stress induction following acute liver-specific deletion of HMG-CoA reductase. J Lipid Res 2020; 61:1675-1686. [PMID: 33109681 PMCID: PMC7707164 DOI: 10.1194/jlr.ra120001006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
HMG-CoA reductase (Hmgcr) is the rate-limiting enzyme in the mevalonate pathway and is inhibited by statins. In addition to cholesterol, Hmgcr activity is also required for synthesizing nonsterol isoprenoids, such as dolichol, ubiquinone, and farnesylated and geranylgeranylated proteins. Here, we investigated the effects of Hmgcr inhibition on nonsterol isoprenoids in the liver. We have generated new genetic models to acutely delete genes in the mevalonate pathway in the liver using AAV-mediated delivery of Cre-recombinase (AAV-Cre) or CRISPR/Cas9 (AAV-CRISPR). The genetic deletion of Hmgcr by AAV-Cre resulted in extensive hepatocyte apoptosis and compensatory liver regeneration. At the biochemical level, we observed decreased levels of sterols and depletion of the nonsterol isoprenoids, dolichol and ubiquinone. At the cellular level, Hmgcr-null hepatocytes showed ER stress and impaired N-glycosylation. We further hypothesized that the depletion of dolichol, essential for N-glycosylation, could be responsible for ER stress. Using AAV-CRISPR, we somatically disrupted dehydrodolichyl diphosphate synthase subunit (Dhdds), encoding a branch point enzyme required for dolichol biosynthesis. Dhdds-null livers showed ER stress and impaired N-glycosylation, along with apoptosis and regeneration. Finally, the combined deletion of Hmgcr and Dhdds synergistically exacerbated hepatocyte ER stress. Our data show a critical role for mevalonate-derived dolichol in the liver and suggest that dolichol depletion is at least partially responsible for ER stress and apoptosis upon potent Hmgcr inhibition.
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Affiliation(s)
- Marco De Giorgi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Kelsey E. Jarrett
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA,Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Jason C. Burton
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA,Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Alexandria M. Doerfler
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Ayrea Hurley
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Ang Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Rachel H. Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Mia Furgurson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Kalyani R. Patel
- Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Jun Han
- Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Christoph H. Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada,Department of Data Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, Russia
| | - William R. Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA,For correspondence: William R. Lagor,
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25
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Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun 2020; 11:5273. [PMID: 33077723 PMCID: PMC7573591 DOI: 10.1038/s41467-020-18970-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor (NgBR) heterodimers. Importantly, the 2.3 Å crystal structure reveals that the tetramer assembles via the DHDDS C-termini as a dimer-of-heterodimers. Moreover, the distal C-terminus of NgBR transverses across the interface with DHDDS, directly participating in active-site formation and the functional coupling between the subunits. Finally, we explored the functional consequences of disease mutations clustered around the active-site, and in combination with molecular dynamics simulations, we propose a mechanism for hcis-PT dysfunction in retinitis pigmentosa. Together, our structure of the hcis-PT complex unveils the dolichol synthesis mechanism and its perturbation in disease. The human cis-prenyltransferase (hcis-PT) complex synthesizes the precursor of the glycosyl carrier dolichol-phosphate and as such it is essential for protein N-glycosylation. The crystal structure of the complex reveals unusual tetrameric architecture and provides insights into dolichol synthesis mechanism and functional consequences of disease-associated hcis-PT mutations.
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26
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Tatour Y, Ben-Yosef T. Syndromic Inherited Retinal Diseases: Genetic, Clinical and Diagnostic Aspects. Diagnostics (Basel) 2020; 10:diagnostics10100779. [PMID: 33023209 PMCID: PMC7600643 DOI: 10.3390/diagnostics10100779] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal diseases (IRDs), which are among the most common genetic diseases in humans, define a clinically and genetically heterogeneous group of disorders. Over 80 forms of syndromic IRDs have been described. Approximately 200 genes are associated with these syndromes. The majority of syndromic IRDs are recessively inherited and rare. Many, although not all, syndromic IRDs can be classified into one of two major disease groups: inborn errors of metabolism and ciliopathies. Besides the retina, the systems and organs most commonly involved in syndromic IRDs are the central nervous system, ophthalmic extra-retinal tissues, ear, skeleton, kidney and the cardiovascular system. Due to the high degree of phenotypic variability and phenotypic overlap found in syndromic IRDs, correct diagnosis based on phenotypic features alone may be challenging and sometimes misleading. Therefore, genetic testing has become the benchmark for the diagnosis and management of patients with these conditions, as it complements the clinical findings and facilitates an accurate clinical diagnosis and treatment.
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Togashi N, Fujita A, Shibuya M, Uneoka S, Miyabayashi T, Sato R, Okubo Y, Endo W, Inui T, Jin K, Matsumoto N, Haginoya K. Fifteen-year follow-up of a patient with a DHDDS variant with non-progressive early onset myoclonic tremor and rare generalized epilepsy. Brain Dev 2020; 42:696-699. [PMID: 32654954 DOI: 10.1016/j.braindev.2020.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/21/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Generalized epilepsy and tremor phenotypes have been reported in some genetic disorders. Among them benign adult familial myoclonus epilepsy (BAFME) has been confirmed as a clearly defined clinical and genetic entity. On the other hand, non-progressive tremor and generalized epilepsy phenotypes have also been reported in patients with DHDDS variants. CASE PRESENTATION We report on a long term follow-up of patient with de novo missense variant of DHDDS, who revealed non progressive nature. This 18-year-old woman presented non-progressive tremor since her early infancy. She had rare seizures. Her tremor was considered as cortical myoclonic tremor with giant somatosensory evoked potentials. CONCLUSION In patients with early onset, non-progressive tremor and rare generalized epilepsy phenotypes, DHDDS variants may be considered in the genetic differential diagnosis.
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Affiliation(s)
- Noriko Togashi
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Moriei Shibuya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Saki Uneoka
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Takuya Miyabayashi
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Ryo Sato
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Yukimune Okubo
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Wakaba Endo
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Takehiko Inui
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Kazutaka Jin
- Department of Epileptology, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan.
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Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A 2020; 117:20794-20802. [PMID: 32817466 PMCID: PMC7456142 DOI: 10.1073/pnas.2008381117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
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Affiliation(s)
- Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Eon Joo Park
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin Siciliano
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Ya Ha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520;
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
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Zhang R, Tang BS, Guo JF. Research advances on neurite outgrowth inhibitor B receptor. J Cell Mol Med 2020; 24:7697-7705. [PMID: 32542927 PMCID: PMC7348171 DOI: 10.1111/jcmm.15391] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 12/24/2022] Open
Abstract
Neurite outgrowth inhibitor‐B (Nogo‐B) is a membrane protein which is extensively expressed in multiple organs, especially in endothelial cells and vascular smooth muscle cells of blood vessels and belongs to the reticulon protein family. Notably, its specific receptor, Nogo‐B receptor (NgBR), encoded by NUS1, has been implicated in many crucial cellular processes, such as cholesterol trafficking, lipid metabolism, dolichol synthesis, protein N‐glycosylation, vascular remodelling, angiogenesis, tumorigenesis and neurodevelopment. In recent years, accumulating studies have demonstrated the statistically significant changes of NgBR expression levels in human diseases, including Niemann‐Pick type C disease, fatty liver, congenital disorders of glycosylation, persistent pulmonary hypertension of the newborn, invasive ductal breast carcinoma, malignant melanoma, non‐small cell lung carcinoma, paediatric epilepsy and Parkinson's disease. Besides, both the in vitro and in vivo studies have shown that NgBR overexpression or knockdown contribute to the alteration of various pathophysiological processes. Thus, there is a broad development potential in therapeutic strategies by modifying the expression levels of NgBR.
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Affiliation(s)
- Rui Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bei-Sha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Ji-Feng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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Ramachandra Rao S, Skelton LA, Wu F, Onysk A, Spolnik G, Danikiewicz W, Butler MC, Stacks DA, Surmacz L, Mu X, Swiezewska E, Pittler SJ, Fliesler SJ. Retinal Degeneration Caused by Rod-Specific Dhdds Ablation Occurs without Concomitant Inhibition of Protein N-Glycosylation. iScience 2020; 23:101198. [PMID: 32526701 PMCID: PMC7287266 DOI: 10.1016/j.isci.2020.101198] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/10/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) catalyzes the committed step in dolichol synthesis. Recessive mutations in DHDDS cause retinitis pigmentosa (RP59), resulting in blindness. We hypothesized that rod photoreceptor-specific ablation of Dhdds would cause retinal degeneration due to diminished dolichol-dependent protein N-glycosylation. Dhddsflx/flx mice were crossed with rod-specific Cre recombinase-expressing (Rho-iCre75) mice to generate rod-specific Dhdds knockout mice (Dhddsflx/flx iCre+). In vivo morphological and electrophysiological evaluation of Dhddsflx/flx iCre+ retinas revealed mild retinal dysfunction at postnatal (PN) 4 weeks, compared with age-matched controls; however, rapid photoreceptor degeneration ensued, resulting in almost complete loss of rods and cones by PN 6 weeks. Retina dolichol levels were markedly decreased by PN 4 weeks in Dhddsflx/flx iCre+ mice, relative to controls; despite this, N-glycosylation of retinal proteins, including opsin (the dominant rod-specific glycoprotein), persisted in Dhddsflx/flx iCre+ mice. These findings challenge the conventional mechanistic view of RP59 as a congenital disorder of glycosylation. Deletion of Dhdds in rod cells caused rapid retinal degeneration in mice Retinal dolichol levels markedly decreased before onset of degeneration Protein N-glycosylation was uncompromised despite Dhdds deletion Degeneration also involved gliosis, microglial activation, and phagoptosis
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Affiliation(s)
- Sriganesh Ramachandra Rao
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Lara A Skelton
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Agnieszka Onysk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Grzegorz Spolnik
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 02106, Poland
| | - Witold Danikiewicz
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 02106, Poland
| | - Mark C Butler
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA
| | - Delores A Stacks
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Xiuqian Mu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA; New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA
| | - Ewa Swiezewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Steven J Pittler
- Department of Optometry and Vision Science, Vision Science Research Center, School of Optometry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Steven J Fliesler
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14209, USA; Research Service, VA Western NY Healthcare System, Buffalo, NY 142015, USA; Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York- University at Buffalo, Buffalo, NY 14203, USA.
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Lack of Overt Retinal Degeneration in a K42E Dhdds Knock-In Mouse Model of RP59. Cells 2020; 9:cells9040896. [PMID: 32272552 PMCID: PMC7226774 DOI: 10.3390/cells9040896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/30/2020] [Accepted: 04/04/2020] [Indexed: 12/17/2022] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) is required for protein N-glycosylation in eukaryotic cells. A K42E point mutation in the DHDDS gene causes an autosomal recessive form of retinitis pigmentosa (RP59), which has been classified as a congenital disease of glycosylation (CDG). We generated K42E Dhdds knock-in mice as a potential model for RP59. Mice heterozygous for the Dhdds K42E mutation were generated using CRISPR/Cas9 technology and crossed to generate DhddsK42E/K42E homozygous mice. Spectral domain-optical coherence tomography (SD-OCT) was performed to assess retinal structure, relative to age-matched wild type (WT) controls. Immunohistochemistry against glial fibrillary acidic protein (GFAP) and opsin (1D4 epitope) was performed on retinal frozen sections to monitor gliosis and opsin localization, respectively, while lectin cytochemistry, plus and minus PNGase-F treatment, was performed to assess protein glycosylation status. Retinas of DhddsK42E/K42E mice exhibited grossly normal histological organization from 1 to 12 months of age. Anti-GFAP immunoreactivity was markedly increased in DhddsK42E/K42E mice, relative to controls. However, opsin immunolocalization, ConA labeling and PNGase-F sensitivity were comparable in mutant and control retinas. Hence, retinas of DhddsK42E/K42E mice exhibited no overt signs of degeneration, yet were markedly gliotic, but without evidence of compromised protein N-glycosylation. These results challenge the notion of RP59 as a DHDDS loss-of-function CDG and highlight the need to investigate unexplored RP59 disease mechanisms.
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DeRamus ML, Davis SJ, Rao SR, Nyankerh C, Stacks D, Kraft TW, Fliesler SJ, Pittler SJ. Selective Ablation of Dehydrodolichyl Diphosphate Synthase in Murine Retinal Pigment Epithelium (RPE) Causes RPE Atrophy and Retinal Degeneration. Cells 2020; 9:E771. [PMID: 32245241 PMCID: PMC7140717 DOI: 10.3390/cells9030771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/06/2020] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
Patients with certain defects in the dehydrodolichyl diphosphate synthase (DHDDS) gene (RP59; OMIM #613861) exhibit classic symptoms of retinitis pigmentosa, as well as macular changes, suggestive of retinal pigment epithelium (RPE) involvement. The DHDDS enzyme is ubiquitously required for several pathways of protein glycosylation. We wish to understand the basis for selective ocular pathology associated with certain DHDDS mutations and the contribution of specific ocular cell types to the pathology of mutant Dhdds-mediated retinal degeneration. To circumvent embryonic lethality associated with Dhdds knockout, we generated a Cre-dependent knockout allele of murine Dhdds (Dhddsflx/flx). We used targeted Cre expression to study the importance of the enzyme in the RPE. Structural alterations of the RPE and retina including reduction in outer retinal thickness, cell layer disruption, and increased RPE hyper-reflectivity were apparent at one postnatal month. At three months, RPE and photoreceptor disruption was observed non-uniformly across the retina as well as RPE transmigration into the photoreceptor layer, external limiting membrane descent towards the RPE, and patchy loss of photoreceptors. Functional loss measured by electroretinography was consistent with structural loss showing scotopic a- and b-wave reductions of 83% and 77%, respectively, at three months. These results indicate that RPE dysfunction contributes to DHDDS mutation-mediated pathology and suggests a more complicated disease mechanism than simply disruption of glycosylation.
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Affiliation(s)
- Marci L. DeRamus
- Department of Optometry and Vision Science, Vision Science Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.L.D.); (S.J.D.); (C.N.); (D.S.); (T.W.K.)
| | - Stephanie J. Davis
- Department of Optometry and Vision Science, Vision Science Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.L.D.); (S.J.D.); (C.N.); (D.S.); (T.W.K.)
| | - Sriganesh Ramachandra Rao
- Departments of Ophthalmology and Biochemistry, State University of New York-University at Buffalo, Buffalo, NY 14209, USA; and Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA; (S.R.R.); (S.J.F.)
| | - Cyril Nyankerh
- Department of Optometry and Vision Science, Vision Science Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.L.D.); (S.J.D.); (C.N.); (D.S.); (T.W.K.)
| | - Delores Stacks
- Department of Optometry and Vision Science, Vision Science Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.L.D.); (S.J.D.); (C.N.); (D.S.); (T.W.K.)
| | - Timothy W. Kraft
- Department of Optometry and Vision Science, Vision Science Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.L.D.); (S.J.D.); (C.N.); (D.S.); (T.W.K.)
| | - Steven J. Fliesler
- Departments of Ophthalmology and Biochemistry, State University of New York-University at Buffalo, Buffalo, NY 14209, USA; and Research Service, VA Western NY Healthcare System, Buffalo, NY 14215, USA; (S.R.R.); (S.J.F.)
| | - Steven J. Pittler
- Department of Optometry and Vision Science, Vision Science Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (M.L.D.); (S.J.D.); (C.N.); (D.S.); (T.W.K.)
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Li N, Gou JH, Xiong J, You JJ, Li ZY. HOXB4 promotes the malignant progression of ovarian cancer via DHDDS. BMC Cancer 2020; 20:222. [PMID: 32178630 PMCID: PMC7077141 DOI: 10.1186/s12885-020-06725-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
Background Homeobox B4 (HOXB4) is correlated with poor prognosis of various cancer types. However, how HOXB4 promotes ovarian cancer (OV) progression remains unclear. Methods The Cancer Genome Atlas (TCGA) database indicated that a high level of HOXB4 in OV was correlated with poor prognosis. The biological functions of HOXB4 were confirmed by colony formation, migration, and invasion assays. The effect of HOXB4 on the expression of EMT cell markers was determined. The transcriptional target of HOXB4 was DHDDS, which was detected by a ChIP assay. A xenograft tumor model was generated in nude mice to detect the role of HOXB4 in tumor proliferation and metastasis. Results The results showed that HOXB4 protein levels were higher in OV tissues than in normal tissues and correlated with poor prognosis of OV. HOXB4 reduction inhibited the proliferation and invasion ability of OV cells in vitro. Conversely, these effects were enhanced by the upregulation of HOXB4 in OV cells. The binding of HOXB4 to two DNA motifs regulated DHDDS expression and contributed to the malignant progression of OV. The role of HOXB4 in contributing to tumor development in vivo was verified in mice. Further results indicated that HOXB4 induced Snail and Zeb1 expression. Conclusion Overall, HOXB4 overexpression was remarkably correlated with poor prognosis of OV. Mechanistically, HOXB4 enhances the proliferation and invasion of tumor cells by activating DHDDS, thereby promoting the malignant progression of OV.
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Affiliation(s)
- Na Li
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China.,Department of Obstetrics and Gynecology, The first affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, 563000, People's Republic of China
| | - Jin-Hai Gou
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China
| | - Jiao Xiong
- Department of Obstetrics and Gynecology, The first affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, 563000, People's Republic of China
| | - Juan-Juan You
- Department of Obstetrics and Gynecology, The first affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, 563000, People's Republic of China
| | - Zheng-Yu Li
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, People's Republic of China. .,Key Laboratory of Obstetrics & Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, 610041, P.R. China.
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Ansar M, Chung H, Waryah YM, Makrythanasis P, Falconnet E, Rao AR, Guipponi M, Narsani AK, Fingerhut R, Santoni FA, Ranza E, Waryah AM, Bellen HJ, Antonarakis SE. Visual impairment and progressive phthisis bulbi caused by recessive pathogenic variant in MARK3. Hum Mol Genet 2019; 27:2703-2711. [PMID: 29771303 DOI: 10.1093/hmg/ddy180] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 12/20/2022] Open
Abstract
Developmental eye defects often severely reduce vision. Despite extensive efforts, for a substantial fraction of these cases the molecular causes are unknown. Recessive eye disorders are frequent in consanguineous populations and such large families with multiple affected individuals provide an opportunity to identify recessive causative genes. We studied a Pakistani consanguineous family with three affected individuals with congenital vision loss and progressive eye degeneration. The family was analyzed by exome sequencing of one affected individual and genotyping of all family members. We have identified a non-synonymous homozygous variant (NM_001128918.2: c.1708C > G: p.Arg570Gly) in the MARK3 gene as the likely cause of the phenotype. Given that MARK3 is highly conserved in flies (I: 55%; S: 67%) we knocked down the MARK3 homologue, par-1, in the eye during development. This leads to a significant reduction in eye size, a severe loss of photoreceptors and loss of vision based on electroretinogram (ERG) recordings. Expression of the par-1 p.Arg792Gly mutation (equivalent to the MARK3 variant found in patients) in developing fly eyes also induces loss of eye tissue and reduces the ERG signals. The data in flies and human indicate that the MARK3 variant corresponds to a loss of function. We conclude that the identified mutation in MARK3 establishes a new gene-disease link, since it likely causes structural abnormalities during eye development and visual impairment in humans, and that the function of MARK3/par-1 is evolutionarily conserved in eye development.
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Affiliation(s)
- Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Hyunglok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Yar M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Ali Raza Rao
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ashok K Narsani
- Institute of Ophthalmology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ralph Fingerhut
- Swiss Newborn Screening Laboratory, University Children's Hospital, Zurich, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Emmanuelle Ranza
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Ali M Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland.,iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
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35
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Structural Characterization of Full-Length Human Dehydrodolichyl Diphosphate Synthase Using an Integrative Computational and Experimental Approach. Biomolecules 2019; 9:biom9110660. [PMID: 31661879 PMCID: PMC6921004 DOI: 10.3390/biom9110660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 01/13/2023] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) is the catalytic subunit of the heteromeric human cis-prenyltransferase complex, synthesizing the glycosyl carrier precursor for N-linked protein glycosylation. Consistent with the important role of N-glycosylation in protein biogenesis, DHDDS mutations result in human diseases. Importantly, DHDDS encompasses a C-terminal region, which does not converge with any known conserved domains. Therefore, despite the clinical importance of DHDDS, our understating of its structure-function relations remains poor. Here, we provide a structural model for the full-length human DHDDS using a multidisciplinary experimental and computational approach. Size-exclusion chromatography multi-angle light scattering revealed that DHDDS forms a monodisperse homodimer in solution. Enzyme kinetics assays revealed that it exhibits catalytic activity, although reduced compared to that reported for the intact heteromeric complex. Our model suggests that the DHDDS C-terminus forms a helix-turn-helix motif, tightly packed against the core catalytic domain. This model is consistent with small-angle X-ray scattering data, indicating that the full-length DHDDS maintains a similar conformation in solution. Moreover, hydrogen-deuterium exchange mass-spectrometry experiments show time-dependent deuterium uptake in the C-terminal domain, consistent with its overall folded state. Finally, we provide a model for the DHDDS-NgBR heterodimer, offering a structural framework for future structural and functional studies of the complex.
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Sharon D, Ben-Yosef T, Goldenberg-Cohen N, Pras E, Gradstein L, Soudry S, Mezer E, Zur D, Abbasi AH, Zeitz C, Cremers FPM, Khan MI, Levy J, Rotenstreich Y, Birk OS, Ehrenberg M, Leibu R, Newman H, Shomron N, Banin E, Perlman I. A nationwide genetic analysis of inherited retinal diseases in Israel as assessed by the Israeli inherited retinal disease consortium (IIRDC). Hum Mutat 2019; 41:140-149. [PMID: 31456290 DOI: 10.1002/humu.23903] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 01/13/2023]
Abstract
Inherited retinal diseases (IRDs) cause visual loss due to dysfunction or progressive degeneration of photoreceptors. These diseases show marked phenotypic and genetic heterogeneity. The Israeli IRD consortium (IIRDC) was established in 2013 with the goal of performing clinical and genetic mapping of the majority of Israeli IRD patients. To date, we recruited 2,420 families including 3,413 individuals with IRDs. On the basis of our estimation, these patients represent approximately 40% of Israeli IRD patients. To the best of our knowledge, this is, by far, the largest reported IRD cohort, and one of the first studies addressing the genetic analysis of IRD patients on a nationwide scale. The most common inheritance pattern in our cohort is autosomal recessive (60% of families). The most common retinal phenotype is retinitis pigmentosa (43%), followed by Stargardt disease and cone/cone-rod dystrophy. We identified the cause of disease in 56% of the families. Overall, 605 distinct mutations were identified, of which 12% represent prevalent founder mutations. The most frequently mutated genes were ABCA4, USH2A, FAM161A, CNGA3, and EYS. The results of this study have important implications for molecular diagnosis, genetic screening, and counseling, as well as for the development of new therapeutic strategies for retinal diseases.
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Affiliation(s)
- Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Nitza Goldenberg-Cohen
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Ophthalmology, Bnai Zion Medical Center, Haifa, Israel.,The Krieger Eye Research Laboratory, Felsenstein Medical Research Center (FMRC), Petach Tikva, Israel
| | - Eran Pras
- Department of Ophthalmology, Assaf-Harofeh Medical Center, Zerifin, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Shiri Soudry
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Ophthalmology, Rambam Healthcare Campus, Haifa, Israel
| | - Eedy Mezer
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Department of Ophthalmology, Rambam Healthcare Campus, Haifa, Israel
| | - Dinah Zur
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Ophthalmology Division, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Anan H Abbasi
- Ziv Medical Center, Safed, Israel.,The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Christina Zeitz
- INSERM, CNRS, Institut de la Vision, Sorbonne Université, Paris, France
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Muhammad I Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaime Levy
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ygal Rotenstreich
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Goldschleger Eye Institute, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev, Ben-Gurion University, Beer Sheva, Israel.,Genetics Institute, Soroka Medical Center, Faculty of Health Sciences, Ben-Gurion University, Beer Sheva, Israel
| | - Miriam Ehrenberg
- Ophthalmology Unit, Schneider Children's Medical Center in Israel, Petach Tikva, Israel
| | - Rina Leibu
- Department of Ophthalmology, Rambam Healthcare Campus, Haifa, Israel
| | - Hadas Newman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Ophthalmology Division, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ido Perlman
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.,Ophthalmology Division, Tel Aviv Medical Center, Tel Aviv, Israel
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Chellappa SA, Pathak AK, Sinha P, Jainarayanan ASHWINK, Jain S, Brahmachari SK. Meta-analysis of genomic variants and gene expression data in schizophrenia suggests the potential need for adjunctive therapeutic interventions for neuropsychiatric disorders. J Genet 2019. [DOI: 10.1007/s12041-019-1101-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Anirudh Chellappa S, Pathak AK, Sinha P, Jainarayanan AK, Jain S, Brahmachari SK. Meta-analysis of genomic variants and gene expression data in schizophrenia suggests the potential need for adjunctive therapeutic interventions for neuropsychiatric disorders. J Genet 2019; 98:60. [PMID: 31204709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Schizophrenia (SZ) is a debilitating mental illness with a multigenic aetiology and significant heritability. Despite extensive genetic studies, the molecular aetiology has remained enigmatic. A recent systems biology study suggested a protein-protein interaction network for SZ with 504 novel interactions. The onset of psychiatric disorders is predominant during adolescence, often accompanied by subtle structural abnormalities in multiple regions of the brain. The availability of BrainSpan Atlas data allowed us to re-examine the genes present in the SZ interactome as a function of space and time. The availability of genomes of healthy centenarians and nonpsychiatric Exome Aggregation Consortium database allowed us to identify the variants of criticality. The expression of the SZ candidate genes responsible for cognition and disease onset was studied in different brain regions during particular developmental stages. A subset of novel interactors detected in the network was further validated using gene expression data of post-mortem brains of patients with psychiatric illness. We have narrowed down the list of drug targets proposed by theprevious interactome study to 10 proteins. These proteins belonging to 81 biological pathways are targeted by 34 known Food and Drug Administration-approved drugs that have distinct potential for the treatment of neuropsychiatric disorders. We also report the possibility of targeting key genes belonging to celecoxib pharmacodynamics, Gα signalling and cGMP-PKG signalling pathwaysthat are not known to be specific to SZ aetiology.
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Affiliation(s)
- S Anirudh Chellappa
- Centre for Open Innovation - Indian Centre for Social Transformation (ICST), Bengaluru 560 001, India
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Albrecht NE, Alevy J, Jiang D, Burger CA, Liu BI, Li F, Wang J, Kim SY, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gaspero A, Justice MJ, Westenskow PD, Yamamoto S, Seavitt JR, Beaudet AL, Dickinson ME, Samuel MA. Rapid and Integrative Discovery of Retina Regulatory Molecules. Cell Rep 2018; 24:2506-2519. [PMID: 30157441 PMCID: PMC6170014 DOI: 10.1016/j.celrep.2018.07.090] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/15/2018] [Accepted: 07/27/2018] [Indexed: 12/26/2022] Open
Abstract
Retinal function relies on precisely organized neurons and synapses and a properly patterned vasculature to support them. Alterations in these features can result in vision loss. However, our understanding of retinal organization pathways remains incomplete because of a lack of methods to rapidly identify neuron and vasculature regulators in mammals. Here we developed a pipeline for the identification of neural and synaptic integrity genes by high-throughput retinal screening (INSiGHT) that analyzes candidate expression, vascular patterning, cellular organization, and synaptic arrangement. Using this system, we examined 102 mutant mouse lines and identified 16 unique retinal regulatory genes. Fifteen of these candidates are identified as novel retina regulators, and many (9 of 16) are associated with human neural diseases. These results expand the genetic landscape involved in retinal circuit organization and provide a road map for continued discovery of mammalian retinal regulators and disease-causing alleles.
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Affiliation(s)
- Nicholas E Albrecht
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan Alevy
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Danye Jiang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney A Burger
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian I Liu
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fenge Li
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julia Wang
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Seon-Young Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sowmya Kalaga
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Uchechukwu Udensi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chinwe Asomugha
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ritu Bohat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angelina Gaspero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Monica J Justice
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Peter D Westenskow
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John R Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary E Dickinson
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Melanie A Samuel
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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Ng BG, Freeze HH. Perspectives on Glycosylation and Its Congenital Disorders. Trends Genet 2018; 34:466-476. [PMID: 29606283 DOI: 10.1016/j.tig.2018.03.002] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/04/2018] [Accepted: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Congenital disorders of glycosylation (CDG) are a rapidly expanding group of metabolic disorders that result from abnormal protein or lipid glycosylation. They are often difficult to clinically diagnose because they broadly affect many organs and functions and lack clinical uniformity. However, recent technological advances in next-generation sequencing have revealed a treasure trove of new genetic disorders, expanded the knowledge of known disorders, and showed a critical role in infectious diseases. More comprehensive genetic tools specifically tailored for mammalian cell-based models have revealed a critical role for glycosylation in pathogen-host interactions, while also identifying new CDG susceptibility genes. We highlight recent advancements that have resulted in a better understanding of human glycosylation disorders, perspectives for potential future therapies, and mysteries for which we continue to seek new insights and solutions.
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Affiliation(s)
- Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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Kimchi A, Khateb S, Wen R, Guan Z, Obolensky A, Beryozkin A, Kurtzman S, Blumenfeld A, Pras E, Jacobson SG, Ben-Yosef T, Newman H, Sharon D, Banin E. Nonsyndromic Retinitis Pigmentosa in the Ashkenazi Jewish Population: Genetic and Clinical Aspects. Ophthalmology 2017; 125:725-734. [PMID: 29276052 DOI: 10.1016/j.ophtha.2017.11.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 01/19/2023] Open
Abstract
PURPOSE To analyze the genetic and clinical findings in retinitis pigmentosa (RP) patients of Ashkenazi Jewish (AJ) descent, aiming to identify genotype-phenotype correlations. DESIGN Cohort study. PARTICIPANTS Retinitis pigmentosa patients from 230 families of AJ origin. METHODS Sanger sequencing was performed to detect specific founder mutations known to be prevalent in the AJ population. Ophthalmologic analysis included a comprehensive clinical examination, visual acuity (VA), visual fields, electroretinography, color vision testing, and retinal imaging by OCT, pseudocolor, and autofluorescence fundus photography. MAIN OUTCOME MEASURES Inheritance pattern and causative mutation; retinal function as assessed by VA, visual fields, and electroretinography results; and retinal structural changes observed on clinical funduscopy as well as by pseudocolor, autofluorescence, and OCT imaging. RESULTS The causative mutation was identified in 37% of families. The most prevalent RP-causing mutations are the Alu insertion (c.1297_8ins353, p.K433Rins31*) in the male germ cell-associated kinase (MAK) gene (39% of families with a known genetic cause for RP) and c.124A>G, p.K42E in dehydrodolichol diphosphate synthase (DHDDS) (33%). Additionally, disease-causing mutations were identified in 11 other genes. Analysis of clinical parameters of patients with mutations in the 2 most common RP-causing genes revealed that MAK patients had better VA and visual fields at relatively older ages in comparison with DHDDS patients. Funduscopic findings of DHDDS patients matched those of MAK patients who were 20 to 30 years older. Patients with DHDDS mutations were referred for electrophysiologic evaluation at earlier ages, and their cone responses became nondetectable at a much younger age than MAK patients. CONCLUSIONS Our AJ cohort of RP patients is the largest reported to date and showed a substantial difference in the genetic causes of RP compared with cohorts of other populations, mainly a high rate of autosomal recessive inheritance and a unique composition of causative genes. The most common RP-causing genes in our cohort, MAK and DHDDS, were not described as major causative genes in other populations. The clinical data show that in general, patients with biallelic MAK mutations had a later age of onset and a milder retinal phenotype compared with patients with biallelic DHDDS mutations.
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Affiliation(s)
- Adva Kimchi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Rong Wen
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida
| | - Ziqiang Guan
- Duke University Medical Center, Durham, North Carolina
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shoshi Kurtzman
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Anat Blumenfeld
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eran Pras
- Department of Ophthalmology, Assaf Harofeh Medical Center, Zerifin, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tamar Ben-Yosef
- The Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Hadas Newman
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Department of Ophthalmology, Sourasky Medical Center, Tel-Aviv, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
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Hamdan FF, Myers CT, Cossette P, Lemay P, Spiegelman D, Laporte AD, Nassif C, Diallo O, Monlong J, Cadieux-Dion M, Dobrzeniecka S, Meloche C, Retterer K, Cho MT, Rosenfeld JA, Bi W, Massicotte C, Miguet M, Brunga L, Regan BM, Mo K, Tam C, Schneider A, Hollingsworth G, FitzPatrick DR, Donaldson A, Canham N, Blair E, Kerr B, Fry AE, Thomas RH, Shelagh J, Hurst JA, Brittain H, Blyth M, Lebel RR, Gerkes EH, Davis-Keppen L, Stein Q, Chung WK, Dorison SJ, Benke PJ, Fassi E, Corsten-Janssen N, Kamsteeg EJ, Mau-Them FT, Bruel AL, Verloes A, Õunap K, Wojcik MH, Albert DV, Venkateswaran S, Ware T, Jones D, Liu YC, Mohammad SS, Bizargity P, Bacino CA, Leuzzi V, Martinelli S, Dallapiccola B, Tartaglia M, Blumkin L, Wierenga KJ, Purcarin G, O’Byrne JJ, Stockler S, Lehman A, Keren B, Nougues MC, Mignot C, Auvin S, Nava C, Hiatt SM, Bebin M, Shao Y, Scaglia F, Lalani SR, Frye RE, Jarjour IT, Jacques S, Boucher RM, Riou E, Srour M, Carmant L, Lortie A, Major P, Diadori P, Dubeau F, D’Anjou G, Bourque G, Berkovic SF, Sadleir LG, Campeau PM, Kibar Z, Lafrenière RG, Girard SL, Mercimek-Mahmutoglu S, Boelman C, Rouleau GA, Scheffer IE, Mefford HC, Andrade DM, Rossignol E, Minassian BA, Michaud JL, Michaud JL. High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. Am J Hum Genet 2017; 101:664-685. [PMID: 29100083 DOI: 10.1016/j.ajhg.2017.09.008] [Citation(s) in RCA: 294] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/11/2017] [Indexed: 12/30/2022] Open
Abstract
Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques L Michaud
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada; Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada; Department of Pediatrics, Université de Montréal, Montreal, QC H3T1C5, Canada.
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Ansar M, Riazuddin S, Sarwar MT, Makrythanasis P, Paracha SA, Iqbal Z, Khan J, Assir MZ, Hussain M, Razzaq A, Polla DL, Taj AS, Holmgren A, Batool N, Misceo D, Iwaszkiewicz J, de Brouwer APM, Guipponi M, Hanquinet S, Zoete V, Santoni FA, Frengen E, Ahmed J, Riazuddin S, van Bokhoven H, Antonarakis SE. Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay. Genet Med 2017; 20:778-784. [DOI: 10.1038/gim.2017.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/31/2017] [Indexed: 02/04/2023] Open
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Grabińska KA, Edani BH, Park EJ, Kraehling JR, Sessa WC. A conserved C-terminal R XG motif in the NgBR subunit of cis-prenyltransferase is critical for prenyltransferase activity. J Biol Chem 2017; 292:17351-17361. [PMID: 28842490 DOI: 10.1074/jbc.m117.806034] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/16/2017] [Indexed: 11/06/2022] Open
Abstract
cis-Prenyltransferases (cis-PTs) constitute a large family of enzymes conserved during evolution and present in all domains of life. In eukaryotes and archaea, cis-PT is the first enzyme committed to the synthesis of dolichyl phosphate, an obligate lipid carrier in protein glycosylation reactions. The homodimeric bacterial enzyme, undecaprenyl diphosphate synthase, generates 11 isoprene units and has been structurally and mechanistically characterized in great detail. Recently, we discovered that unlike undecaprenyl diphosphate synthase, mammalian cis-PT is a heteromer consisting of NgBR (Nus1) and hCIT (dehydrodolichol diphosphate synthase) subunits, and this composition has been confirmed in plants and fungal cis-PTs. Here, we establish the first purification system for heteromeric cis-PT and show that both NgBR and hCIT subunits function in catalysis and substrate binding. Finally, we identified a critical RXG sequence in the C-terminal tail of NgBR that is conserved and essential for enzyme activity across phyla. In summary, our findings show that eukaryotic cis-PT is composed of the NgBR and hCIT subunits. The strong conservation of the RXG motif among NgBR orthologs indicates that this subunit is critical for the synthesis of polyprenol diphosphates and cellular function.
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Affiliation(s)
- Kariona A Grabińska
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Ban H Edani
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eon Joo Park
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Jan R Kraehling
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
| | - William C Sessa
- From the Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, Connecticut 06520
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Edri I, Goldenberg M, Lisnyansky M, Strulovich R, Newman H, Loewenstein A, Khananshvili D, Giladi M, Haitin Y. Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli. J Vis Exp 2017. [PMID: 28809830 DOI: 10.3791/56430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple condensation reactions. DHDDS (dehydrodolichyl diphosphate synthase) is a eukaryotic long-chain cis-PT (forming cis double bonds from the condensation reaction) that catalyzes chain elongation of farnesyl diphosphate (FPP, an allylic diphosphate) via multiple condensations with isopentenyl diphosphate (IPP). DHDDS is of biomedical importance, as a non-conservative mutation (K42E) in the enzyme results in retinitis pigmentosa, ultimately leading to blindness. Therefore, the present protocol was developed in order to acquire large quantities of purified DHDDS, suitable for mechanistic studies. Here, the usage of protein fusion, optimized culture conditions and codon-optimization were used to allow the overexpression and purification of functionally active human DHDDS in E. coli. The described protocol is simple, cost-effective and time sparing. The homology of cis-PT among different species suggests that this protocol may be applied for other eukaryotic cis-PT as well, such as those involved in natural rubber synthesis.
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Affiliation(s)
- Ilan Edri
- Sackler Faculty of Medicine, Tel Aviv University
| | | | - Michal Lisnyansky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University
| | - Roi Strulovich
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University
| | - Hadas Newman
- Sackler Faculty of Medicine, Tel Aviv University; Department of Ophthalmology, Tel Aviv Sourasky Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University
| | - Anat Loewenstein
- Sackler Faculty of Medicine, Tel Aviv University; Department of Ophthalmology, Tel Aviv Sourasky Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University; Tel Aviv Sourasky Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University;
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University;
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46
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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47
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Vincent AL, Abeysekera N, van Bysterveldt KA, Oliver VF, Ellingford JM, Barton S, Black GC. Next-generation sequencing targeted disease panel in rod-cone retinal dystrophies in Māori and Polynesian reveals novel changes and a common founder mutation. Clin Exp Ophthalmol 2017; 45:901-910. [PMID: 28488341 DOI: 10.1111/ceo.12983] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/02/2017] [Indexed: 01/20/2023]
Abstract
IMPORTANCE This study identifies unique genetic variation observed in a cohort of Māori and Polynesian patients with rod-cone retinal dystrophies using a targeted next-generation sequencing retinal disease gene panel. BACKGROUND With over 250 retinal disease genes identified, genetic diagnosis is still only possible in 60-70% of individuals and even less within unique ethnic groups. DESIGN Prospective genetic testing in patients with rod-cone retinal dystrophies identified from the New Zealand Inherited Retinal Disease Database, PARTICIPANTS: Sixteen patients of Māori and Polynesian ancestry. METHODS Next-generation sequencing of a targeted retinal gene panel. Sanger sequencing for a novel PDE6B mutation in subsequent Māori patients. MAIN OUTCOME MEASURES Genetic diagnosis, genotype-phenotype correlation. RESULTS Thirteen unique pathogenic variants were identified in 9 of 16 (56.25%) patients in 10 different genes. A definitive genetic diagnosis was made in 7/16 patients (43.7%). Six changes were novel and not in public databases of human variation. In four patients, a homozygous, novel pathogenic variant (c.2197G > C, p.(Ala 733Pro)) in PDE6B was identified and also present in a further five similarly affected Māori patients. CONCLUSIONS AND RELEVANCE Over half of the Māori and Polynesian patients with inherited rod-cone diseases have no pathogenic variant(s) detected with a targeted retinal next-generation sequencing strategy, which is supportive of novel genetic mechanisms in this population. A novel PDE6B founder variant is likely to account for 16% of recessive inherited retinal dystrophy in Māori. Careful characterization of the clinical presentation permits identification of further Māori patients with a similar phenotype and simplifies the diagnostic algorithm.
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Affiliation(s)
- Andrea L Vincent
- Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand.,Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Nandoun Abeysekera
- Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Katherine A van Bysterveldt
- Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Verity F Oliver
- Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester, UK
| | - Graeme Cm Black
- Manchester Centre for Genomic Medicine, Institute of Human Development, University of Manchester, Manchester, UK
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48
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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: 71] [Impact Index Per Article: 10.1] [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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49
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Giladi M, Edri I, Goldenberg M, Newman H, Strulovich R, Khananshvili D, Haitin Y, Loewenstein A. Purification and characterization of human dehydrodolychil diphosphate synthase (DHDDS) overexpressed in E. coli. Protein Expr Purif 2017; 132:138-142. [PMID: 28167250 DOI: 10.1016/j.pep.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 01/09/2023]
Abstract
Protein asparagine (N)-linked glycosylation is a post-translational modification that occurs in the endoplasmic reticulum; it plays an important role in protein folding, oligomerization, quality control, sorting, and transport. Accordingly, disorders of glycosylation may affect practically every organ system. Dehydrodolichyl diphosphate synthase (DHDDS) is an eukaryotic cis prenyltransferase (cis-PT) that catalyzes chain elongation of farnesyl diphosphate via multiple condensations with isopentenyl diphosphate to form dehydrodolichyl diphosphate, a precursor for the glycosyl carrier dolichylpyrophophate involved in N-linked glycosylation. Mutations in DHDDS were shown to result in retinitis pigmentosa, ultimately leading to blindness, but the exact molecular mechanism by which the mutations affect DHDDS function remains elusive. In addition, bacterial cis-PT homologs are involved in bacterial wall synthesis and are therefore potential targets for new antibacterial agents. However, as eukaryotic cis-PT were not thoroughly characterized structurally and functionally, rational design of prokaryotic cis-PT specific drugs is currently impossible. Here, we present a simple protocol for purification of functionally active human DHDDS under non-denaturating conditions using a codon-optimized construct. The purified protein forms a stable homodimer, similar to its bacterial homologs, and shows time- and substrate-dependent activity. Purification of this protein requires the presence of a detergent for protein solubility. The protocol described here may be utilized for the overexpression of other eukaryotic cis-PT. Future structural and functional studies of the recombinant DHDDS may shed light on the mechanisms underlying DHDDS-related retinitis pigmentosa and lead to novel therapeutic approaches.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Ilan Edri
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Hadas Newman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Roi Strulovich
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Khananshvili
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Anat Loewenstein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Ophthalmology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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50
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Biswas P, Duncan JL, Maranhao B, Kozak I, Branham K, Gabriel L, Lin JH, Barteselli G, Navani M, Suk J, Parke M, Schlechter C, Weleber RG, Heckenlively JR, Dagnelie G, Lee P, Riazuddin SA, Ayyagari R. Genetic analysis of 10 pedigrees with inherited retinal degeneration by exome sequencing and phenotype-genotype association. Physiol Genomics 2017; 49:216-229. [PMID: 28130426 PMCID: PMC5407181 DOI: 10.1152/physiolgenomics.00096.2016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 12/31/2022] Open
Abstract
Our purpose was to identify causative mutations and characterize the phenotype associated with the genotype in 10 unrelated families with autosomal recessive retinal degeneration. Ophthalmic evaluation and DNA isolation were carried out in 10 pedigrees with inherited retinal degenerations (IRD). Exomes of probands from eight pedigrees were captured using Nimblegen V2/V3 or Agilent V5+UTR kits, and sequencing was performed on Illumina HiSeq. The DHDDS gene was screened for mutations in the remaining two pedigrees with Ashkenazi Jewish ancestry. Exome variants were filtered to detect candidate causal variants using exomeSuite software. Segregation and ethnicity-matched control sample analysis were performed by dideoxy sequencing. Retinal histology of a patient with DHDDS mutation was studied by microscopy. Genetic analysis identified six known mutations in ABCA4 (p.Gly1961Glu, p.Ala1773Val, c.5461-10T>C), RPE65 (p.Tyr249Cys, p.Gly484Asp), PDE6B (p.Lys706Ter) and DHDDS (p.Lys42Glu) and ten novel potentially pathogenic variants in CERKL (p.Met323Val fsX20), RPE65 (p.Phe252Ser, Thr454Leu fsX31), ARL6 (p.Arg121His), USH2A (p.Gly3142Ter, p.Cys3294Trp), PDE6B (p.Gln652Ter), and DHDDS (p.Thr206Ala) genes. Among these, variants/mutations in two separate genes were observed to segregate with IRD in two pedigrees. Retinal histopathology of a patient with a DHDDS mutation showed severe degeneration of retinal layers with relative preservation of the retinal pigment epithelium. Analysis of exome variants in ten pedigrees revealed nine novel potential disease-causing variants and nine previously reported homozygous or compound heterozygous mutations in the CERKL, ABCA4, RPE65, ARL6, USH2A, PDE6B, and DHDDS genes. Mutations that could be sufficient to cause pathology were observed in more than one gene in one pedigree.
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Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Jacque L Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California
| | - Bruno Maranhao
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Igor Kozak
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Jonathan H Lin
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Giulio Barteselli
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Mili Navani
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - Michelle Parke
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | | | - Richard G Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon; and
| | - John R Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan
| | - Gislin Dagnelie
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Pauline Lee
- Shiley Eye Institute, University of California San Diego, La Jolla, California
| | - S Amer Riazuddin
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California;
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