1
|
Brotto D, Sorrentino F, Cenedese R, Avato I, Bovo R, Trevisi P, Manara R. Genetics of Inner Ear Malformations: A Review. Audiol Res 2021; 11:524-536. [PMID: 34698066 PMCID: PMC8544219 DOI: 10.3390/audiolres11040047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/02/2022] Open
Abstract
Inner ear malformations are present in 20% of patients with sensorineural hearing loss. Although the first descriptions date to the 18th century, in recent years the knowledge about these conditions has experienced terrific improvement. Currently, most of these conditions have a rehabilitative option. Much less is known about the etiology of these anomalies. In particular, the evolution of genetics has provided new data about the possible relationship between inner ear malformations and genetic anomalies. In addition, in syndromic condition, the well-known presence of sensorineural hearing loss can now be attributed to the presence of an inner ear anomaly. In some cases, the presence of these abnormalities should be considered as a characteristic feature of the syndrome. The present paper aims to summarize the available knowledge about the possible relationships between inner ear malformations and genetic mutations.
Collapse
Affiliation(s)
- Davide Brotto
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padua, 35128 Padua, Italy; (F.S.); (R.C.); (R.B.); (P.T.)
- Correspondence:
| | - Flavia Sorrentino
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padua, 35128 Padua, Italy; (F.S.); (R.C.); (R.B.); (P.T.)
| | - Roberta Cenedese
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padua, 35128 Padua, Italy; (F.S.); (R.C.); (R.B.); (P.T.)
| | - Irene Avato
- Department of Diagnostic, Paediatric, Clinical and Surgical Science, University of Pavia, 35128 Pavia, Italy;
| | - Roberto Bovo
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padua, 35128 Padua, Italy; (F.S.); (R.C.); (R.B.); (P.T.)
| | - Patrizia Trevisi
- Section of Otorhinolaryngology—Head and Neck Surgery, Department of Neurosciences, University of Padua, 35128 Padua, Italy; (F.S.); (R.C.); (R.B.); (P.T.)
| | - Renzo Manara
- Neuroradiology Unit, Department of Neurosciences, University of Padua, 35128 Padua, Italy;
| |
Collapse
|
2
|
Santos D, Mahtab M, Boavida A, Pisani FM. Role of the DDX11 DNA Helicase in Warsaw Breakage Syndrome Etiology. Int J Mol Sci 2021; 22:2308. [PMID: 33669056 PMCID: PMC7956524 DOI: 10.3390/ijms22052308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 12/23/2022] Open
Abstract
Warsaw breakage syndrome (WABS) is a genetic disorder characterized by sister chromatid cohesion defects, growth retardation, microcephaly, hearing loss and other variable clinical manifestations. WABS is due to biallelic mutations of the gene coding for the super-family 2 DNA helicase DDX11/ChlR1, orthologous to the yeast chromosome loss protein 1 (Chl1). WABS is classified in the group of "cohesinopathies", rare hereditary diseases that are caused by mutations in genes coding for subunits of the cohesin complex or protein factors having regulatory roles in the sister chromatid cohesion process. In fact, among the cohesion regulators, an important player is DDX11, which is believed to be important for the functional coupling of DNA synthesis and cohesion establishment at the replication forks. Here, we will review what is known about the molecular and cellular functions of human DDX11 and its role in WABS etiopathogenesis, even in light of recent findings on the role of cohesin and its regulator network in promoting chromatin loop formation and regulating chromatin spatial organization.
Collapse
Affiliation(s)
- Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| | - Francesca M. Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy; (D.S.); (M.M.); (A.B.)
| |
Collapse
|
3
|
Toraman B, Bilginer SÇ, Hesapçıoğlu ST, Göker Z, Soykam HO, Ergüner B, Dinçer T, Yıldız G, Ünsal S, Kasap BK, Kandil S, Kalay E. Finding underlying genetic mechanisms of two patients with autism spectrum disorder carrying familial apparently balanced chromosomal translocations. J Gene Med 2021; 23:e3322. [PMID: 33591602 DOI: 10.1002/jgm.3322] [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: 11/11/2020] [Revised: 01/26/2021] [Accepted: 02/14/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Genetic etiologies of autism spectrum disorders (ASD) are complex, and the genetic factors identified so far are very diverse. In complex genetic diseases such as ASD, de novo or inherited chromosomal abnormalities are valuable findings for researchers with respect to identifying the underlying genetic risk factors. With gene mapping studies on these chromosomal abnormalities, dozens of genes have been associated with ASD and other neurodevelopmental genetic diseases. In the present study, we aimed to idenitfy the causative genetic factors in patients with ASD who have an apparently balanced chromosomal translocation in their karyotypes. METHODS For mapping the broken genes as a result of chromosomal translocations, we performed whole genome DNA sequencing. Chromosomal breakpoints and large DNA copy number variations (CNV) were determined after genome alignment. Identified CNVs and single nucleotide variations (SNV) were evaluated with VCF-BED intersect and Gemini tools, respectively. A targeted resequencing approach was performed on the JMJD1C gene in all of the ASD cohorts (220 patients). For molecular modeling, we used a homology modeling approach via the SWISS-MODEL. RESULTS We found that there was no contribution of the broken genes or regulator DNA sequences to ASD, whereas the SNVs on the JMJD1C, CNKSR2 and DDX11 genes were the most convincing genetic risk factors for underlying ASD phenotypes. CONCLUSIONS Genetic etiologies of ASD should be analyzed comprehensively by taking into account of the all chromosomal structural abnormalities and de novo or inherited CNV/SNVs with all possible inheritance patterns.
Collapse
Affiliation(s)
- Bayram Toraman
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Samiye Çilem Bilginer
- Faculty of Medicine Child and Adolescent Psychiatry Department, Karadeniz Technical University, Trabzon, Turkey
| | - Selma Tural Hesapçıoğlu
- Child and Adolescent Psychiatry Department, Yildirim Beyazit University Faculty of Medicine, Ankara, Turkey
| | - Zeynep Göker
- Ministry of Health Ankara City Hospital, Child-Adolescent and Mental Health, Cankaya, Ankara, Turkey
| | - Hüseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, İstanbul, Turkey
| | - Bekir Ergüner
- Sabanci University Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bio engineering, Istanbul, Turkey
| | - Tuba Dinçer
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Gökhan Yıldız
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Serbülent Ünsal
- Graduate School of Health Science, Biostatistics and Medical Informatics Department, PhD Candidate, Karadeniz Technical University, Trabzon, Turkey
| | - Burak Kaan Kasap
- Graduate School of Health Science, Medical Biology Department, PhD Candidate, Karadeniz Technical University, Trabzon, Turkey
| | - Sema Kandil
- Faculty of Medicine Child and Adolescent Psychiatry Department, Karadeniz Technical University, Trabzon, Turkey
| | - Ersan Kalay
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| |
Collapse
|
4
|
Bottega R, Ravera S, Napolitano LMR, Chiappetta V, Zini N, Crescenzi B, Arniani S, Faleschini M, Cortone G, Faletra F, Medagli B, Sirchia F, Moretti M, de Lange J, Cappelli E, Mecucci C, Onesti S, Pisani FM, Savoia A. Genomic integrity and mitochondrial metabolism defects in Warsaw syndrome cells: a comparison with Fanconi anemia. J Cell Physiol 2021; 236:5664-5675. [PMID: 33432587 DOI: 10.1002/jcp.30265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/25/2022]
Abstract
Warsaw breakage syndrome (WABS), is caused by biallelic mutations of DDX11, a gene coding a DNA helicase. We have recently reported two affected sisters, compound heterozygous for a missense (p.Leu836Pro) and a frameshift (p.Lys303Glufs*22) variant. By investigating the pathogenic mechanism, we demonstrate the inability of the DDX11 p.Leu836Pro mutant to unwind forked DNA substrates, while retaining DNA binding activity. We observed the accumulation of patient-derived cells at the G2/M phase and increased chromosomal fragmentation after mitomycin C treatment. The phenotype partially overlaps with features of the Fanconi anemia cells, which shows not only genomic instability but also defective mitochondria. This prompted us to examine mitochondrial functionality in WABS cells and revealed an altered aerobic metabolism. This opens the door to the further elucidation of the molecular and cellular basis of an impaired mitochondrial phenotype and sheds light on this fundamental process in cell physiology and the pathogenesis of these diseases.
Collapse
Affiliation(s)
- Roberta Bottega
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Silvia Ravera
- Department of Experimental Medicine, University of Genova, Genova, Italy
| | | | - Viviana Chiappetta
- Istituto di Biochimica e Biologia Cellulare (IBBC), Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Nicoletta Zini
- CNR-National Research Council of Italy, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza"-Unit of Bologna, Bologna, Italy.,IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Barbara Crescenzi
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Silvia Arniani
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Michela Faleschini
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Giuseppe Cortone
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy.,International School for Advanced Studies (SISSA), Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Barbara Medagli
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy.,Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Fabio Sirchia
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy
| | - Martina Moretti
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Job de Lange
- Amsterdam UMC, Clinical Genetics, Section Oncogenetics, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Enrico Cappelli
- UO Ematologia, IRCCS Istituto Giannina Gaslini, Genova, Italy, Genova, Italy
| | - Cristina Mecucci
- Sezione di Ematologia ed Immunologia Clinica, Centro Ricerche Emato-Oncologiche, University of Perugia, Perugia, Italy
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare (IBBC), Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy.,Department of Medical Sciences, University of Trieste, Trieste, Italy
| |
Collapse
|
5
|
Lerner LK, Holzer S, Kilkenny ML, Šviković S, Murat P, Schiavone D, Eldridge CB, Bittleston A, Maman JD, Branzei D, Stott K, Pellegrini L, Sale JE. Timeless couples G-quadruplex detection with processing by DDX11 helicase during DNA replication. EMBO J 2020; 39:e104185. [PMID: 32705708 PMCID: PMC7506991 DOI: 10.15252/embj.2019104185] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022] Open
Abstract
Regions of the genome with the potential to form secondary DNA structures pose a frequent and significant impediment to DNA replication and must be actively managed in order to preserve genetic and epigenetic integrity. How the replisome detects and responds to secondary structures is poorly understood. Here, we show that a core component of the fork protection complex in the eukaryotic replisome, Timeless, harbours in its C-terminal region a previously unappreciated DNA-binding domain that exhibits specific binding to G-quadruplex (G4) DNA structures. We show that this domain contributes to maintaining processive replication through G4-forming sequences, and exhibits partial redundancy with an adjacent PARP-binding domain. Further, this function of Timeless requires interaction with and activity of the helicase DDX11. Loss of both Timeless and DDX11 causes epigenetic instability at G4-forming sequences and DNA damage. Our findings indicate that Timeless contributes to the ability of the replisome to sense replication-hindering G4 formation and ensures the prompt resolution of these structures by DDX11 to maintain processive DNA synthesis.
Collapse
Affiliation(s)
- Leticia K Lerner
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Centre de Recherche des CordeliersCell Death and Drug Resistance in Hematological Disorders TeamINSERM UMRS 1138Sorbonne UniversitéParisFrance
| | - Sandro Holzer
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | | | | | | | | | | | | - Joseph D Maman
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Dana Branzei
- IFOMFondazione Italiana per la Ricerca sul CancroInstitute of Molecular OncologyMilanItaly
| | - Katherine Stott
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Luca Pellegrini
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | | |
Collapse
|
6
|
van Schie JJM, Faramarz A, Balk JA, Stewart GS, Cantelli E, Oostra AB, Rooimans MA, Parish JL, de Almeida Estéves C, Dumic K, Barisic I, Diderich KEM, van Slegtenhorst MA, Mahtab M, Pisani FM, Te Riele H, Ameziane N, Wolthuis RMF, de Lange J. Warsaw Breakage Syndrome associated DDX11 helicase resolves G-quadruplex structures to support sister chromatid cohesion. Nat Commun 2020; 11:4287. [PMID: 32855419 PMCID: PMC7452896 DOI: 10.1038/s41467-020-18066-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Warsaw Breakage Syndrome (WABS) is a rare disorder related to cohesinopathies and Fanconi anemia, caused by bi-allelic mutations in DDX11. Here, we report multiple compound heterozygous WABS cases, each displaying destabilized DDX11 protein and residual DDX11 function at the cellular level. Patient-derived cell lines exhibit sensitivity to topoisomerase and PARP inhibitors, defective sister chromatid cohesion and reduced DNA replication fork speed. Deleting DDX11 in RPE1-TERT cells inhibits proliferation and survival in a TP53-dependent manner and causes chromosome breaks and cohesion defects, independent of the expressed pseudogene DDX12p. Importantly, G-quadruplex (G4) stabilizing compounds induce chromosome breaks and cohesion defects which are strongly aggravated by inactivation of DDX11 but not FANCJ. The DNA helicase domain of DDX11 is essential for sister chromatid cohesion and resistance to G4 stabilizers. We propose that DDX11 is a DNA helicase protecting against G4 induced double-stranded breaks and concomitant loss of cohesion, possibly at DNA replication forks.
Collapse
Affiliation(s)
- Janne J M van Schie
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Atiq Faramarz
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Jesper A Balk
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Erika Cantelli
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Anneke B Oostra
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Martin A Rooimans
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
| | - Joanna L Parish
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | | | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Hospital Centre Zagreb, University of Zagreb Medical School, Zagreb, Croatia
| | - Ingeborg Barisic
- Children's Hospital Zagreb, Center of Excellence for Reproductive and Regenerative Medicine, Medical School University of Zagreb, Zagreb, Croatia
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Mohammad Mahtab
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Hein Te Riele
- Netherlands Cancer Institute, Division of Tumor Biology and Immunology, Amsterdam, The Netherlands
| | - Najim Ameziane
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands
- Centogene, Am Strande 7, 18055, Rostock, Germany
| | - Rob M F Wolthuis
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| | - Job de Lange
- Section of Oncogenetics, Cancer Center Amsterdam and Department of Clinical Genetics, Amsterdam University Medical Centers, De Boelelaan 1118, 1081, HV, Amsterdam, the Netherlands.
| |
Collapse
|
7
|
Brotto D, Manara R, Scimemi P, Sorrentino F, Montino S, Maritan F, Caserta E, Lovo E, Martini A, Santarelli R, Trevisi P. An audiological perspective on ''Two further patients with Warsaw breakage syndrome. Is a mild phenotype possible?". Mol Genet Genomic Med 2020; 8:e1283. [PMID: 32500959 PMCID: PMC7507339 DOI: 10.1002/mgg3.1283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/26/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
- Davide Brotto
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Renzo Manara
- Neuroradiology, Neurosciences Department, University of Padova, Padova, Italy
| | - Pietro Scimemi
- Neurosciences Department, University of Padova, Padova, Italy.,Audiology Service, Ospedale Santi Giovanni e Paolo, Venezia, Italy
| | - Flavia Sorrentino
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Silvia Montino
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Francesca Maritan
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Ezio Caserta
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Elisa Lovo
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Alessandro Martini
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| | - Rosamaria Santarelli
- Neurosciences Department, University of Padova, Padova, Italy.,Audiology Service, Ospedale Santi Giovanni e Paolo, Venezia, Italy
| | - Patrizia Trevisi
- Neurosciences Department, University of Padova, Padova, Italy.,ENT Unit, Azienda Ospedaliera Università di Padova, Padova, Italy
| |
Collapse
|
8
|
Simon AK, Kummer S, Wild S, Lezaja A, Teloni F, Jozwiakowski SK, Altmeyer M, Gari K. The iron-sulfur helicase DDX11 promotes the generation of single-stranded DNA for CHK1 activation. Life Sci Alliance 2020; 3:3/3/e201900547. [PMID: 32071282 PMCID: PMC7032568 DOI: 10.26508/lsa.201900547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
The iron–sulfur cluster helicase DDX11 promotes the generation of ssDNA and the phosphorylation of CHK1 at serine-345, possibly by unwinding replication-dependent DNA secondary structures. The iron–sulfur (FeS) cluster helicase DDX11 is associated with a human disorder termed Warsaw Breakage Syndrome. Interestingly, one disease-associated mutation affects the highly conserved arginine-263 in the FeS cluster-binding motif. Here, we demonstrate that the FeS cluster in DDX11 is required for DNA binding, ATP hydrolysis, and DNA helicase activity, and that arginine-263 affects FeS cluster binding, most likely because of its positive charge. We further show that DDX11 interacts with the replication factors DNA polymerase delta and WDHD1. In vitro, DDX11 can remove DNA obstacles ahead of Pol δ in an ATPase- and FeS domain-dependent manner, and hence generate single-stranded DNA. Accordingly, depletion of DDX11 causes reduced levels of single-stranded DNA, a reduction of chromatin-bound replication protein A, and impaired CHK1 phosphorylation at serine-345. Taken together, we propose that DDX11 plays a role in dismantling secondary structures during DNA replication, thereby promoting CHK1 activation.
Collapse
Affiliation(s)
- Anna K Simon
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Sandra Kummer
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Sebastian Wild
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Aleksandra Lezaja
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Federico Teloni
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | | | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kerstin Gari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| |
Collapse
|
9
|
Pisani FM. Spotlight on Warsaw Breakage Syndrome. APPLICATION OF CLINICAL GENETICS 2019; 12:239-248. [PMID: 31824187 PMCID: PMC6901054 DOI: 10.2147/tacg.s186476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
Abstract
Warsaw breakage syndrome (WABS) is a very rare recessive hereditary disease caused by mutations in the gene coding for the DNA helicase DDX11, involved in genome stability maintenance and sister cohesion establishment. Typical clinical features observed in WABS patients include growth retardation, facial dysmorphia, microcephaly, hearing loss due to cochlear malformations and, at cytological level, sister chromatid cohesion defects. Molecular bases of WABS have not yet been elucidated, due to lack of disease animal model systems and limited knowledge of the DDX11 physiological functions. However, WABS is considered to belong to the group of cohesinopathies, genetic disorders due to mutations of subunits or regulators of cohesin, the protein complex responsible for tethering sister chromatids from the time of their synthesis till they separate in mitosis. Recent evidences suggest that cohesin and its regulators have additional key roles in chromatin organization by promoting the formation of chromatin loops. This “non-canonical” function of cohesin is expected to impact gene transcription during cell differentiation and embryonic development and its dis-regulation, caused by mutation/loss of genes encoding cohesin subunits or regulators, could originate the developmental defects observed in cohesinopathies. Ethiopathogenesis of WABS is discussed in line with these recent findings and evidence of a possible role of DDX11 as a cohesin regulator.
Collapse
Affiliation(s)
- Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples 80131, Italy
| |
Collapse
|
10
|
Rabin R, Hirsch Y, Johansson MM, Ekstein J, Zeevi DA, Keena B, Zackai EH, Pappas J. Study of carrier frequency of Warsaw breakage syndrome in the Ashkenazi Jewish population and presentation of two cases. Am J Med Genet A 2019; 179:2144-2151. [DOI: 10.1002/ajmg.a.61284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/18/2019] [Accepted: 06/23/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Rachel Rabin
- Clinical Genetic Services, Department of PediatricsNYU School of Medicine New York New York
| | - Yoel Hirsch
- Dor Yeshorim, Committee for Prevention Jewish Genetic Diseases Brooklyn New York
| | - Martin M. Johansson
- Dor Yeshorim, Committee for Prevention Jewish Genetic Diseases Brooklyn New York
| | - Joseph Ekstein
- Dor Yeshorim, Committee for Prevention Jewish Genetic Diseases Brooklyn New York
| | - David A. Zeevi
- Dor Yeshorim, Committee for Prevention Jewish Genetic Diseases Jerusalem Israel
| | - Beth Keena
- Division of Human GeneticsChildren's Hospital of Philadelphia Philadelphia Pennsylvania
| | - Elaine H. Zackai
- Division of Human GeneticsChildren's Hospital of Philadelphia Philadelphia Pennsylvania
| | - John Pappas
- Clinical Genetic Services, Department of PediatricsNYU School of Medicine New York New York
- Clinical GeneticsNYU Orthopedic Hospital New York New York
| |
Collapse
|
11
|
Bottega R, Napolitano LMR, Carbone A, Cappelli E, Corsolini F, Onesti S, Savoia A, Gasparini P, Faletra F. Two further patients with Warsaw breakage syndrome. Is a mild phenotype possible? Mol Genet Genomic Med 2019; 7:e639. [PMID: 30924321 PMCID: PMC6503064 DOI: 10.1002/mgg3.639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/15/2019] [Accepted: 02/08/2019] [Indexed: 01/10/2023] Open
Abstract
Background Warsaw Breakage Syndrome (WABS) is an ultra rare cohesinopathy caused by biallelic mutation of DDX11 gene. It is clinically characterized by pre and postnatal growth delay, microcephaly, hearing loss with cochlear hypoplasia, skin color abnormalities, and dysmorphisms. Methods Mutational screening and functional analyses (protein expression and 3D‐modeling) were performed in order to investigate the presence and pathogenicity of DDX11 variant identified in our patients. Results We report the clinical history of two sisters affected by WABS with a pathological mytomicin C test carrying compound heterozygous mutations (c.2507T > C / c.907_920del) of the DDX11 gene. The pathogenicity of this variant was confirmed in the light of a bioinformatic study and protein three‐dimensional modeling, as well as expression analysis. Conclusion These findings further extend the clinical and molecular knowledge about the WABS showing a possible mild phenotype without major malformations or intellectual disability.
Collapse
Affiliation(s)
- Roberta Bottega
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Luisa M R Napolitano
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Anna Carbone
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Fabio Corsolini
- U.O.S.D. Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, "G. Gaslini" Children's Hospital, Genoa, Italy
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste, Italy
| | - Anna Savoia
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.,Department of Medical Science, University of Trieste, Trieste, Italy
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy.,Department of Medical Science, University of Trieste, Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| |
Collapse
|
12
|
Lerner LK, Sale JE. Replication of G Quadruplex DNA. Genes (Basel) 2019; 10:genes10020095. [PMID: 30700033 PMCID: PMC6409989 DOI: 10.3390/genes10020095] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
A cursory look at any textbook image of DNA replication might suggest that the complex machine that is the replisome runs smoothly along the chromosomal DNA. However, many DNA sequences can adopt non-B form secondary structures and these have the potential to impede progression of the replisome. A picture is emerging in which the maintenance of processive DNA replication requires the action of a significant number of additional proteins beyond the core replisome to resolve secondary structures in the DNA template. By ensuring that DNA synthesis remains closely coupled to DNA unwinding by the replicative helicase, these factors prevent impediments to the replisome from causing genetic and epigenetic instability. This review considers the circumstances in which DNA forms secondary structures, the potential responses of the eukaryotic replisome to these impediments in the light of recent advances in our understanding of its structure and operation and the mechanisms cells deploy to remove secondary structure from the DNA. To illustrate the principles involved, we focus on one of the best understood DNA secondary structures, G quadruplexes (G4s), and on the helicases that promote their resolution.
Collapse
Affiliation(s)
- Leticia Koch Lerner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| |
Collapse
|
13
|
Pisani FM, Napolitano E, Napolitano LMR, Onesti S. Molecular and Cellular Functions of the Warsaw Breakage Syndrome DNA Helicase DDX11. Genes (Basel) 2018; 9:genes9110564. [PMID: 30469382 PMCID: PMC6266566 DOI: 10.3390/genes9110564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/17/2018] [Accepted: 11/19/2018] [Indexed: 12/23/2022] Open
Abstract
DDX11/ChlR1 (Chl1 in yeast) is a DNA helicase involved in sister chromatid cohesion and in DNA repair pathways. The protein belongs to the family of the iron–sulphur cluster containing DNA helicases, whose deficiencies have been linked to a number of diseases affecting genome stability. Mutations of human DDX11 are indeed associated with the rare genetic disorder named Warsaw breakage syndrome, showing both chromosomal breakages and chromatid cohesion defects. Moreover, growing evidence of a potential role in oncogenesis further emphasizes the clinical relevance of DDX11. Here, we illustrate the biochemical and structural features of DDX11 and how it cooperates with multiple protein partners in the cell, acting at the interface of DNA replication/repair/recombination and sister chromatid cohesion to preserve genome stability.
Collapse
Affiliation(s)
- Francesca M Pisani
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, 80131 Napoli, Italy.
| | - Ettore Napolitano
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino, 111, 80131 Napoli, Italy.
| | - Luisa M R Napolitano
- Elettra⁻Sincrotrone Trieste S.C.p.A., AREA Science Park Basovizza, 34149 Trieste, Italy.
| | - Silvia Onesti
- Elettra⁻Sincrotrone Trieste S.C.p.A., AREA Science Park Basovizza, 34149 Trieste, Italy.
| |
Collapse
|