1
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Waskow ER, Emrick LT, Rosenfeld JA, Ketkar S, Burrage LC, Scott DA. Recessive loss-of-function variants in DPH1 identified as the molecular cause in a sibling pair previously diagnosed with Fine-Lubinsky syndrome. Am J Med Genet A 2024:e63845. [PMID: 39166428 DOI: 10.1002/ajmg.a.63845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/04/2024] [Accepted: 07/31/2024] [Indexed: 08/22/2024]
Abstract
Fine-Lubinsky syndrome is a rare clinically defined syndrome sometimes referred to as brachycephaly, deafness, cataract, microstomia, and impaired intellectual development syndrome. Here we provide a clinical and molecular update for a sibling pair diagnosed with Fine-Lubinsky syndrome. An extensive genetic work-up, including chromosomal microarray analysis and quad exome sequencing, was nondiagnostic. However, a research reanalysis of their exome sequencing data revealed that both were homozygous for an intronic c.749+39G>A [NM_001383.6] variant in DPH1. RNAseq analysis performed on RNA from fibroblasts revealed significantly reduced expression of DPH1 transcripts suggestive of abnormal splicing followed by nonsense mediated mRNA decay. Since the phenotypes of this sibling pair were consistent with those associated with the inheritance of biallelic pathogenic variants in DPH1, they were given a diagnosis of developmental delay with short stature, dysmorphic facial features, and sparse hair 1 (DEDSSH1). This leads us to recommend that all individuals with a clinical diagnosis of Fine-Lubinsky syndrome be screened for variants in DPH1. The clinical histories of this sibling pair emphasize that hearing loss associated with DEDSSH1 may remit over time and that individuals with DEDSSH1 should be monitored for the development of cardiomyopathy. This case also demonstrates the clinical utility of RNAseq as a means of functionally validating the effects of intronic variants that may affect splicing.
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Affiliation(s)
- Emily R Waskow
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Lisa T Emrick
- Texas Children's Hospital, Houston, Texas, USA
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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2
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Ütkür K, Mayer K, Liu S, Brinkmann U, Schaffrath R. Functional Integrity of Radical SAM Enzyme Dph1•Dph2 Requires Non-Canonical Cofactor Motifs with Tandem Cysteines. Biomolecules 2024; 14:470. [PMID: 38672486 PMCID: PMC11048331 DOI: 10.3390/biom14040470] [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: 03/24/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The Dph1•Dph2 heterodimer from yeast is a radical SAM (RS) enzyme that generates the 3-amino-3-carboxy-propyl (ACP) precursor for diphthamide, a clinically relevant modification on eukaryotic elongation factor 2 (eEF2). ACP formation requires SAM cleavage and atypical Cys-bound Fe-S clusters in each Dph1 and Dph2 subunit. Intriguingly, the first Cys residue in each motif is found next to another ill-defined cysteine that we show is conserved across eukaryotes. As judged from structural modeling, the orientation of these tandem cysteine motifs (TCMs) suggests a candidate Fe-S cluster ligand role. Hence, we generated, by site-directed DPH1 and DPH2 mutagenesis, Dph1•Dph2 variants with cysteines from each TCM replaced individually or in combination by serines. Assays diagnostic for diphthamide formation in vivo reveal that while single substitutions in the TCM of Dph2 cause mild defects, double mutations almost entirely inactivate the RS enzyme. Based on enhanced Dph1 and Dph2 subunit instability in response to cycloheximide chases, the variants with Cys substitutions in their cofactor motifs are particularly prone to protein degradation. In sum, we identify a fourth functionally cooperative Cys residue within the Fe-S motif of Dph2 and show that the Cys-based cofactor binding motifs in Dph1 and Dph2 are critical for the structural integrity of the dimeric RS enzyme in vivo.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Shihui Liu
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany;
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3
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Schaffrath R, Brinkmann U. Diphthamide - a conserved modification of eEF2 with clinical relevance. Trends Mol Med 2024; 30:164-177. [PMID: 38097404 DOI: 10.1016/j.molmed.2023.11.008] [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: 09/28/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 02/17/2024]
Abstract
Diphthamide, a complex modification on eukaryotic translation elongation factor 2 (eEF2), assures reading-frame fidelity during translation. Diphthamide and enzymes for its synthesis are conserved in eukaryotes and archaea. Originally identified as target for diphtheria toxin (DT) in humans, its clinical relevance now proves to be broader than the link to pathogenic bacteria. Diphthamide synthesis enzymes (DPH1 and DPH3) are associated with cancer, and DPH gene mutations can cause diphthamide deficiency syndrome (DDS). Finally, new analyses provide evidence that diphthamide may restrict propagation of viruses including SARS-CoV-2 and HIV-1, and that DPH enzymes are targeted by viruses for degradation to overcome this restriction. This review describes how diphthamide is synthesized and functions in translation, and covers its clinical relevance in human development, cancer, and infectious diseases.
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Affiliation(s)
- Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany.
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4
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Pinilla M, Mazars R, Vergé R, Gorse L, Paradis M, Suire B, Santoni K, Robinson KS, Toh GA, Prouvensier L, Leon-Icaza SA, Hessel A, Péricat D, Murris M, Guet-Revillet H, Henras A, Buyck J, Ravet E, Zhong FL, Cougoule C, Planès R, Meunier E. EEF2-inactivating toxins engage the NLRP1 inflammasome and promote epithelial barrier disruption. J Exp Med 2023; 220:e20230104. [PMID: 37642996 PMCID: PMC10465324 DOI: 10.1084/jem.20230104] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/31/2023] Open
Abstract
Human airway and corneal epithelial cells, which are critically altered during chronic infections mediated by Pseudomonas aeruginosa, specifically express the inflammasome sensor NLRP1. Here, together with a companion study, we report that the NLRP1 inflammasome detects exotoxin A (EXOA), a ribotoxin released by P. aeruginosa type 2 secretion system (T2SS), during chronic infection. Mechanistically, EXOA-driven eukaryotic elongation factor 2 (EEF2) ribosylation and covalent inactivation promote ribotoxic stress and subsequent NLRP1 inflammasome activation, a process shared with other EEF2-inactivating toxins, diphtheria toxin and cholix toxin. Biochemically, irreversible EEF2 inactivation triggers ribosome stress-associated kinases ZAKα- and P38-dependent NLRP1 phosphorylation and subsequent proteasome-driven functional degradation. Finally, cystic fibrosis cells from patients exhibit exacerbated P38 activity and hypersensitivity to EXOA-induced ribotoxic stress-dependent NLRP1 inflammasome activation, a process inhibited by the use of ZAKα inhibitors. Altogether, our results show the importance of P. aeruginosa virulence factor EXOA at promoting NLRP1-dependent epithelial damage and identify ZAKα as a critical sensor of virulence-inactivated EEF2.
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Affiliation(s)
- Miriam Pinilla
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Raoul Mazars
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Romain Vergé
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Leana Gorse
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Margaux Paradis
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Bastien Suire
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Karin Santoni
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Kim Samirah Robinson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Gee Ann Toh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Laure Prouvensier
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Audrey Hessel
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - David Péricat
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Marlène Murris
- Department of Pneumology, Hospital Larrey, Toulouse, France
- University Hospital of Toulouse, Toulouse, France
| | | | - Anthony Henras
- Center of Integrative Biology, University of Toulouse, CNRS, Toulouse, France
| | - Julien Buyck
- UFR Medicine and Pharmacy, INSERM U1070, University of Poitiers, Poitiers, France
| | | | - Franklin L. Zhong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Skin Research Institute of Singapore, Singapore, Singapore
| | - Céline Cougoule
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Rémi Planès
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
- Invivogen, Toulouse, France
| | - Etienne Meunier
- Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
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5
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Ütkür K, Mayer K, Khan M, Manivannan T, Schaffrath R, Brinkmann U. DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models. Dis Model Mech 2023; 16:dmm050207. [PMID: 37675463 PMCID: PMC10538292 DOI: 10.1242/dmm.050207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023] Open
Abstract
The autosomal-recessive diphthamide deficiency syndrome presents as intellectual disability with developmental abnormalities, seizures, craniofacial and additional morphological phenotypes. It is caused by reduced activity of proteins that synthesize diphthamide on human translation elongation factor 2. Diphthamide synthesis requires seven proteins (DPH1-DPH7), with clinical deficiency described for DPH1, DPH2 and DPH5. A limited set of variant alleles from syndromic patients has been functionally analyzed, but databases (gnomAD) list additional so far uncharacterized variants in human DPH1 and DPH2. Because DPH enzymes are conserved among eukaryotes, their functionality can be assessed in yeast and mammalian cells. Our experimental assessment of known and uncharacterized DPH1 and DPH2 missense alleles showed that six variants are tolerated despite inter-species conservation. Ten additional human DPH1 (G113R, A114T, H132P, H132R, S136R, C137F, L138P, Y152C, S221P, H240R) and two DPH2 (H105P, C341Y) variants showed reduced functionality and hence are deficiency-susceptibility alleles. Some variants locate close to the active enzyme center and may affect catalysis, while others may impact on enzyme activation. In sum, our study has identified functionally compromised alleles of DPH1 and DPH2 genes that likely cause diphthamide deficiency syndrome.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maliha Khan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Thirishika Manivannan
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie,Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
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6
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Baik AH, Haribowo AG, Chen X, Queliconi BB, Barrios AM, Garg A, Maishan M, Campos AR, Matthay MA, Jain IH. Oxygen toxicity causes cyclic damage by destabilizing specific Fe-S cluster-containing protein complexes. Mol Cell 2023; 83:942-960.e9. [PMID: 36893757 PMCID: PMC10148707 DOI: 10.1016/j.molcel.2023.02.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 01/12/2023] [Accepted: 02/14/2023] [Indexed: 03/11/2023]
Abstract
Oxygen is toxic across all three domains of life. Yet, the underlying molecular mechanisms remain largely unknown. Here, we systematically investigate the major cellular pathways affected by excess molecular oxygen. We find that hyperoxia destabilizes a specific subset of Fe-S cluster (ISC)-containing proteins, resulting in impaired diphthamide synthesis, purine metabolism, nucleotide excision repair, and electron transport chain (ETC) function. Our findings translate to primary human lung cells and a mouse model of pulmonary oxygen toxicity. We demonstrate that the ETC is the most vulnerable to damage, resulting in decreased mitochondrial oxygen consumption. This leads to further tissue hyperoxia and cyclic damage of the additional ISC-containing pathways. In support of this model, primary ETC dysfunction in the Ndufs4 KO mouse model causes lung tissue hyperoxia and dramatically increases sensitivity to hyperoxia-mediated ISC damage. This work has important implications for hyperoxia pathologies, including bronchopulmonary dysplasia, ischemia-reperfusion injury, aging, and mitochondrial disorders.
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Affiliation(s)
- Alan H Baik
- Department of Medicine, Division of Cardiology, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Augustinus G Haribowo
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Xuewen Chen
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bruno B Queliconi
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alec M Barrios
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ankur Garg
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mazharul Maishan
- Cardiovascular Research Institute, UCSF, San Francisco, CA 94143, USA
| | - Alexandre R Campos
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Michael A Matthay
- Cardiovascular Research Institute, UCSF, San Francisco, CA 94143, USA; Departments of Medicine and Anesthesia, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isha H Jain
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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7
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Bielopolski N, Heyman E, Bassan H, BenZeev B, Tzadok M, Ginsberg M, Blumkin L, Michaeli Y, Sokol R, Yosha-Orpaz N, Hady-Cohen R, Banne E, Lev D, Lerman-Sagie T, Wald-Altman S, Nissenkorn A. "Virtual patch clamp analysis" for predicting the functional significance of pathogenic variants in sodium channels. Epilepsy Res 2022; 186:107002. [PMID: 36027690 DOI: 10.1016/j.eplepsyres.2022.107002] [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: 05/31/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVE Opening of voltage-gated sodium channels is crucial for neuronal depolarization. Proper channel opening and influx of Na+ through the ion pore, is dependent upon binding of Na+ ion to a specific amino-acid motif (DEKA) within the pore. In this study we used molecular dynamic simulations, an advanced bioinformatic tool, to research the dysfunction caused by pathogenic variants in SCN1a, SCN2a and SCN8a genes. METHOD Molecular dynamic simulations were performed in six patients: three patients with Dravet syndrome (p.Gly177Ala,p.Ser259Arg and p.Met1267Ile, SCN1a), two patients with early onset drug resistant epilepsy(p.Ala263Val, SCN2a and p.Ile251Arg, SCN8a), and a patient with autism (p.Thr155Ala, SCN2a). After predicting the 3D-structure of mutated proteins by homology modeling, time dependent molecular dynamic simulations were performed, using the Schrödinger algorithm. The opening of the sodium channel, including the detachment of the sodium ion to the DEKA motif and pore diameter were assessed. Results were compared to the existent patch clamp analysis in four patients, and consistency with clinical phenotype was noted. RESULTS The Na+ ion remained attached to DEKA filter longer when compared to wild type in the p.Gly177Ala, p.Ser259Arg,SCN1a, and p.Thr155Ala, SCN2a variants, consistent with loss-of-function. In contrast, it detached quicker from DEKA than wild type in the p.Ala263Val,SCN2a variant, consistent with gain-of-function. In the p.Met1267Ile,SCN1a variant, detachment from DEKA was quicker, but pore diameter decreased, suggesting partial loss-of-function. In the p.Leu251Arg,SCN8a variant, the pore remained opened longer when compared to wild type, consistent with a gain-of-function. The molecular dynamic simulation results were consistent with the existing patch-clamp analysis studies, as well as the clinical phenotype. SIGNIFICANCE Molecular dynamic simulation can be useful in predicting pathogenicity of variants and the disease phenotype, and selecting targeted treatment based on channel dysfunction. Further development of these bioinformatic tools may lead to "virtual patch-clamp analysis".
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Affiliation(s)
| | - E Heyman
- Pediatric Epilepsy Department, Shamir Medical Center, Asaf Ha Rofeh, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - H Bassan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Neurology Unit, Shamir Medical Center, Asaf HaRofeh, Israel.
| | - B BenZeev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center, Tel HaShomer, Israel.
| | - M Tzadok
- Pediatric Neurology Unit, Safra Children's Hospital, Sheba Medical Center, Tel HaShomer, Israel.
| | - M Ginsberg
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - L Blumkin
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - Y Michaeli
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - R Sokol
- Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - N Yosha-Orpaz
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | - R Hady-Cohen
- Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel.
| | - E Banne
- Pediatric Epilepsy Department, Shamir Medical Center, Asaf Ha Rofeh, Israel; Genetics Institute, Edith Wolfson Medical Center, Holon, Israel
| | - D Lev
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Genetics Institute, Edith Wolfson Medical Center, Holon, Israel.
| | - T Lerman-Sagie
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
| | | | - A Nissenkorn
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Rare Diseases Institute-Magen, Edith Wolfson Medical Center, Holon, Israel; Pediatric Neurology Unit, Edith Wolfson Medical Center, Holon, Israel.
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8
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Zhang H, Quintana J, Ütkür K, Adrian L, Hawer H, Mayer K, Gong X, Castanedo L, Schulten A, Janina N, Peters M, Wirtz M, Brinkmann U, Schaffrath R, Krämer U. Translational fidelity and growth of Arabidopsis require stress-sensitive diphthamide biosynthesis. Nat Commun 2022; 13:4009. [PMID: 35817801 PMCID: PMC9273596 DOI: 10.1038/s41467-022-31712-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/30/2022] [Indexed: 11/09/2022] Open
Abstract
Diphthamide, a post-translationally modified histidine residue of eukaryotic TRANSLATION ELONGATION FACTOR2 (eEF2), is the human host cell-sensitizing target of diphtheria toxin. Diphthamide biosynthesis depends on the 4Fe-4S-cluster protein Dph1 catalyzing the first committed step, as well as Dph2 to Dph7, in yeast and mammals. Here we show that diphthamide modification of eEF2 is conserved in Arabidopsis thaliana and requires AtDPH1. Ribosomal -1 frameshifting-error rates are increased in Arabidopsis dph1 mutants, similar to yeast and mice. Compared to the wild type, shorter roots and smaller rosettes of dph1 mutants result from fewer formed cells. TARGET OF RAPAMYCIN (TOR) kinase activity is attenuated, and autophagy is activated, in dph1 mutants. Under abiotic stress diphthamide-unmodified eEF2 accumulates in wild-type seedlings, most strongly upon heavy metal excess, which is conserved in human cells. In summary, our results suggest that diphthamide contributes to the functionality of the translational machinery monitored by plants to regulate growth.
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Affiliation(s)
- Hongliang Zhang
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Julia Quintana
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Koray Ütkür
- Microbiology, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Lorenz Adrian
- Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, 04318, Leipzig, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, 13355, Berlin, Germany
| | - Harmen Hawer
- Microbiology, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Xiaodi Gong
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
| | - Leonardo Castanedo
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Anna Schulten
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Nadežda Janina
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany
| | - Marcus Peters
- Molecular Immunology, Medical Faculty, Ruhr University Bochum, 44801, Bochum, Germany
| | - Markus Wirtz
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
| | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377, Penzberg, Germany
| | - Raffael Schaffrath
- Microbiology, Institute for Biology, University of Kassel, 34132, Kassel, Germany
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, Box 44 ND3/30, 44801, Bochum, Germany.
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9
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Tu WL, Chih YC, Shih YT, Yu YR, You LR, Chen CM. Context-specific roles of diphthamide deficiency in hepatocellular carcinogenesis. J Pathol 2022; 258:149-163. [PMID: 35781884 DOI: 10.1002/path.5986] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 11/07/2022]
Abstract
Diphthamide biosynthesis protein 1 (DPH1) is biochemically involved in the first step of diphthamide biosynthesis, a post-translational modification of eukaryotic elongation factor 2 (EEF2). Earlier studies showed that DPH1, also known as ovarian cancer-associated gene 1 (OVCA1), is involved in ovarian carcinogenesis. However, the role of DPH1 in hepatocellular carcinoma (HCC) remains unclear. To investigate the impact of DPH1 in hepatocellular carcinogenesis, we have performed data mining from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset. We found that reduced DPH1 levels were associated with advanced stages and poor survival of patients with HCC. Also, we generated hepatocyte-specific Dph1 deficient mice and showed that diphthamide deficient EEF2 resulted in a reduced translation elongation rate in the hepatocytes and let to mild liver damage with fatty accumulation. After N-diethylnitrosamine (DEN) -induced acute liver injury, p53-mediated pericentral hepatocyte death was increased, and compensatory proliferation was reduced in Dph1-deficient mice. Consistent with these effects, Dph1 deficiency decreased the incidence of DEN-induced pericentral-derived HCC and revealed a protective effect against p53 loss. In contrast, Dph1 deficiency combined with Trp53- or Trp53/Pten-deficient hepatocytes led to increased tumor loads associated with KRT19 (K19)-positive periportal-like cell expansion in mice. Further gene set enrichment analysis also revealed that HCC patients with lower levels of DPH1 and TP53 expression had enriched gene-sets related to the cell cycle and K19-upregulated HCC. Additionally, liver tumor organoids obtained from 6-month-old Pten/Trp53/Dph1-triple-mutant mice had a higher frequency of organoid re-initiation cells and higher proliferative index compared with those of the Pten/Trp53-double-mutant. Pten/Trp53/Dph1-triple-mutant liver tumor organoids showed expression of genes associated with stem/progenitor phenotypes, including Krt19 and Prominin-1 (Cd133) progenitor markers, combined with low hepatocyte-expressed fibrinogen genes. These findings indicate that diphthamide deficiency differentially regulates hepatocellular carcinogenesis, which inhibits pericentral hepatocytes-derived tumor and promotes periportal progenitors-associated liver tumors. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wei-Ling Tu
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Yu-Chan Chih
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Ya-Tung Shih
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Yi-Ru Yu
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan
| | - Li-Ru You
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chun-Ming Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming, Chiao Tung University, Taipei, Taiwan.,Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
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10
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Malone TJ, Kaczmarek LK. The role of altered translation in intellectual disability and epilepsy. Prog Neurobiol 2022; 213:102267. [PMID: 35364140 PMCID: PMC10583652 DOI: 10.1016/j.pneurobio.2022.102267] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Abstract
A very high proportion of cases of intellectual disability are genetic in origin and are associated with the occurrence of epileptic seizures during childhood. These two disorders together effect more than 5% of the world's population. One feature linking the two diseases is that learning and memory require the synthesis of new synaptic components and ion channels, while maintenance of overall excitability also requires synthesis of similar proteins in response to altered neuronal stimulation. Many of these disorders result from mutations in proteins that regulate mRNA processing, translation initiation, translation elongation, mRNA stability or upstream translation modulators. One theme that emerges on reviewing this field is that mutations in proteins that regulate changes in translation following neuronal stimulation are more likely to result in epilepsy with intellectual disability than general translation regulators with no known role in activity-dependent changes. This is consistent with the notion that activity-dependent translation in neurons differs from that in other cells types in that the changes in local cellular composition, morphology and connectivity that occur generally in response to stimuli are directly coupled to local synaptic activity and persist for months or years after the original stimulus.
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Affiliation(s)
- Taylor J Malone
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA
| | - Leonard K Kaczmarek
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA.
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11
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Shankar SP, Grimsrud K, Lanoue L, Egense A, Willis B, Hörberg J, AlAbdi L, Mayer K, Ütkür K, Monaghan KG, Krier J, Stoler J, Alnemer M, Shankar PR, Schaffrath R, Alkuraya FS, Brinkmann U, Eriksson LA, Lloyd K, Rauen KA. A novel DPH5-related diphthamide-deficiency syndrome causing embryonic lethality or profound neurodevelopmental disorder. Genet Med 2022; 24:1567-1582. [PMID: 35482014 DOI: 10.1016/j.gim.2022.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Diphthamide is a post-translationally modified histidine essential for messenger RNA translation and ribosomal protein synthesis. We present evidence for DPH5 as a novel cause of embryonic lethality and profound neurodevelopmental delays (NDDs). METHODS Molecular testing was performed using exome or genome sequencing. A targeted Dph5 knockin mouse (C57BL/6Ncrl-Dph5em1Mbp/Mmucd) was created for a DPH5 p.His260Arg homozygous variant identified in 1 family. Adenosine diphosphate-ribosylation assays in DPH5-knockout human and yeast cells and in silico modeling were performed for the identified DPH5 potential pathogenic variants. RESULTS DPH5 variants p.His260Arg (homozygous), p.Asn110Ser and p.Arg207Ter (heterozygous), and p.Asn174LysfsTer10 (homozygous) were identified in 3 unrelated families with distinct overlapping craniofacial features, profound NDDs, multisystem abnormalities, and miscarriages. Dph5 p.His260Arg homozygous knockin was embryonically lethal with only 1 subviable mouse exhibiting impaired growth, craniofacial dysmorphology, and multisystem dysfunction recapitulating the human phenotype. Adenosine diphosphate-ribosylation assays showed absent to decreased function in DPH5-knockout human and yeast cells. In silico modeling of the variants showed altered DPH5 structure and disruption of its interaction with eEF2. CONCLUSION We provide strong clinical, biochemical, and functional evidence for DPH5 as a novel cause of embryonic lethality or profound NDDs with multisystem involvement and expand diphthamide-deficiency syndromes and ribosomopathies.
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Affiliation(s)
- Suma P Shankar
- Division of Genomic Medicine, UC Davis Health MIND Institute, Department of Pediatrics, UC Davis Health, University of California, Davis, Sacramento, CA; Department of Ophthalmology and Vision Science, UC Davis Health, University of California, Davis, Sacramento, CA.
| | - Kristin Grimsrud
- Department of Pathology and Laboratory Medicine, UC Davis Health, University of California, Davis, Sacramento, CA; UC Davis Mouse Biology Program, University of California, Davis, Davis, CA
| | - Louise Lanoue
- UC Davis Mouse Biology Program, University of California, Davis, Davis, CA
| | - Alena Egense
- Division of Genomic Medicine, UC Davis Health MIND Institute, Department of Pediatrics, UC Davis Health, University of California, Davis, Sacramento, CA
| | - Brandon Willis
- UC Davis Mouse Biology Program, University of California, Davis, Davis, CA
| | - Johanna Hörberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia; Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich (RICM), Penzberg, Germany
| | - Koray Ütkür
- Division of Microbiology, Institute of Biology, University of Kassel, Kassel, Germany
| | | | - Joel Krier
- Division of Genetics, Brigham and Women's Hospital, Boston, MA; Undiagnosed Diseases Network
| | - Joan Stoler
- Undiagnosed Diseases Network; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Maha Alnemer
- Department of Obstetrics & Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Prabhu R Shankar
- Division of Health Informatics, Department of Public Health Sciences, School of Medicine, University of California, Davis, Sacramento, CA
| | - Raffael Schaffrath
- Division of Microbiology, Institute of Biology, University of Kassel, Kassel, Germany
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich (RICM), Penzberg, Germany
| | - Leif A Eriksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Kent Lloyd
- UC Davis Mouse Biology Program, University of California, Davis, Davis, CA; Department of Surgery, UC Davis Health, University of California, Davis, Sacramento, CA
| | - Katherine A Rauen
- Division of Genomic Medicine, UC Davis Health MIND Institute, Department of Pediatrics, UC Davis Health, University of California, Davis, Sacramento, CA
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- Undiagnosed Diseases Network
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12
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Cheng SSW, Luk HM, Lo IFM. An adult Chinese patient with developmental delay with short stature, dysmorphic features, and sparse hair (Loucks-Innes syndrome). Am J Med Genet A 2021; 185:1925-1931. [PMID: 33704902 DOI: 10.1002/ajmg.a.62164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/07/2021] [Accepted: 02/24/2021] [Indexed: 11/09/2022]
Abstract
Variants of the diphthamide biosynthesis I (DPH1, OMIM*603527) are associated with developmental delay, short stature, and sparse hair syndrome (DEDSSH/DPH1 syndrome) (OMIM# 616901). Another name is Loucks-Innes syndrome. DPH1 syndrome is an ultrarare and severe neurodevelopmental disorder. Less than 20 patients were reported from different ethnicities. Here, we described the first Chinese adult with genetically confirmed DPH1 syndrome. We summarized previously reported patients in the literature and found that developmental delay, unusual skull shape, sparse hair, and facial dysmorphism were consistently present in all DPH1 syndrome patients. Dysplastic toenails and dental abnormalities are age-dependent characteristics of DPH1 syndrome. Our patient was the first reported patient with documented growth hormone deficiency. Dental and endocrine checkup should be considered in the routine follow-up of DPH1 syndrome patients.
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Affiliation(s)
- Shirley S W Cheng
- Department of Health, HKSAR, Clinical Genetic Service, Hong Kong, Hong Kong
| | - Ho-Ming Luk
- Department of Health, HKSAR, Clinical Genetic Service, Hong Kong, Hong Kong
| | - Ivan F M Lo
- Department of Health, HKSAR, Clinical Genetic Service, Hong Kong, Hong Kong
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13
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Kyryachenko S, Georges A, Yu M, Barrandou T, Guo L, Bruneval P, Rubio T, Gronwald J, Baraki H, Kutschka I, Aras KK, Efimov IR, Norris RA, Voigt N, Bouatia-Naji N. Chromatin Accessibility of Human Mitral Valves and Functional Assessment of MVP Risk Loci. Circ Res 2021; 128:e84-e101. [PMID: 33508947 PMCID: PMC8316483 DOI: 10.1161/circresaha.120.317581] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
RATIONALE Mitral valve prolapse (MVP) is a common valvopathy that leads to mitral insufficiency, heart failure, and sudden death. Functional genomic studies in mitral valves are needed to better characterize MVP-associated variants and target genes. OBJECTIVE To establish the chromatin accessibility profiles and assess functionality of variants and narrow down target genes at MVP loci. METHODS AND RESULTS We mapped the open chromatin regions in nuclei from 11 human pathogenic and 7 nonpathogenic mitral valves by an assay for transposase-accessible chromatin with high-throughput sequencing. Open chromatin peaks were globally similar between pathogenic and nonpathogenic valves. Compared with the heart tissue and cardiac fibroblasts, we found that MV-specific assay for transposase-accessible chromatin with high-throughput sequencing peaks are enriched near genes involved in extracellular matrix organization, chondrocyte differentiation, and connective tissue development. One of the most enriched motifs in MV-specific open chromatin peaks was for the nuclear factor of activated T cells family of TFs (transcription factors) involved in valve endocardial and interstitial cell formation. We also found that MVP-associated variants were significantly enriched (P<0.05) in mitral valve open chromatin peaks. Integration of the assay for transposase-accessible chromatin with high-throughput sequencing data with risk loci, extensive functional annotation, and gene reporter assay suggest plausible causal variants for rs2641440 at the SMG6/SRR locus and rs6723013 at the IGFBP2/IGFBP5/TNS1 locus. CRISPR-Cas9 deletion of the sequence including rs6723013 in human fibroblasts correlated with increased expression only for TNS1. Circular chromatin conformation capture followed by high-throughput sequencing experiments provided evidence for several target genes, including SRR, HIC1, and DPH1 at the SMG6/SRR locus and further supported TNS1 as the most likely target gene on chromosome 2. CONCLUSIONS Here, we describe unprecedented genome-wide open chromatin profiles from human pathogenic and nonpathogenic MVs and report specific gene regulation profiles, compared with the heart. We also report in vitro functional evidence for potential causal variants and target genes at MVP risk loci involving established and new biological mechanisms. Graphic Abstract: A graphic abstract is available for this article.
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Affiliation(s)
| | | | - Mengyao Yu
- Université de Paris, PARCC, Inserm, Paris,
France
| | | | - Lilong Guo
- Department of Regenerative Medicine and Cell Biology,
Medical University of South Carolina, Charleston, SC, USA
- Department of Medicine, Medical University of South
Carolina, Charleston, SC, USA
| | | | - Tony Rubio
- Institute of Pharmacology and Toxicology, University
Medical Center Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
| | - Judith Gronwald
- Institute of Pharmacology and Toxicology, University
Medical Center Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
| | - Hassina Baraki
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
- Department of Thoracic and Cardiovascular Surgery,
University Medical Center, Göttingen, Germany
| | - Ingo Kutschka
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
- Department of Thoracic and Cardiovascular Surgery,
University Medical Center, Göttingen, Germany
| | - Kedar K. Aras
- Department of Biomedical Engineering, George Washington
University, Washington, DC, USA
| | - Igor R. Efimov
- Department of Biomedical Engineering, George Washington
University, Washington, DC, USA
| | - Russel A. Norris
- Department of Regenerative Medicine and Cell Biology,
Medical University of South Carolina, Charleston, SC, USA
- Department of Medicine, Medical University of South
Carolina, Charleston, SC, USA
| | - Niels Voigt
- Institute of Pharmacology and Toxicology, University
Medical Center Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner
Site Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from
Molecular Machines to Networks of Excitable Cells (MBExC), University of
Göttingen, Germany
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14
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Nabais Sá MJ, Olson AN, Yoon G, Nimmo GAM, Gomez CM, Willemsen MA, Millan F, Schneider A, Pfundt R, de Brouwer APM, Dinman JD, de Vries BBA. De Novo variants in EEF2 cause a neurodevelopmental disorder with benign external hydrocephalus. Hum Mol Genet 2020; 29:3892-3899. [PMID: 33355653 DOI: 10.1093/hmg/ddaa270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 11/15/2022] Open
Abstract
Eukaryotic translation elongation factor 2 (eEF2) is a key regulatory factor in gene expression that catalyzes the elongation stage of translation. A functionally impaired eEF2, due to a heterozygous missense variant in the EEF2 gene, was previously reported in one family with spinocerebellar ataxia-26 (SCA26), an autosomal dominant adult-onset pure cerebellar ataxia. Clinical exome sequencing identified de novo EEF2 variants in three unrelated children presenting with a neurodevelopmental disorder (NDD). Individuals shared a mild phenotype comprising motor delay and relative macrocephaly associated with ventriculomegaly. Populational data and bioinformatic analysis underscored the pathogenicity of all de novo missense variants. The eEF2 yeast model strains demonstrated that patient-derived variants affect cellular growth, sensitivity to translation inhibitors and translational fidelity. Consequently, we propose that pathogenic variants in the EEF2 gene, so far exclusively associated with late-onset SCA26, can cause a broader spectrum of neurologic disorders, including childhood-onset NDDs and benign external hydrocephalus.
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Affiliation(s)
- Maria J Nabais Sá
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands.,Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar/Universidade do Porto, 4050-313 Porto, Portugal
| | - Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Grace Yoon
- Division of Clinical and Metabolic Genetics and Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Graeme A M Nimmo
- Fred A Litwin Family Centre for Genetic Medicine, University Health Network/Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | | | - Michèl A Willemsen
- Department of Pediatric Neurology, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Amalia Children's Hospital, 6525 GA Nijmegen, The Netherlands
| | | | - Alexandra Schneider
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, 6525 GA Nijmegen, The Netherlands
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15
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Hawer H, Mendelsohn BA, Mayer K, Kung A, Malhotra A, Tuupanen S, Schleit J, Brinkmann U, Schaffrath R. Diphthamide-deficiency syndrome: a novel human developmental disorder and ribosomopathy. Eur J Hum Genet 2020; 28:1497-1508. [PMID: 32576952 PMCID: PMC7575589 DOI: 10.1038/s41431-020-0668-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/06/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
We describe a novel type of ribosomopathy that is defined by deficiency in diphthamidylation of translation elongation factor 2. The ribosomopathy was identified by correlating phenotypes and biochemical properties of previously described patients with diphthamide biosynthesis gene 1 (DPH1) deficiencies with a new patient that carried inactivating mutations in both alleles of the human diphthamide biosynthesis gene 2 (DPH2). The human DPH1 syndrome is an autosomal recessive disorder associated with developmental delay, abnormal head circumference (microcephaly or macrocephaly), short stature, and congenital heart disease. It is defined by variants with reduced functionality of the DPH1 gene observed so far predominantly in consanguineous homozygous patients carrying identical mutant alleles of DPH1. Here we report a child with a very similar phenotype carrying biallelic variants of the human DPH2. The gene products DPH1 and DPH2 are components of a heterodimeric enzyme complex that mediates the first step of the posttranslational diphthamide modification on the nonredundant eukaryotic translation elongation factor 2 (eEF2). Diphthamide deficiency was shown to reduce the accuracy of ribosomal protein biosynthesis. Both DPH2 variants described here severely impair diphthamide biosynthesis as demonstrated in human and yeast cells. This is the first report of a patient carrying compound heterozygous DPH2 loss-of-function variants with a DPH1 syndrome-like phenotype and implicates diphthamide deficiency as the root cause of this patient's clinical phenotype as well as of DPH1-syndrome. These findings define "diphthamide-deficiency syndrome" as a special ribosomopathy due to reduced functionality of components of the cellular machinery for eEF2-diphthamide synthesis.
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Affiliation(s)
- Harmen Hawer
- Fachgebiet Mikrobiologie, Institut für Biologie, Universität Kassel, D-34132, Kassel, Hessen, Germany
| | | | - Klaus Mayer
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, D-82377, Penzberg, Bavaria, Germany
| | - Ann Kung
- Kaiser Permanente Oakland Medical Center, Oakland, CA, 94611, USA
| | - Amit Malhotra
- Kaiser Permanente Oakland Medical Center, Oakland, CA, 94611, USA
| | - Sari Tuupanen
- Blueprint Genetics Oy, Keilaranta 16 A-B, 02150, Espoo, Finland
| | | | - Ulrich Brinkmann
- Roche Pharma Research & Early Development, Large Molecule Research, Roche Innovation Center Munich, D-82377, Penzberg, Bavaria, Germany.
| | - Raffael Schaffrath
- Fachgebiet Mikrobiologie, Institut für Biologie, Universität Kassel, D-34132, Kassel, Hessen, Germany
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