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Shi Y, Huang D, Song C, Cao R, Wang Z, Wang D, Zhao L, Xu X, Lu C, Xiong F, Zhao H, Li S, Zhou Q, Luo S, Hu D, Zhang Y, Wang C, Shen Y, Su W, Wu Y, Schmitz K, Wei S, Song W. Diphthamide deficiency promotes association of eEF2 with p53 to induce p21 expression and neural crest defects. Nat Commun 2024; 15:3301. [PMID: 38671004 PMCID: PMC11053169 DOI: 10.1038/s41467-024-47670-1] [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: 12/16/2022] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Diphthamide is a modified histidine residue unique for eukaryotic translation elongation factor 2 (eEF2), a key ribosomal protein. Loss of this evolutionarily conserved modification causes developmental defects through unknown mechanisms. In a patient with compound heterozygous mutations in Diphthamide Biosynthesis 1 (DPH1) and impaired eEF2 diphthamide modification, we observe multiple defects in neural crest (NC)-derived tissues. Knockin mice harboring the patient's mutations and Xenopus embryos with Dph1 depleted also display NC defects, which can be attributed to reduced proliferation in the neuroepithelium. DPH1 depletion facilitates dissociation of eEF2 from ribosomes and association with p53 to promote transcription of the cell cycle inhibitor p21, resulting in inhibited proliferation. Knockout of one p21 allele rescues the NC phenotypes in the knockin mice carrying the patient's mutations. These findings uncover an unexpected role for eEF2 as a transcriptional coactivator for p53 to induce p21 expression and NC defects, which is regulated by diphthamide modification.
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Affiliation(s)
- Yu Shi
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, 136 Zhongshan 2nd Rd, Chongqing, 400014, China.
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Daochao Huang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Cui Song
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Ruixue Cao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zhao Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Dan Wang
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Li Zhao
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Xiaolu Xu
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Congyu Lu
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Feng Xiong
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Haowen Zhao
- Department of Clinical Laboratory, Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Neurodevelopment and Cognitive Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Shuxiang Li
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Quansheng Zhou
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
- Department of Endocrinology and Genetic Metabolism Disease, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Shuyue Luo
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Dongjie Hu
- Department of Pediatric Research Institute, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Yun Zhang
- Department of Radiology, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Cui Wang
- Department of Radiology, Children's Hospital of Chongqing Medical University, 136 Zhongshan 2nd Rd, Chongqing, 400014, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Weiting Su
- Kunming Institute of Zoology, Chinese Academy of Science, Kunming, 650223, Yunnan, China
| | - Yili Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Karl Schmitz
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Shuo Wei
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA.
| | - Weihong Song
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, School of Mental Health and Kangning Hospital, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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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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3
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Tang J, Li N, Li G, Wang J, Yu T, Yao R. Assessment of Rare Genetic Variants to Identify Candidate Modifier Genes Underlying Neurological Manifestations in Neurofibromatosis 1 Patients. Genes (Basel) 2022; 13:genes13122218. [PMID: 36553485 PMCID: PMC9778305 DOI: 10.3390/genes13122218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/30/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Neurological phenotypes such as intellectual disability occur in almost half of patients with neurofibromatosis 1 (NF1). Current genotype-phenotype studies have failed to reveal the mechanism underlying this clinical variability. Despite the presence of pathogenic variants of NF1, modifier genes likely determine the occurrence and severity of neurological phenotypes. Exome sequencing data were used to identify genetic variants in 13 NF1 patients and 457 healthy controls, and this information was used to identify candidate modifier genes underlying neurological phenotypes based on an optimal sequence kernel association test. Thirty-six genes were identified as significant modifying factors in patients with neurological phenotypes and all are highly expressed in the nervous system. A review of the literature confirmed that 19 genes including CUL7, DPH1, and BCO1 are clearly associated with the alteration of neurological functioning and development. Our study revealed the enrichment of rare variants of 19 genes closely related to neurological development and functioning in NF1 patients with neurological phenotypes, indicating possible modifier genes and variants affecting neurodevelopment. Further studies on rare genetic variants of candidate modifier genes may help explain the clinical heterogeneity of NF1.
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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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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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Liu X, Bennison SA, Robinson L, Toyo-oka K. Responsible Genes for Neuronal Migration in the Chromosome 17p13.3: Beyond Pafah1b1(Lis1), Crk and Ywhae(14-3-3ε). Brain Sci 2021; 12:brainsci12010056. [PMID: 35053800 PMCID: PMC8774252 DOI: 10.3390/brainsci12010056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/13/2021] [Accepted: 12/23/2021] [Indexed: 01/07/2023] Open
Abstract
The 17p13.3 chromosome region is often deleted or duplicated in humans, resulting in severe neurodevelopmental disorders such as Miller–Dieker syndrome (MDS) and 17p13.3 duplication syndrome. Lissencephaly can also be caused by gene mutations or deletions of a small piece of the 17p13.3 region, including a single gene or a few genes. PAFAH1B1 gene, coding for LIS1 protein, is a responsible gene for lissencephaly and MDS and regulates neuronal migration by controlling microtubules (MTs) and cargo transport along MTs via dynein. CRK is a downstream regulator of the reelin signaling pathways and regulates neuronal migration. YWHAE, coding for 14-3-3ε, is also responsible for MDS and regulates neuronal migration by binding to LIS1-interacting protein, NDEL1. Although these three proteins are known to be responsible for neuronal migration defects in MDS, there are 23 other genes in the MDS critical region on chromosome 17p13.3, and little is known about their functions in neurodevelopment, especially in neuronal migration. This review will summarize the recent progress on the functions of LIS1, CRK, and 14-3-3ε and describe the recent findings of other molecules in the MDS critical regions in neuronal migration.
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Affiliation(s)
- Xiaonan Liu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, PA 19129, USA;
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA; (S.A.B.); (L.R.)
| | - Sarah A. Bennison
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA; (S.A.B.); (L.R.)
| | - Lozen Robinson
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA; (S.A.B.); (L.R.)
| | - Kazuhito Toyo-oka
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19129, USA; (S.A.B.); (L.R.)
- Correspondence: ; Tel.: +1-(215)-991-8288
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7
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Diphthamide promotes TOR signaling by increasing the translation of proteins in the TORC1 pathway. Proc Natl Acad Sci U S A 2021; 118:2104577118. [PMID: 34507998 PMCID: PMC8449394 DOI: 10.1073/pnas.2104577118] [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] [Accepted: 07/23/2021] [Indexed: 01/31/2023] Open
Abstract
Diphthamide, a modification found only on translation elongation factor 2 (EF2), was proposed to suppress -1 frameshifting in translation. Although diphthamide is conserved among all eukaryotes, exactly what proteins are affected by diphthamide deletion is not clear in cells. Through genome-wide profiling for a potential -1 frameshifting site, we identified that the target of rapamycin complex 1 (TORC1)/mammalian TORC1 (mTORC1) signaling pathway is affected by deletion of diphthamide. Diphthamide deficiency in yeast suppresses the translation of TORC1-activating proteins Vam6 and Rtc1. Interestingly, TORC1 signaling also promotes diphthamide biosynthesis, suggesting that diphthamide forms a positive feedback loop to promote translation under nutrient-rich conditions. Our results provide an explanation for why diphthamide is evolutionarily conserved and why diphthamide deletion can cause severe developmental defects.
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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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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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10
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Nam KH, Yi SA, Jang HJ, Han JW, Lee J. In vitro modeling for inherited neurological diseases using induced pluripotent stem cells: from 2D to organoid. Arch Pharm Res 2020; 43:877-889. [PMID: 32761309 DOI: 10.1007/s12272-020-01260-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
Stem cells are characterized by self-renewal and by their ability to differentiate into cells of various organs. With massive progress in 2D and 3D cell culture techniques, in vitro generation of various types of such organoids from patient-derived stem cells is now possible. As in vitro differentiation protocols are usually made to resemble human developmental processes, organogenesis of patient-derived stem cells can provide key information regarding a range of developmental diseases. Human stem cell-based in vitro modeling as opposed to using animal models can particularly benefit the evaluation of neurological diseases because of significant differences in structure and developmental processes between the human and the animal brain. This review focuses on stem cell-based in vitro modeling of neurodevelopmental disorders, more specifically, the fundamentals and technical advancements in monolayer neuron and brain organoid cultures. Furthermore, we discuss the drawbacks of the conventional culture method and explore the advanced, cutting edge 3D organoid models for several neurodevelopmental diseases, including genetic diseases such as Down syndrome, Rett syndrome, and Miller-Dieker syndrome, as well as brain malformations like macrocephaly and microcephaly. Finally, we discuss the limitations of the current organoid techniques and some potential solutions that pave the way for accurate modeling of neurological disorders in a dish.
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Affiliation(s)
- Ki Hong Nam
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sang Ah Yi
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Ji Jang
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea. .,Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon, 16419, Republic of Korea. .,Imnewrun Biosciences Inc., Suwon, 16419, Republic of Korea.
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11
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A Genome-Wide Screen in Mice To Identify Cell-Extrinsic Regulators of Pulmonary Metastatic Colonisation. G3-GENES GENOMES GENETICS 2020; 10:1869-1877. [PMID: 32245826 PMCID: PMC7263671 DOI: 10.1534/g3.120.401128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Metastatic colonization, whereby a disseminated tumor cell is able to survive and proliferate at a secondary site, involves both tumor cell-intrinsic and -extrinsic factors. To identify tumor cell-extrinsic (microenvironmental) factors that regulate the ability of metastatic tumor cells to effectively colonize a tissue, we performed a genome-wide screen utilizing the experimental metastasis assay on mutant mice. Mutant and wildtype (control) mice were tail vein-dosed with murine metastatic melanoma B16-F10 cells and 10 days later the number of pulmonary metastatic colonies were counted. Of the 1,300 genes/genetic locations (1,344 alleles) assessed in the screen 34 genes were determined to significantly regulate pulmonary metastatic colonization (15 increased and 19 decreased; P < 0.005 and genotype effect <-55 or >+55). While several of these genes have known roles in immune system regulation (Bach2, Cyba, Cybb, Cybc1, Id2, Igh-6, Irf1, Irf7, Ncf1, Ncf2, Ncf4 and Pik3cg) most are involved in a disparate range of biological processes, ranging from ubiquitination (Herc1) to diphthamide synthesis (Dph6) to Rho GTPase-activation (Arhgap30 and Fgd4), with no previous reports of a role in the regulation of metastasis. Thus, we have identified numerous novel regulators of pulmonary metastatic colonization, which may represent potential therapeutic targets.
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Urreizti R, Mayer K, Evrony GD, Said E, Castilla-Vallmanya L, Cody NAL, Plasencia G, Gelb BD, Grinberg D, Brinkmann U, Webb BD, Balcells S. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. Eur J Hum Genet 2019; 28:64-75. [PMID: 30877278 DOI: 10.1038/s41431-019-0374-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/21/2019] [Accepted: 03/01/2019] [Indexed: 11/09/2022] Open
Abstract
DPH1 variants have been associated with an ultra-rare and severe neurodevelopmental disorder, mainly characterized by variable developmental delay, short stature, dysmorphic features, and sparse hair. We have identified four new patients (from two different families) carrying novel variants in DPH1, enriching the clinical delineation of the DPH1 syndrome. Using a diphtheria toxin ADP-ribosylation assay, we have analyzed the activity of seven identified variants and demonstrated compromised function for five of them [p.(Leu234Pro); p.(Ala411Argfs*91); p.(Leu164Pro); p.(Leu125Pro); and p.(Tyr112Cys)]. We have built a homology model of the human DPH1-DPH2 heterodimer and have performed molecular dynamics simulations to study the effect of these variants on the catalytic sites as well as on the interactions between subunits of the heterodimer. The results show correlation between loss of activity, reduced size of the opening to the catalytic site, and changes in the size of the catalytic site with clinical severity. This is the first report of functional tests of DPH1 variants associated with the DPH1 syndrome. We demonstrate that the in vitro assay for DPH1 protein activity, together with structural modeling, are useful tools for assessing the effect of the variants on DPH1 function and may be used for predicting patient outcomes and prognoses.
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Affiliation(s)
- Roser Urreizti
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain.
| | - Klaus Mayer
- Roche Pharma Research and Early Development. Large Molecule Research, Roche Innovation Center, Munich, Nonnenwald 2, 82377, Penzberg, Germany
| | - Gilad D Evrony
- Center for Human Genetics & Genomics, New York University Langone Health, New York, NY, USA
| | - Edith Said
- Section of Medical Genetics, Mater dei Hospital, Msida, Malta.,Department of Anatomy and Cell Biology, University of Malta, Msida, Malta
| | - Laura Castilla-Vallmanya
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Neal A L Cody
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Sema4, Stamford, CT, USA
| | | | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Grinberg
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development. Large Molecule Research, Roche Innovation Center, Munich, Nonnenwald 2, 82377, Penzberg, Germany
| | - Bryn D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susanna Balcells
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, IBUB, IRSJD, CIBERER, Barcelona, Spain
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13
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Lin Y, Kong F, Li Y, Wang Y, Song L, Zhao C. The tumor suppressor OVCA1 is a short half-life protein degraded by the ubiquitin-proteasome pathway. Oncol Lett 2019; 17:2328-2334. [PMID: 30675298 PMCID: PMC6341780 DOI: 10.3892/ol.2018.9852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 11/19/2018] [Indexed: 12/14/2022] Open
Abstract
Ovarian cancer gene 1 (OVCA1) is a tumor suppressor associated with ovarian cancer, which is involved in cell proliferation regulation, embryonic development and tumorigenesis. Loss of heterozygosity in the OVCA1 gene occurs in 50-86% of cases of ovarian cancer; however, the physiological and biochemical functions of OVCA1 are not yet clear. In the present study, the stability and degradation of OVCA1 were investigated in A2780, Hela and 293 cells. The results revealed that the OVCA1 protein was unstable by MG132 inhibiting proteasome mediated degradation, co-immunoprecipitation and half-life measurement experiments. The cellular protein levels of endogenous OVCA1 were too low to be detected by western blotting. In addition, carbobenzoxy-L-leucyl-L-leucyl-L-leucinal inhibited the degradation of OVCA1 in cells. The co-immunoprecipitation assay revealed that the OVCA1 protein interacted with ubiquitin to form a poly-ubiquitinated complex in cells. The half-life of OVCA1, measured by inhibiting protein synthesis with cycloheximide, was <2 h. The present study demonstrated that OVCA1 may be degraded by the ubiquitin-mediated proteasome pathway and may be considered a short half-life protein. In conclusion, the regulation of OVCA1 protein degradation via the ubiquitin-proteasome pathway may represent a novel direction in the development of ovarian cancer therapy.
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Affiliation(s)
- Yingwei Lin
- Department of Clinical Laboratory, The Second Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
| | - Fandou Kong
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Yan Li
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Yinghui Wang
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Ling Song
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Chunyan Zhao
- College of Laboratory Medicine, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
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14
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Tsuda-Sakurai K, Miura M. The hidden nature of protein translational control by diphthamide: the secrets under the leather. J Biochem 2019; 165:1-8. [PMID: 30204891 DOI: 10.1093/jb/mvy071] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/27/2018] [Indexed: 01/16/2023] Open
Abstract
The protein translation elongation factor eEF2 undergoes a unique posttranslational modification called diphthamidation. eEF2 is an essential factor in protein translation, and the diphthamide modification has been a famous target of the diphtheria toxin for a long time. On the other hand, the physiological function of this rare modification in vivo remains unknown. Recent studies have suggested that diphthamide has specific functions for the cellular stress response and active proliferation. In this review, we summarize the history and findings of diphthamide obtained to date and discuss the possibility of a specific function for diphthamide in regulating protein translation.
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Affiliation(s)
- Kayoko Tsuda-Sakurai
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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15
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Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer. Genes (Basel) 2018; 10:genes10010019. [PMID: 30597914 PMCID: PMC6356722 DOI: 10.3390/genes10010019] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA modifications in prevention of neurodegeneration, certain cancer types upregulate tRNA modification genes to sustain cancer cell gene expression and metastasis. Multiple associations of defects in genes encoding subunits of the tRNA modifier complex Elongator with human disease highlight the importance of proper anticodon wobble uridine modifications (xm⁵U34) for health. Elongator functionality requires communication with accessory proteins and dynamic phosphorylation, providing regulatory control of its function. Here, we summarized recent insights into molecular functions of the complex and the role of Elongator dependent tRNA modification in human disease.
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16
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Narrowe AB, Spang A, Stairs CW, Caceres EF, Baker BJ, Miller CS, Ettema TJG. Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids. Genome Biol Evol 2018; 10:2380-2393. [PMID: 30060184 PMCID: PMC6143161 DOI: 10.1093/gbe/evy154] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.
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Affiliation(s)
- Adrienne B Narrowe
- Department of Integrative Biology, University of Colorado Denver, Denver
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Courtney W Stairs
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Eva F Caceres
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas Austin, Port Aransas
| | | | - Thijs J G Ettema
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Sweden
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Abstract
In 1993, Jabs et al. were the first to describe a genetic origin of craniosynostosis. Since this discovery, the genetic causes of the most common syndromes have been described. In 2015, a total of 57 human genes were reported for which there had been evidence that mutations were causally related to craniosynostosis. Facilitated by rapid technological developments, many others have been identified since then. Reviewing the literature, we characterize the most common craniosynostosis syndromes followed by a description of the novel causes that were identified between January 2015 and December 2017.
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Affiliation(s)
- Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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18
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Dever TE, Dinman JD, Green R. Translation Elongation and Recoding in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a032649. [PMID: 29610120 DOI: 10.1101/cshperspect.a032649] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this review, we highlight the current understanding of translation elongation and recoding in eukaryotes. In addition to providing an overview of the process, recent advances in our understanding of the role of the factor eIF5A in both translation elongation and termination are discussed. We also highlight mechanisms of translation recoding with a focus on ribosomal frameshifting during elongation. We see that the balance between the basic steps in elongation and the less common recoding events is determined by the kinetics of the different processes as well as by specific sequence determinants.
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Affiliation(s)
- Thomas E Dever
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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19
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Zhao H, Zhong W, Leng C, Zhang J, Zhang M, Huang W, Zhang Y, Li W, Jia P, Lin J, Maimaitili G, Chen F. A novel PTCH1
mutation underlies nonsyndromic cleft lip and/or palate in a Han Chinese family. Oral Dis 2018; 24:1318-1325. [PMID: 29908092 DOI: 10.1111/odi.12915] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 05/25/2018] [Accepted: 06/11/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Huaxiang Zhao
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Wenjie Zhong
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Chuntao Leng
- Department of Stomatology; The Fifth Affiliated Hospital of Xinjiang Medical University; Urumqi China
| | - Jieni Zhang
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Mengqi Zhang
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Wenbin Huang
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Yunfan Zhang
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Weiran Li
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Peizeng Jia
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Jiuxiang Lin
- Department of Orthodontics; Peking University School and Hospital of Stomatology; Beijing China
| | - Gulibaha Maimaitili
- Department of Stomatology; The Fifth Affiliated Hospital of Xinjiang Medical University; Urumqi China
| | - Feng Chen
- Central Laboratory; Peking University School and Hospital of Stomatology; Beijing China
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20
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Blazejewski SM, Bennison SA, Smith TH, Toyo-Oka K. Neurodevelopmental Genetic Diseases Associated With Microdeletions and Microduplications of Chromosome 17p13.3. Front Genet 2018; 9:80. [PMID: 29628935 PMCID: PMC5876250 DOI: 10.3389/fgene.2018.00080] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 02/26/2018] [Indexed: 01/24/2023] Open
Abstract
Chromosome 17p13.3 is a region of genomic instability that is linked to different rare neurodevelopmental genetic diseases, depending on whether a deletion or duplication of the region has occurred. Chromosome microdeletions within 17p13.3 can result in either isolated lissencephaly sequence (ILS) or Miller-Dieker syndrome (MDS). Both conditions are associated with a smooth cerebral cortex, or lissencephaly, which leads to developmental delay, intellectual disability, and seizures. However, patients with MDS have larger deletions than patients with ILS, resulting in additional symptoms such as poor muscle tone, congenital anomalies, abnormal spasticity, and craniofacial dysmorphisms. In contrast to microdeletions in 17p13.3, recent studies have attracted considerable attention to a condition known as a 17p13.3 microduplication syndrome. Depending on the genes involved in their microduplication, patients with 17p13.3 microduplication syndrome may be categorized into either class I or class II. Individuals in class I have microduplications of the YWHAE gene encoding 14-3-3ε, as well as other genes in the region. However, the PAFAH1B1 gene encoding LIS1 is never duplicated in these patients. Class I microduplications generally result in learning disabilities, autism, and developmental delays, among other disorders. Individuals in class II always have microduplications of the PAFAH1B1 gene, which may include YWHAE and other genetic microduplications. Class II microduplications generally result in smaller body size, developmental delays, microcephaly, and other brain malformations. Here, we review the phenotypes associated with copy number variations (CNVs) of chromosome 17p13.3 and detail their developmental connection to particular microdeletions or microduplications. We also focus on existing single and double knockout mouse models that have been used to study human phenotypes, since the highly limited number of patients makes a study of these conditions difficult in humans. These models are also crucial for the study of brain development at a mechanistic level since this cannot be accomplished in humans. Finally, we emphasize the usefulness of the CRISPR/Cas9 system and next generation sequencing in the study of neurodevelopmental diseases.
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Affiliation(s)
- Sara M Blazejewski
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Sarah A Bennison
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Trevor H Smith
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Kazuhito Toyo-Oka
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States
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21
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A novel homozygous DPH1 mutation causes intellectual disability and unique craniofacial features. J Hum Genet 2018; 63:487-491. [DOI: 10.1038/s10038-017-0404-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 11/08/2022]
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22
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COUP-TFII is required for morphogenesis of the neural crest-derived tympanic ring. Sci Rep 2017; 7:12386. [PMID: 28959031 PMCID: PMC5620064 DOI: 10.1038/s41598-017-12665-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/18/2017] [Indexed: 12/27/2022] Open
Abstract
Chicken Ovalbumin Upstream Promoter-Transcription Factor II (COUP-TFII) plays pivotal roles in cell growth, cell differentiation, and cell fate determination. Although genome-wide studies have identified COUP-TFII binding on gene sets mainly involved in neural crest cell (NCC) development and craniofacial morphogenesis, the direct functional connection between COUP-TFII and NCCs in vivo has not been well characterized. In this study, we show that COUP-TFII is expressed in the subpopulation of NCCs and its derivatives, and targeted ablation of COUP-TFII in mouse NCCs results in markedly shortened and bifurcated tympanic rings, which in turn disturb the caudal direction of external acoustic meatus invagination. However, formation of the manubrium of the malleus (MM) in Wnt1-Cre/+;COUP-TFIIflox/flox mice is not perturbed, suggesting that the rostral half of the tympanic ring is sufficient to support proper MM development. Interestingly, we found that loss of COUP-TFII up-regulates Sox9 in the tympanic ring primordium and affects the distribution of preosteoblasts before mesenchymal condensation. Together, our results demonstrate that COUP-TFII plays an essential role in regulating the patterning of the NCC-derived tympanic ring.
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23
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Elp3 and Dph3 of Schizosaccharomyces pombe mediate cellular stress responses through tRNA LysUUU modifications. Sci Rep 2017; 7:7225. [PMID: 28775286 PMCID: PMC5543170 DOI: 10.1038/s41598-017-07647-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/30/2017] [Indexed: 01/31/2023] Open
Abstract
Efficient protein synthesis in eukaryotes requires diphthamide modification of translation elongation factor eEF2 and wobble uridine modifications of tRNAs. In higher eukaryotes, these processes are important for preventing neurological and developmental defects and cancer. In this study, we used Schizosaccharomyces pombe as a model to analyse mutants defective in eEF2 modification (dph1Δ), in tRNA modifications (elp3Δ), or both (dph3Δ) for sensitivity to cytotoxic agents and thermal stress. The dph3Δ and elp3Δ mutants were sensitive to a range of drugs and had growth defects at low temperature. dph3Δ was epistatic with dph1Δ for sensitivity to hydroxyurea and methyl methanesulfonate, and with elp3Δ for methyl methanesulfonate and growth at 16 °C. The dph1Δ and dph3Δ deletions rescued growth defects of elp3Δ in response to thiabendazole and at 37 °C. Elevated tRNALysUUU levels suppressed the elp3Δ phenotypes and some of the dph3Δ phenotypes, indicating that lack of tRNALysUUU modifications were responsible. Furthermore, we found positive genetic interactions of elp3Δ and dph3Δ with sty1Δ and atf1Δ, indicating that Elp3/Dph3-dependent tRNA modifications are important for efficient biosynthesis of key factors required for accurate responses to cytotoxic stress conditions.
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24
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Barros Fontes MI, Dos Santos AP, Rossi Torres F, Lopes-Cendes I, Cendes F, Appenzeller S, Kawasaki de Araujo T, Lopes Monlleó I, Gil-da-Silva-Lopes VL. 17p13.3 Microdeletion: Insights on Genotype-Phenotype Correlation. Mol Syndromol 2016; 8:36-41. [PMID: 28232781 DOI: 10.1159/000452753] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2016] [Indexed: 01/13/2023] Open
Abstract
Microdeletions in the chromosomal region 17p13.3 are associated with neuronal migration disorders, and PAFAB1H1 is the main gene involved. The largest genomic imbalances, including the YWHAE and CRK genes, cause more severe structural abnormalities of the brain and other associated dysmorphic features. Here, we describe a 3-year-old boy with a microdeletion in 17p13.3 presenting with minor facial dysmorphisms, a cleft palate, neurodevelopmental delay, and behavioral disorder with no structural malformation of the brain. The patient was evaluated by a clinician using a standard protocol. Laboratory investigation included GTG-banding, whole-genome AGH, and array-CGH. Whole-genome AGH and array-CGH analysis identified an estimated 2.1-Mb deletion in the 17p13.3 region showing haploinsufficiency of the YWHAE, CRK, H1C1, and OVCA1 genes and no deletion of PAFAH1B1. The complex gene interaction on brain development and function is illustrated in the genotype-phenotype correlation described here. This report reinforces the importance of the 17p13.3 region in developmental abnormalities and highlights the weak implication of the HIC1 and OVCA1 genes in palatogenesis.
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Affiliation(s)
- Marshall I Barros Fontes
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil; Department of Medical Genetics Sector, State University of Health Sciences of Alagoas (UNCISAL), Maceió, Brazil
| | - Ana P Dos Santos
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fábio Rossi Torres
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernando Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Simone Appenzeller
- Department of Internal Medicine, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Tânia Kawasaki de Araujo
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
| | - Isabella Lopes Monlleó
- Department of Clinical Genetics Service, Faculty of Medicine, University Hospital, Federal University of Alagoas (UFAL), Maceió, Brazil
| | - Vera L Gil-da-Silva-Lopes
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, Brazil
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25
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Wang CY, Tang MC, Chang WC, Furushima K, Jang CW, Behringer RR, Chen CM. PiggyBac Transposon-Mediated Mutagenesis in Rats Reveals a Crucial Role of Bbx in Growth and Male Fertility. Biol Reprod 2016; 95:51. [PMID: 27465138 PMCID: PMC5394979 DOI: 10.1095/biolreprod.116.141739] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/14/2016] [Indexed: 12/14/2022] Open
Abstract
Bobby sox homolog (Bbx) is an evolutionally conserved gene, but its biological function remains elusive. Here, we characterized defects of Bbx mutant rats that were created by PiggyBac-mediated insertional mutagenesis. Smaller body size and male infertility were the two major phenotypes of homozygous Bbx mutants. Bbx expression profile analysis showed that Bbx was more highly expressed in the testis and pituitary gland than in other organs. Histology and hormonal gene expression analysis of control and Bbx-null pituitary glands showed that loss of Bbx appeared to be dispensable for pituitary histogenesis and the expression of major hormones. BBX was localized in the nuclei of postmeiotic spermatids and Sertoli cells in wild-type testes, but absent in mutant testes. An increased presence of aberrant multinuclear giant cells and apoptotic cells was observed in mutant seminiferous tubules. TUNEL-positive cells costained with CREM (round spermatid marker), but not PLZF (spermatogonia marker), gammaH2Ax (meiotic spermatocyte marker), or GATA4 (Sertoli cell marker). Finally, there were drastically reduced numbers and motility of epididymal sperm from Bbx-null rats. These results suggest that loss of BBX induces apoptosis of postmeiotic spermatids and results in spermiogenesis defects and infertility.
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Affiliation(s)
- Chieh-Ying Wang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Chu Tang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan Laboratory Animal Center, National Yang-Ming University, Taipei, Taiwan
| | - Wen-Chi Chang
- Laboratory Animal Center, National Yang-Ming University, Taipei, Taiwan
| | - Kenryo Furushima
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Chuan-Wei Jang
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Richard R Behringer
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | - Chun-Ming Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan Laboratory Animal Center, National Yang-Ming University, Taipei, Taiwan
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Wit JM, Oostdijk W, Losekoot M, van Duyvenvoorde HA, Ruivenkamp CAL, Kant SG. MECHANISMS IN ENDOCRINOLOGY: Novel genetic causes of short stature. Eur J Endocrinol 2016; 174:R145-73. [PMID: 26578640 DOI: 10.1530/eje-15-0937] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/16/2015] [Indexed: 12/17/2022]
Abstract
The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFκB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. Heterozygous NPR2 or SHOX defects may be found in ∼3% of short children, and also rasopathies (e.g., Noonan syndrome) can be found in children without clear syndromic appearance. Numerous other syndromes associated with short stature are caused by genetic defects in fundamental cellular processes, chromosomal abnormalities, CNVs, and imprinting disorders.
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Affiliation(s)
- Jan M Wit
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilma Oostdijk
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Monique Losekoot
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Hermine A van Duyvenvoorde
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Sarina G Kant
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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Loucks CM, Parboosingh JS, Shaheen R, Bernier FP, McLeod DR, Seidahmed MZ, Puffenberger EG, Ober C, Hegele RA, Boycott KM, Alkuraya FS, Innes AM. Matching two independent cohorts validates DPH1 as a gene responsible for autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. Hum Mutat 2015. [PMID: 26220823 DOI: 10.1002/humu.22843] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Recently, Alazami et al. (2015) identified 33 putative candidate disease genes for neurogenetic disorders. One such gene was DPH1, in which a homozygous missense mutation was associated with a 3C syndrome-like phenotype in four patients from a single extended family. Here, we report a second homozygous missense variant in DPH1, seen in four members of a founder population, and associated with a phenotype initially reminiscent of Sensenbrenner syndrome. This postpublication "match" validates DPH1 as a gene underlying syndromic intellectual disability with short stature and craniofacial and ectodermal anomalies, reminiscent of, but distinct from, 3C and Sensenbrenner syndromes. This validation took several years after the independent discoveries due to the absence of effective methods for sharing both candidate phenotype and genotype data between investigators. Sharing of data via Web-based anonymous data exchange servers will play an increasingly important role toward more efficient identification of the molecular basis for rare Mendelian disorders.
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Affiliation(s)
- Catrina M Loucks
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jillian S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyhadh, 11211, Saudi Arabia
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
| | - D Ross McLeod
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Carole Ober
- Department of Human Genetics, and Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois
| | - Robert A Hegele
- Department of Paediatrics, University of Western Ontario, London, Ontario, Canada
| | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyhadh, 11211, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, Alberta, Canada
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Differential requirements for β-catenin in murine prostate cancer originating from basal versus luminal cells. J Pathol 2015; 236:290-301. [DOI: 10.1002/path.4521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 02/12/2015] [Accepted: 02/19/2015] [Indexed: 01/01/2023]
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Price KE, Haddad Y, Fakhouri WD. Analysis of the Relationship Between Micrognathia and Cleft Palate: A Systematic Review. Cleft Palate Craniofac J 2015; 53:e34-44. [PMID: 25658963 DOI: 10.1597/14-238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective To gather data from relevant experimental and observational studies to determine the relationship between micrognathia and cleft palate. The goal is to raise awareness and motivate clinicians to consider the cause and effect relationship when confronted with patients with cleft palate, even if there is no clearly noticeable mandibular abnormality. Design Several electronic databases were systematically examined to find articles for this review, using search terms including "cleft palate," "micrognathia," "tongue," and "airway obstruction." PubMed was the source of all the articles chosen to be included. Exclusion criteria included case reports, articles focused on treatment options, and articles only tangentially related to cleft palate and/or micrognathia. Results A total of 930 articles were screened for relevance, and 82 articles were chosen for further analysis. Evidence gathered in this review includes a variety of etiological factors that are causative or associated with both micrognathia and cleft palate. Observational studies relating the two abnormalities are also included. Much of the included literature recognizes a cause-and-effect relationship between micrognathia and cleft palate. Conclusion On the basis of the published data, we suggest that micrognathia does induce cleft palate in humans and animals. With knowledge of this causative relationship, clinicians should consider the importance of gathering cephalometric data on the mandibles and tongues of patients presenting with isolated cleft palate to determine whether they have micrognathia as well. With more data, patterns may emerge that could give insight into the complex etiology of nonsyndromic cleft palate.
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Schaffrath R, Abdel-Fattah W, Klassen R, Stark MJR. The diphthamide modification pathway from Saccharomyces cerevisiae--revisited. Mol Microbiol 2014; 94:1213-26. [PMID: 25352115 DOI: 10.1111/mmi.12845] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2014] [Indexed: 01/09/2023]
Abstract
Diphthamide is a conserved modification in archaeal and eukaryal translation elongation factor 2 (EF2). Its name refers to the target function for diphtheria toxin, the disease-causing agent that, through ADP ribosylation of diphthamide, causes irreversible inactivation of EF2 and cell death. Although this clearly emphasizes a pathobiological role for diphthamide, its physiological function is unclear, and precisely why cells need EF2 to contain diphthamide is hardly understood. Nonetheless, the conservation of diphthamide biosynthesis together with syndromes (i.e. ribosomal frame-shifting, embryonic lethality, neurodegeneration and cancer) typical of mutant cells that cannot make it strongly suggests that diphthamide-modified EF2 occupies an important and translation-related role in cell proliferation and development. Whether this is structural and/or regulatory remains to be seen. However, recent progress in dissecting the diphthamide gene network (DPH1-DPH7) from the budding yeast Saccharomyces cerevisiae has significantly advanced our understanding of the mechanisms required to initiate and complete diphthamide synthesis on EF2. Here, we review recent developments in the field that not only have provided novel, previously overlooked and unexpected insights into the pathway and the biochemical players required for diphthamide synthesis but also are likely to foster innovative studies into the potential regulation of diphthamide, and importantly, its ill-defined biological role.
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Affiliation(s)
- Raffael Schaffrath
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK; Institut für Biologie, Abteilung Mikrobiologie, Universität Kassel, 34132, Kassel, Germany
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