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Di Nardo M, Musio A. Cohesin - bridging the gap among gene transcription, genome stability, and human diseases. FEBS Lett 2024. [PMID: 38852996 DOI: 10.1002/1873-3468.14949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024]
Abstract
The intricate landscape of cellular processes governing gene transcription, chromatin organization, and genome stability is a fascinating field of study. A key player in maintaining this delicate equilibrium is the cohesin complex, a molecular machine with multifaceted roles. This review presents an in-depth exploration of these intricate connections and their significant impact on various human diseases.
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Affiliation(s)
- Maddalena Di Nardo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
| | - Antonio Musio
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Pisa, Italy
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2
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Joseph CR, Dusi S, Giannattasio M, Branzei D. Rad51-mediated replication of damaged templates relies on monoSUMOylated DDK kinase. Nat Commun 2022; 13:2480. [PMID: 35513396 PMCID: PMC9072374 DOI: 10.1038/s41467-022-30215-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/21/2022] [Indexed: 12/24/2022] Open
Abstract
DNA damage tolerance (DDT), activated by replication stress during genome replication, is mediated by translesion synthesis and homologous recombination (HR). Here we uncover that DDK kinase, essential for replication initiation, is critical for replication-associated recombination-mediated DDT. DDK relies on its multi-monoSUMOylation to facilitate HR-mediated DDT and optimal retention of Rad51 recombinase at replication damage sites. Impairment of DDK kinase activity, reduced monoSUMOylation and mutations in the putative SUMO Interacting Motifs (SIMs) of Rad51 impair replication-associated recombination and cause fork uncoupling with accumulation of large single-stranded DNA regions at fork branching points. Notably, genetic activation of salvage recombination rescues the uncoupled fork phenotype but not the recombination-dependent gap-filling defect of DDK mutants, revealing that the salvage recombination pathway operates preferentially proximal to fork junctions at stalled replication forks. Overall, we uncover that monoSUMOylated DDK acts with Rad51 in an axis that prevents replication fork uncoupling and mediates recombination-dependent gap-filling.
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Affiliation(s)
- Chinnu Rose Joseph
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Sabrina Dusi
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
| | - Michele Giannattasio
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy
- Università degli Studi di Milano, Dipartimento di Oncologia ed Emato-Oncologia, Via S. Sofia 9/1, 20122, Milano, Italy
| | - Dana Branzei
- IFOM, Istituto Fondazione di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy.
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 27100, Pavia, Italy.
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Saeed M, Ibáñez-Costa A, Patiño-Trives AM, Muñoz-Barrera L, Collantes Estévez E, Aguirre MÁ, López-Pedrera C. Expression of DDX11 and DNM1L at the 12p11 Locus Modulates Systemic Lupus Erythematosus Susceptibility. Int J Mol Sci 2021; 22:ijms22147624. [PMID: 34299244 PMCID: PMC8304828 DOI: 10.3390/ijms22147624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/03/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives: This study employed genetic and functional analyses using OASIS meta-analysis of multiple existing GWAS and gene-expression datasets to identify novel SLE genes. Methods: Four hundred and ten genes were mapped using SNIPPER to 30 SLE GWAS loci and investigated for expression in three SLE GEO-datasets and the Cordoba GSE50395-dataset. Blood eQTL for significant SNPs in SLE loci and STRING for functional pathways of differentially expressed genes were used. Confirmatory qPCR on SLE monocytes was performed. The entire 12p11 locus was investigated for genetic association using two additional GWAS. Expression of 150 genes at this locus was assessed. Based on this significance, qPCRs for DNM1L and KRAS were performed. Results: Fifty genes were differentially expressed in at least two SLE GEO-datasets, with all probes directionally aligned. DDX11, an RNA helicase involved in genome stability, was downregulated in both GEO and Cordoba datasets. The most significant SNP, rs3741869 in OASIS locus 12p11.21, containing DDX11, was a cis-eQTL regulating DDX11 expression. DDX11 was found repressed. The entire 12p11 locus showed three association peaks. Gene expression in GEO datasets identified DNM1L and KRAS, besides DDX11. Confirmatory qPCR validated DNM1L as an SLE susceptibility gene. DDX11, DNM1L and KRAS interact with each other and multiple known SLE genes including STAT1/STAT4 and major components of IFN-dependent gene expression, and are responsible for signal transduction of cytokines, hormones, and growth-factors, deregulation of which is involved in SLE-development. Conclusion: A genomic convergence approach with OASIS analysis of multiple GWAS and expression datasets identified DDX11 and DNM1L as novel SLE-genes, the expression of which is altered in monocytes from SLE patients. This study lays the foundation for understanding the pathogenic involvement of DDX11 and DNM1L in SLE by identifying them using a systems-biology approach, while the 12p11 locus harboring these genes was previously missed by four independent GWAS.
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Affiliation(s)
| | - Alejandro Ibáñez-Costa
- Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain; (A.I.-C.); (A.M.P.-T.); (L.M.-B.); (E.C.E.); (M.Á.A.)
| | - Alejandra María Patiño-Trives
- Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain; (A.I.-C.); (A.M.P.-T.); (L.M.-B.); (E.C.E.); (M.Á.A.)
| | - Laura Muñoz-Barrera
- Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain; (A.I.-C.); (A.M.P.-T.); (L.M.-B.); (E.C.E.); (M.Á.A.)
| | - Eduardo Collantes Estévez
- Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain; (A.I.-C.); (A.M.P.-T.); (L.M.-B.); (E.C.E.); (M.Á.A.)
| | - María Ángeles Aguirre
- Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain; (A.I.-C.); (A.M.P.-T.); (L.M.-B.); (E.C.E.); (M.Á.A.)
| | - Chary López-Pedrera
- Rheumatology Service, Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Reina Sofia Hospital, University of Cordoba, 14004 Cordoba, Spain; (A.I.-C.); (A.M.P.-T.); (L.M.-B.); (E.C.E.); (M.Á.A.)
- Correspondence:
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4
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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.
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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.)
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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.
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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
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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.
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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
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7
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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.
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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.
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8
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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.
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Affiliation(s)
- Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples 80131, Italy
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9
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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
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10
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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.
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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
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11
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Abe T, Branzei D, Hirota K. DNA Damage Tolerance Mechanisms Revealed from the Analysis of Immunoglobulin V Gene Diversification in Avian DT40 Cells. Genes (Basel) 2018; 9:genes9120614. [PMID: 30544644 PMCID: PMC6316486 DOI: 10.3390/genes9120614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/19/2023] Open
Abstract
DNA replication is an essential biochemical reaction in dividing cells that frequently stalls at damaged sites. Homologous/homeologous recombination (HR)-mediated template switch and translesion DNA synthesis (TLS)-mediated bypass processes release arrested DNA replication forks. These mechanisms are pivotal for replication fork maintenance and play critical roles in DNA damage tolerance (DDT) and gap-filling. The avian DT40 B lymphocyte cell line provides an opportunity to examine HR-mediated template switch and TLS triggered by abasic sites by sequencing the constitutively diversifying immunoglobulin light-chain variable gene (IgV). During IgV diversification, activation-induced deaminase (AID) converts dC to dU, which in turn is excised by uracil DNA glycosylase and yields abasic sites within a defined window of around 500 base pairs. These abasic sites can induce gene conversion with a set of homeologous upstream pseudogenes via the HR-mediated template switch, resulting in templated mutagenesis, or can be bypassed directly by TLS, resulting in non-templated somatic hypermutation at dC/dG base pairs. In this review, we discuss recent works unveiling IgV diversification mechanisms in avian DT40 cells, which shed light on DDT mode usage in vertebrate cells and tolerance of abasic sites.
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Affiliation(s)
- Takuya Abe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.
| | - Dana Branzei
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy.
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100 Pavia, Italy.
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan.
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12
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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.
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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.
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13
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Alkhunaizi E, Shaheen R, Bharti SK, Joseph-George AM, Chong K, Abdel-Salam GMH, Alowain M, Blaser SI, Papsin BC, Butt M, Hashem M, Martin N, Godoy R, Brosh RM, Alkuraya FS, Chitayat D. Warsaw breakage syndrome: Further clinical and genetic delineation. Am J Med Genet A 2018; 176:2404-2418. [PMID: 30216658 DOI: 10.1002/ajmg.a.40482] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 01/01/2023]
Abstract
Warsaw breakage syndrome (WBS) is a recently recognized DDX11-related rare cohesinopathy, characterized by severe prenatal and postnatal growth restriction, microcephaly, developmental delay, cochlear anomalies, and sensorineural hearing loss. Only seven cases have been reported in the English literature, and thus the information on the phenotype and genotype of this interesting condition is limited. We provide clinical and molecular information on five additional unrelated patients carrying novel bi-allelic variants in the DDX11 gene, identified via whole exome sequencing. One of the variants was found to be a novel Saudi founder variant. All identified variants were classified as pathogenic or likely pathogenic except for one that was initially classified as a variant of unknown significance (VOUS) (p.Arg378Pro). Functional characterization of this VOUS using heterologous expression of wild type and mutant DDX11 revealed a marked effect on protein stability, thus confirming pathogenicity of this variant. The phenotypic data of the seven WBS reported patients were compared to our patients for further phenotypic delineation. Although all the reported patients had cochlear hypoplasia, one patient also had posterior labyrinthine anomaly. We conclude that while the cardinal clinical features in WBS (microcephaly, growth retardation, and cochlear anomalies) are almost universally present, the breakage phenotype is highly variable and can be absent in some cases. This report further expands the knowledge of the phenotypic and molecular features of WBS.
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Affiliation(s)
- Ebba Alkhunaizi
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sanjay Kumar Bharti
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland
| | - Ann M Joseph-George
- Cytogenomics Laboratory, Division of Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Karen Chong
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Mohammed Alowain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Susan I Blaser
- Division of Neuroradiology, Department of Diagnostic Imaging, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Blake C Papsin
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Mohammed Butt
- Department of Radiology, King Abdulaziz University Hospital, King Saud University, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nicole Martin
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Ruth Godoy
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
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14
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Warsaw breakage syndrome DDX11 helicase acts jointly with RAD17 in the repair of bulky lesions and replication through abasic sites. Proc Natl Acad Sci U S A 2018; 115:8412-8417. [PMID: 30061412 PMCID: PMC6099846 DOI: 10.1073/pnas.1803110115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Warsaw breakage syndrome, a developmental disorder caused by mutations in the conserved DDX11/ChlR1 DNA helicase, shows features of genome instability partly overlapping with those of Fanconi anemia (FA). Here, using avian cellular models of DDX11 deficiency, we find that DDX11 functions as backup to the FA pathway and facilitates, jointly with the checkpoint clamp 9-1-1, a homologous recombination pathway of DNA bulky-lesion repair that does not affect replication fork speed and stalled fork stability. DDX11 also promotes diversification of the immunoglobulin-variable gene locus by facilitating hypermutation and gene conversion at programmed abasic sites that constitute endogenous replication blocks. The results suggest commonality between postreplicative gap filling and replication through abasic sites and pinpoint DDX11 as a critical player in both these processes. Warsaw breakage syndrome, a developmental disorder caused by mutations in the DDX11/ChlR1 helicase, shows cellular features of genome instability similar to Fanconi anemia (FA). Here we report that DDX11-deficient avian DT40 cells exhibit interstrand crosslink (ICL)-induced chromatid breakage, with DDX11 functioning as backup for the FA pathway in regard to ICL repair. Importantly, we establish that DDX11 acts jointly with the 9-1-1 checkpoint clamp and its loader, RAD17, primarily in a postreplicative fashion, to promote homologous recombination repair of bulky lesions, but is not required for intra-S checkpoint activation or efficient fork progression. Notably, we find that DDX11 also promotes diversification of the chicken Ig-variable gene, a process triggered by programmed abasic sites, by facilitating both hypermutation and homeologous recombination-mediated gene conversion. Altogether, our results uncover that DDX11 orchestrates jointly with 9-1-1 and its loader, RAD17, DNA damage tolerance at sites of bulky lesions, and endogenous abasic sites. These functions may explain the essential roles of DDX11 and its similarity with 9-1-1 during development.
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