1
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Tummala H, Walne AJ, Badat M, Patel M, Walne AM, Alnajar J, Chow CC, Albursan I, Frost JM, Ballard D, Killick S, Szitányi P, Kelly AM, Raghavan M, Powell C, Raymakers R, Todd T, Mantadakis E, Polychronopoulou S, Pontikos N, Liao T, Madapura P, Hossain U, Vulliamy T, Dokal I. The evolving genetic landscape of telomere biology disorder dyskeratosis congenita. EMBO Mol Med 2024; 16:2560-2582. [PMID: 39198715 DOI: 10.1038/s44321-024-00118-x] [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: 04/10/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 09/01/2024] Open
Abstract
Dyskeratosis congenita (DC) is a rare inherited bone marrow failure syndrome, caused by genetic mutations that principally affect telomere biology. Approximately 35% of cases remain uncharacterised at the genetic level. To explore the genetic landscape, we conducted genetic studies on a large collection of clinically diagnosed cases of DC as well as cases exhibiting features resembling DC, referred to as 'DC-like' (DCL). This led us to identify several novel pathogenic variants within known genetic loci and in the novel X-linked gene, POLA1. In addition, we have also identified several novel variants in POT1 and ZCCHC8 in multiple cases from different families expanding the allelic series of DC and DCL phenotypes. Functional characterisation of novel POLA1 and POT1 variants, revealed pathogenic effects on protein-protein interactions with primase, CTC1-STN1-TEN1 (CST) and shelterin subunit complexes, that are critical for telomere maintenance. ZCCHC8 variants demonstrated ZCCHC8 deficiency and signs of pervasive transcription, triggering inflammation in patients' blood. In conclusion, our studies expand the current genetic architecture and broaden our understanding of disease mechanisms underlying DC and DCL disorders.
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Affiliation(s)
- Hemanth Tummala
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK.
- Barts Health NHS Trust, London, UK.
| | - Amanda J Walne
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Mohsin Badat
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
| | - Manthan Patel
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Abigail M Walne
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Jenna Alnajar
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Chi Ching Chow
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Ibtehal Albursan
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Jennifer M Frost
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - David Ballard
- Department of Analytical, Environmental & Forensic Sciences, Kings College London, Franklin-Wilkins Building, Stamford Street, London, SE1 9NH, UK
| | - Sally Killick
- Department of Haematology, Royal Bournemouth Hospital NHS Foundation Trust, Bournemouth, BH7 7DW, UK
| | - Peter Szitányi
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 2, 128 08 Praha 2, Prague, Czech Republic
| | - Anne M Kelly
- Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Manoj Raghavan
- Clinical Haematology, Queen Elizabeth Hospital, Edgbaston, Birmingham, B15 2TH, UK
| | - Corrina Powell
- Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, B15 2TG, UK
| | - Reinier Raymakers
- University Medical Center Utrecht, 3508 GA, Utrecht, The Netherlands
| | - Tony Todd
- Department of Haematology, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
| | - Elpis Mantadakis
- Department of Pediatrics' University General Hospital of Alexandroupolis, Democritus University of Thrace Faculty of Medicine, 6th Kilometer Alexandroupolis-Makris, 68 100 Alexandroupolis, Thrace, Greece
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology-Oncology, Aghia Sophia Children's Hospital, Athens, Greece
| | - Nikolas Pontikos
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, Gower St, London, WC1E 6BT, UK
| | - Tianyi Liao
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Pradeep Madapura
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Upal Hossain
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
| | - Tom Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
| | - Inderjeet Dokal
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, Newark Street, London, E12AT, UK
- Barts Health NHS Trust, London, UK
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2
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Morimoto M, Ryu E, Steger BJ, Dixit A, Saito Y, Yoo J, van der Ven AT, Hauser N, Steinbach PJ, Oura K, Huang AY, Kortüm F, Ninomiya S, Rosenthal EA, Robinson HK, Guegan K, Denecke J, Subramony SH, Diamonstein CJ, Ping J, Fenner M, Balton EV, Strohbehn S, Allworth A, Bamshad MJ, Gandhi M, Dipple KM, Blue EE, Jarvik GP, Lau CC, Holm IA, Weisz-Hubshman M, Solomon BD, Nelson SF, Nishino I, Adams DR, Kang S, Gahl WA, Toro C, Myung K, Malicdan MCV. Expanding the genetic and phenotypic landscape of replication factor C complex-related disorders: RFC4 deficiency is linked to a multisystemic disorder. Am J Hum Genet 2024; 111:1970-1993. [PMID: 39106866 PMCID: PMC11393705 DOI: 10.1016/j.ajhg.2024.07.008] [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: 11/20/2023] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 08/09/2024] Open
Abstract
The precise regulation of DNA replication is vital for cellular division and genomic integrity. Central to this process is the replication factor C (RFC) complex, encompassing five subunits, which loads proliferating cell nuclear antigen onto DNA to facilitate the recruitment of replication and repair proteins and enhance DNA polymerase processivity. While RFC1's role in cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) is known, the contributions of RFC2-5 subunits on human Mendelian disorders is largely unexplored. Our research links bi-allelic variants in RFC4, encoding a core RFC complex subunit, to an undiagnosed disorder characterized by incoordination and muscle weakness, hearing impairment, and decreased body weight. We discovered across nine affected individuals rare, conserved, predicted pathogenic variants in RFC4, all likely to disrupt the C-terminal domain indispensable for RFC complex formation. Analysis of a previously determined cryo-EM structure of RFC bound to proliferating cell nuclear antigen suggested that the variants disrupt interactions within RFC4 and/or destabilize the RFC complex. Cellular studies using RFC4-deficient HeLa cells and primary fibroblasts demonstrated decreased RFC4 protein, compromised stability of the other RFC complex subunits, and perturbed RFC complex formation. Additionally, functional studies of the RFC4 variants affirmed diminished RFC complex formation, and cell cycle studies suggested perturbation of DNA replication and cell cycle progression. Our integrated approach of combining in silico, structural, cellular, and functional analyses establishes compelling evidence that bi-allelic loss-of-function RFC4 variants contribute to the pathogenesis of this multisystemic disorder. These insights broaden our understanding of the RFC complex and its role in human health and disease.
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Affiliation(s)
- Marie Morimoto
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eunjin Ryu
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Benjamin J Steger
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yoshihiko Saito
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Juyeong Yoo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Amelie T van der Ven
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Natalie Hauser
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Peter J Steinbach
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kazumasa Oura
- Division of Neurology and Gerontology, Department of Internal Medicine, School of Medicine Iwate Medical University, Morioka, Japan
| | - Alden Y Huang
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shinsuke Ninomiya
- Department of Clinical Genetics, Kurashiki Central Hospital, Okayama, Japan
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hannah K Robinson
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Katie Guegan
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Callie J Diamonstein
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mark Fenner
- Nottingham University Hospital, Nottingham, UK
| | - Elsa V Balton
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sam Strohbehn
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Aimee Allworth
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Mahi Gandhi
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Katrina M Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; University of Washington School of Public Health, Institute for Public Health Genetics, Seattle, WA, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - C Christopher Lau
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benjamin D Solomon
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Stanley F Nelson
- Institute for Precision Health, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - David R Adams
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - William A Gahl
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea; Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - May Christine V Malicdan
- National Institutes of Health Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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3
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Chee CW, Mohd Hashim N, Abdullah I, Nor Rashid N. RNA Sequencing and Bioinformatics Analysis Reveals the Downregulation of DNA Replication Genes by Morindone in Colorectal Cancer Cells. Appl Biochem Biotechnol 2024; 196:3216-3233. [PMID: 37642925 DOI: 10.1007/s12010-023-04690-9] [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] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Morindone, a natural anthraquinone compound, has been reported to have significant pharmacological properties in different cancers. However, its anticancer effects in colorectal cancer (CRC) and the underlying molecular mechanisms remain obscure. In this study, RNA sequencing was used to assess the differentially expressed genes (DEGs) following morindone treatment in two CRC cell lines, HCT116 and HT29 cells. Functional enrichment analysis of overlapping DEGs revealed that negative regulation of cell development from biological processes and the MAPK signalling pathway were the most significant Gene Ontology terms and Kyoto Encyclopaedia of Genes and Genome pathway, respectively. Seven hub genes were identified among the overlapping genes, including MCM5, MCM6, MCM10, GINS2, POLE2, PRIM1, and WDHD1. All hub genes were found downregulated and involved in DNA replication fork. Among these, GINS2 was identified as the most cancer-dependent gene in both cells with better survival outcomes. Validation was performed on seven hub genes with rt-qPCR, and the results were consistent with the RNA sequencing findings. Collectively, this study provides corroboration of the potential therapeutic benefits and suitable pharmacological targets of morindone in the treatment of CRC.
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Affiliation(s)
- Cheok Wui Chee
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Najihah Mohd Hashim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Centre for Natural Products Research and Drug Discovery, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Iskandar Abdullah
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nurshamimi Nor Rashid
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Centre for Natural Products Research and Drug Discovery, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
- Drug Design and Development Research Group, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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4
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Toskov V, Kaiser-Labusch P, Lee-Kirsch MA, Ehl S, Wegehaupt O. Variable Syndromic Immunodeficiency in Patients with Biallelic PRIM1 Mutations. J Clin Immunol 2024; 44:129. [PMID: 38773012 PMCID: PMC11108906 DOI: 10.1007/s10875-024-01733-6] [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: 12/20/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
Mutations in genes of the DNA polymerase complex have been linked to impaired immunological function next to distinct syndromic features. Biallelic mutations in PRIM1 are associated with a primordial dwarfism syndrome with variable hypogammaglobulinemia. The disease is mostly lethal in infancy due to pulmonary infections as well as hepatic cirrhosis. We studied 3 novel patients with PRIM1-deficiency with a focus on immunological consequences. All three shared dysmorphic features including a prominent forehead, triangular face and bilateral cryptorchidism. P1 carried the novel homozygous PRIM1 splice variant c.103+2T>G, allowing residual protein expression and associated with a mild clinical phenotype. P2 and P3 carried the known homozygous variant c.638+36C>G and died in infancy. Paradoxically, B cell lymphopenia was most pronounced in P1. No other significant lymphocyte abnormalities were detected. Interestingly, all 3 patients showed variable, but intermittently excessive Type I interferon signatures. In summary, the B-cell deficiency in PRIM1-deficiency is markedly variable and the severity of syndromic manifestations is not predictive of the immunological phenotype. We highlight a potential contribution of pathological type I interferon activation to disease pathogenesis which warrants further investigations.
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Affiliation(s)
- Vasil Toskov
- Clinic of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Petra Kaiser-Labusch
- Prof. Hess Children's Hospital, Klinikum Bremen-Mitte, Gesundheit Nord gGmbH, Bremen, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacher Str. 115, 79106, Freiburg, Germany.
| | - Oliver Wegehaupt
- Clinic of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacher Str. 115, 79106, Freiburg, Germany.
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5
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [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: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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6
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Lim Y, Tamayo-Orrego L, Schmid E, Tarnauskaite Z, Kochenova OV, Gruar R, Muramatsu S, Lynch L, Schlie AV, Carroll PL, Chistol G, Reijns MAM, Kanemaki MT, Jackson AP, Walter JC. In silico protein interaction screening uncovers DONSON's role in replication initiation. Science 2023; 381:eadi3448. [PMID: 37590370 PMCID: PMC10801813 DOI: 10.1126/science.adi3448] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
CDC45-MCM2-7-GINS (CMG) helicase assembly is the central event in eukaryotic replication initiation. In yeast, a multi-subunit "pre-loading complex" (pre-LC) accompanies GINS to chromatin-bound MCM2-7, leading to CMG formation. Here, we report that DONSON, a metazoan protein mutated in microcephalic primordial dwarfism, is required for CMG assembly in vertebrates. Using AlphaFold to screen for protein-protein interactions followed by experimental validation, we show that DONSON scaffolds a vertebrate pre-LC containing GINS, TOPBP1, and DNA pol ε. Our evidence suggests that DONSON docks the pre-LC onto MCM2-7, delivering GINS to its binding site in CMG. A patient-derived DONSON mutation compromises CMG assembly and recapitulates microcephalic dwarfism in mice. These results unify our understanding of eukaryotic replication initiation, implicate defective CMG assembly in microcephalic dwarfism, and illustrate how in silico protein-protein interaction screening accelerates mechanistic discovery.
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Affiliation(s)
- Yang Lim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
| | - Lukas Tamayo-Orrego
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Ernst Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
| | - Zygimante Tarnauskaite
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Olga V. Kochenova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Rhian Gruar
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
| | - Sachiko Muramatsu
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS); Mishima, Shizuoka 411-8540, Japan
| | - Luke Lynch
- Biochemistry Department, Stanford School of Medicine; Stanford, CA 94305, USA
| | - Aitana Verdu Schlie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Paula L. Carroll
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Gheorghe Chistol
- Chemical and Systems Biology Department, Stanford School of Medicine; Stanford, CA 94305, USA
| | - Martin A. M. Reijns
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Masato T. Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS); Mishima, Shizuoka 411-8540, Japan
- Graduate Institute for Advanced Studies, SOKENDAI; Mishima, Shizuoka 411-8540, Japan
- Department of Biological Science, The University of Tokyo; Tokyo 113-0033, Japan
| | - Andrew P. Jackson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh; Edinburgh, EH4 2XU, UK
| | - Johannes C. Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute; Boston, MA 02115, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
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7
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Willemsen M, Barber JS, Nieuwenhove EV, Staels F, Gerbaux M, Neumann J, Prezzemolo T, Pasciuto E, Lagou V, Boeckx N, Filtjens J, De Visscher A, Matthys P, Schrijvers R, Tousseyn T, O'Driscoll M, Bucciol G, Schlenner S, Meyts I, Humblet-Baron S, Liston A. Homozygous DBF4 mutation as a cause of severe congenital neutropenia. J Allergy Clin Immunol 2023; 152:266-277. [PMID: 36841265 DOI: 10.1016/j.jaci.2023.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND Severe congenital neutropenia presents with recurrent infections early in life as a result of arrested granulopoiesis. Multiple genetic defects are known to block granulocyte differentiation; however, a genetic cause remains unknown in approximately 40% of cases. OBJECTIVE We aimed to characterize a patient with severe congenital neutropenia and syndromic features without a genetic diagnosis. METHODS Whole exome sequencing results were validated using flow cytometry, Western blotting, coimmunoprecipitation, quantitative PCR, cell cycle and proliferation analysis of lymphocytes and fibroblasts and granulocytic differentiation of primary CD34+ and HL-60 cells. RESULTS We identified a homozygous missense mutation in DBF4 in a patient with mild extra-uterine growth retardation, facial dysmorphism and severe congenital neutropenia. DBF4 is the regulatory subunit of the CDC7 kinase, together known as DBF4-dependent kinase (DDK), the complex essential for DNA replication initiation. The DBF4 variant demonstrated impaired ability to bind CDC7, resulting in decreased DDK-mediated phosphorylation, defective S-phase entry and progression and impaired differentiation of granulocytes associated with activation of the p53-p21 pathway. The introduction of wild-type DBF4 into patient CD34+ cells rescued the promyelocyte differentiation arrest. CONCLUSION Hypomorphic DBF4 mutation causes autosomal-recessive severe congenital neutropenia with syndromic features.
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Affiliation(s)
- Mathijs Willemsen
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - John S Barber
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Erika Van Nieuwenhove
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Frederik Staels
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Margaux Gerbaux
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julika Neumann
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Teresa Prezzemolo
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Emanuela Pasciuto
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Vasiliki Lagou
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Nancy Boeckx
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Jessica Filtjens
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuve, Belgium
| | - Amber De Visscher
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuve, Belgium
| | - Patrick Matthys
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuve, Belgium
| | - Rik Schrijvers
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Giorgia Bucciol
- Department of Microbiology, Immunology, and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven
| | - Susan Schlenner
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Microbiology, Immunology, and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven.
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.
| | - Adrian Liston
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
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8
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Yamaguchi M, Cotterill S. Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies. Int J Mol Sci 2023; 24:ijms24098078. [PMID: 37175782 PMCID: PMC10178534 DOI: 10.3390/ijms24098078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Replicative DNA polymerases, such as DNA polymerase α-primase, δ and ε, are multi-subunit complexes that are responsible for the bulk of nuclear DNA replication during the S phase. Over the last decade, extensive genome-wide association studies and expression profiling studies of the replicative DNA polymerase genes in human patients have revealed a link between the replicative DNA polymerase genes and various human diseases and disorders including cancer, intellectual disability, microcephalic primordial dwarfism and immunodeficiency. These studies suggest the importance of dissecting the mechanisms involved in the functioning of replicative DNA polymerases in understanding and treating a range of human diseases. Previous studies in Drosophila have established this organism as a useful model to understand a variety of human diseases. Here, we review the studies on Drosophila that explored the link between DNA polymerases and human disease. First, we summarize the recent studies linking replicative DNA polymerases to various human diseases and disorders. We then review studies on replicative DNA polymerases in Drosophila. Finally, we suggest the possible use of Drosophila models to study human diseases and disorders associated with replicative DNA polymerases.
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Affiliation(s)
| | - Sue Cotterill
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
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9
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley T, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532415. [PMID: 36993543 PMCID: PMC10054921 DOI: 10.1101/2023.03.13.532415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Genetic information is duplicated via the highly regulated process of DNA replication. The machinery coordinating this process, the replisome, encounters many challenges, including replication fork-stalling lesions that threaten the accurate and timely transmission of genetic information. Cells have multiple mechanisms to repair or bypass lesions that would otherwise compromise DNA replication1,2. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2) function to regulate Replication Termination Factor 2 (RTF2) at the stalled replisome, allowing for replication fork stabilization and restart3. Here we show that RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme responsible for removing RNA in the context of RNA-DNA heteroduplexes4-6. We show that during unperturbed DNA replication, RTF2, like RNase H2, is required to maintain normal replication fork speeds. However, persistent RTF2 and RNase H2 at stalled replication forks compromises the replication stress response, preventing efficient replication restart. Such restart is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for regulation of replication-coupled ribonucleotide incorporation during normal replication and the replication stress response that is achieved through RTF2. We also provide evidence for PRIM1 function in direct replication restart following replication stress in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University
| | | | | | | | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Tom Wiley
- Laboratory of Genome Maintenance, The Rockefeller University
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University
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10
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Willemsen M, Staels F, Gerbaux M, Neumann J, Schrijvers R, Meyts I, Humblet-Baron S, Liston A. DNA replication-associated inborn errors of immunity. J Allergy Clin Immunol 2023; 151:345-360. [PMID: 36395985 DOI: 10.1016/j.jaci.2022.11.003] [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: 09/13/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Inborn errors of immunity are a heterogeneous group of monogenic immunologic disorders caused by mutations in genes with critical roles in the development, maintenance, or function of the immune system. The genetic basis is frequently a mutation in a gene with restricted expression and/or function in immune cells, leading to an immune disorder. Several classes of inborn errors of immunity, however, result from mutation in genes that are ubiquitously expressed. Despite the genes participating in cellular processes conserved between cell types, immune cells are disproportionally affected, leading to inborn errors of immunity. Mutations in DNA replication, DNA repair, or DNA damage response factors can result in monogenic human disease, some of which are classified as inborn errors of immunity. Genetic defects in the DNA repair machinery are a well-known cause of T-B-NK+ severe combined immunodeficiency. An emerging class of inborn errors of immunity is those caused by mutations in DNA replication factors. Considerable heterogeneity exists within the DNA replication-associated inborn errors of immunity, with diverse immunologic defects and clinical manifestations observed. These differences are suggestive for differential sensitivity of certain leukocyte subsets to deficiencies in specific DNA replication factors. Here, we provide an overview of DNA replication-associated inborn errors of immunity and discuss the emerging mechanistic insights that can explain the observed immunologic heterogeneity.
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Affiliation(s)
- Mathijs Willemsen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.
| | - Frederik Staels
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Margaux Gerbaux
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julika Neumann
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Rik Schrijvers
- Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven, Belgium; ERN-RITA Core Center Member, Leuven, Belgium
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.
| | - Adrian Liston
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge.
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11
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Hocking LJ, Andrews C, Armstrong C, Ansari M, Baty D, Berg J, Bradley T, Clark C, Diamond A, Doherty J, Lampe A, McGowan R, Moore DJ, O'Sullivan D, Purvis A, Santoyo-Lopez J, Westwood P, Abbott M, Williams N, Aitman TJ, Miedzybrodzka Z, Humphrey WI, Martin S, Meynert A, Murphy F, Nourse C, Semple CA, Williams N, Dean J, Foley P, Robertson L, Ross A, Williamson K, Berg J, Goudie D, McWilliam C, Fitzpatrick D, Fletcher E, Jackson A, Lam W, Porteous M, Barr K, Bradshaw N, Davidson R, Gardiner C, Gorrie J, Hague R, Hamilton M, Joss S, Kinning E, Longman C, Martin N, McGowan R, Paterson J, Pilz D, Snadden L, Tobias E, Wedderburn S, Whiteford M, Aitman TJ, Miedzybrodzka Z. Genome sequencing with gene panel-based analysis for rare inherited conditions in a publicly funded healthcare system: implications for future testing. Eur J Hum Genet 2023; 31:231-238. [PMID: 36474026 PMCID: PMC9905562 DOI: 10.1038/s41431-022-01226-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/14/2022] [Accepted: 10/25/2022] [Indexed: 12/12/2022] Open
Abstract
NHS genetics centres in Scotland sought to investigate the Genomics England 100,000 Genomes Project diagnostic utility to evaluate genome sequencing for in rare, inherited conditions. Four regional services recruited 999 individuals from 394 families in 200 rare phenotype categories, with negative historic genetic testing. Genome sequencing was performed at Edinburgh Genomics, and phenotype and sequence data were transferred to Genomics England for variant calling, gene-based filtering and variant prioritisation. NHS Scotland genetics laboratories performed interpretation, validation and reporting. New diagnoses were made in 23% cases - 19% in genes implicated in disease at the time of variant prioritisation, and 4% from later review of additional genes. Diagnostic yield varied considerably between phenotype categories and was minimal in cases with prior exome testing. Genome sequencing with gene panel filtering and reporting achieved improved diagnostic yield over previous historic testing but not over now routine trio-exome sequence tests. Re-interpretation of genomic data with updated gene panels modestly improved diagnostic yield at minimal cost. However, to justify the additional costs of genome vs exome sequencing, efficient methods for analysis of structural variation will be required and / or cost of genome analysis and storage will need to decrease.
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Affiliation(s)
- Lynne J Hocking
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK
| | - Claire Andrews
- East of Scotland Regional Genetics Service, NHS Tayside, Ninewells Hospital, Dundee, Scotland, UK
| | - Christine Armstrong
- North of Scotland Medical Genetic Service, NHS Grampian, Polwarth Building, Foresterhill, Aberdeen, Scotland, UK
| | - Morad Ansari
- South East Scotland Genetic Service, NHS Lothian, Western General Hospital, Edinburgh, Scotland, UK
| | - David Baty
- East of Scotland Regional Genetics Service, NHS Tayside, Ninewells Hospital, Dundee, Scotland, UK
| | - Jonathan Berg
- East of Scotland Regional Genetics Service, NHS Tayside, Ninewells Hospital, Dundee, Scotland, UK.,School of Medicine, University of Dundee, Dundee, Scotland, UK
| | - Therese Bradley
- West of Scotland Centre for Genomic Medicine, NHS Greater Glasgow & Clyde, Queen Elizabeth University Hospital, Glasgow, Scotland, UK
| | - Caroline Clark
- North of Scotland Medical Genetic Service, NHS Grampian, Polwarth Building, Foresterhill, Aberdeen, Scotland, UK
| | - Austin Diamond
- South East Scotland Genetic Service, NHS Lothian, Western General Hospital, Edinburgh, Scotland, UK
| | - Jill Doherty
- West of Scotland Centre for Genomic Medicine, NHS Greater Glasgow & Clyde, Queen Elizabeth University Hospital, Glasgow, Scotland, UK
| | - Anne Lampe
- South East Scotland Genetic Service, NHS Lothian, Western General Hospital, Edinburgh, Scotland, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, NHS Greater Glasgow & Clyde, Queen Elizabeth University Hospital, Glasgow, Scotland, UK.,School of Medicine, Dentistry & Nursing, University of Glasgow, Glasgow, Scotland, UK
| | - David J Moore
- South East Scotland Genetic Service, NHS Lothian, Western General Hospital, Edinburgh, Scotland, UK
| | - Dawn O'Sullivan
- North of Scotland Medical Genetic Service, NHS Grampian, Polwarth Building, Foresterhill, Aberdeen, Scotland, UK
| | - Andrew Purvis
- West of Scotland Centre for Genomic Medicine, NHS Greater Glasgow & Clyde, Queen Elizabeth University Hospital, Glasgow, Scotland, UK
| | | | - Paul Westwood
- West of Scotland Centre for Genomic Medicine, NHS Greater Glasgow & Clyde, Queen Elizabeth University Hospital, Glasgow, Scotland, UK
| | - Michael Abbott
- Health Economics Research Unit, University of Aberdeen, Aberdeen, Scotland, UK
| | - Nicola Williams
- West of Scotland Centre for Genomic Medicine, NHS Greater Glasgow & Clyde, Queen Elizabeth University Hospital, Glasgow, Scotland, UK
| | | | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland, UK.
| | - Zosia Miedzybrodzka
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK. .,North of Scotland Medical Genetic Service, NHS Grampian, Polwarth Building, Foresterhill, Aberdeen, Scotland, UK. .,North of Scotland Regional Genetic Service, NHS Grampian, Ashgrove House, Foresterhill, Aberdeen, Scotland, UK.
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12
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Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res 2023; 323:199016. [PMID: 36473671 PMCID: PMC9721189 DOI: 10.1016/j.virusres.2022.199016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it. METHODS In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different. RESULTS Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively. CONCLUSION According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.
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Affiliation(s)
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mahsa Mousakhan Bakhtiari
- Pediatric Cell Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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13
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Chun S, Akle S, Teodosiadis A, Cade BE, Wang H, Sofer T, Evans DS, Stone KL, Gharib SA, Mukherjee S, Palmer LJ, Hillman D, Rotter JI, Hanis CL, Stamatoyannopoulos JA, Redline S, Cotsapas C, Sunyaev SR. Leveraging pleiotropy to discover and interpret GWAS results for sleep-associated traits. PLoS Genet 2022; 18:e1010557. [PMID: 36574455 PMCID: PMC9829185 DOI: 10.1371/journal.pgen.1010557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/09/2023] [Accepted: 12/06/2022] [Indexed: 12/28/2022] Open
Abstract
Genetic association studies of many heritable traits resulting from physiological testing often have modest sample sizes due to the cost and burden of the required phenotyping. This reduces statistical power and limits discovery of multiple genetic associations. We present a strategy to leverage pleiotropy between traits to both discover new loci and to provide mechanistic hypotheses of the underlying pathophysiology. Specifically, we combine a colocalization test with a locus-level test of pleiotropy. In simulations, we show that this approach is highly selective for identifying true pleiotropy driven by the same causative variant, thereby improves the chance to replicate the associations in underpowered validation cohorts and leads to higher interpretability. Here, as an exemplar, we use Obstructive Sleep Apnea (OSA), a common disorder diagnosed using overnight multi-channel physiological testing. We leverage pleiotropy with relevant cellular and cardio-metabolic phenotypes and gene expression traits to map new risk loci in an underpowered OSA GWAS. We identify several pleiotropic loci harboring suggestive associations to OSA and genome-wide significant associations to other traits, and show that their OSA association replicates in independent cohorts of diverse ancestries. By investigating pleiotropic loci, our strategy allows proposing new hypotheses about OSA pathobiology across many physiological layers. For example, we identify and replicate the pleiotropy across the plateletcrit, OSA and an eQTL of DNA primase subunit 1 (PRIM1) in immune cells. We find suggestive links between OSA, a measure of lung function (FEV1/FVC), and an eQTL of matrix metallopeptidase 15 (MMP15) in lung tissue. We also link a previously known genome-wide significant peak for OSA in the hexokinase 1 (HK1) locus to hematocrit and other red blood cell related traits. Thus, the analysis of pleiotropic associations has the potential to assemble diverse phenotypes into a chain of mechanistic hypotheses that provide insight into the pathogenesis of complex human diseases.
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Affiliation(s)
- Sung Chun
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sebastian Akle
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Katie L. Stone
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Sina A. Gharib
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, Washington, United States of America
- Computational Medicine Core at Center for Lung Biology, University of Washington, Seattle, Washington, United States of America
| | - Sutapa Mukherjee
- Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
- Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia, Australia
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - David Hillman
- Centre for Sleep Science, University of Western Australia, Perth, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, Australia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Craig L. Hanis
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - John A. Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Chris Cotsapas
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
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Begemann A, Oneda B, Baumer A, Guldimann M, Tutschek B, Rauch A. A Xp22.11-p21.3 microdeletion in a three-generation family supports male lethality of POLA1 nullisomy resulting in reduced fertility of female carriers. Eur J Med Genet 2022; 65:104628. [PMID: 36182037 DOI: 10.1016/j.ejmg.2022.104628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/19/2022] [Accepted: 09/25/2022] [Indexed: 11/03/2022]
Abstract
POLA1 encodes a subunit of the DNA polymerase alpha, a key enzyme for the initiation of DNA synthesis. In males, hemizygous hypomorphic variants in POLA1 have been identified as the cause of X-linked pigmentary reticulate disorder (XLPDR) and a novel X-linked neurodevelopmental disorder termed Van Esch-O'Driscoll syndrome (VEODS), while female carriers have been reported to be healthy. Nullisomy for POLA1 was speculated to be lethal due to its crucial function, while the effect of loss of one allele in females remained unknown. Here, we report on a three-generation family harboring a deletion of POLA1 in females showing subfertility as the only phenotype. Our findings show that heterozygous deletions or truncating variants in females with skewed X inactivation do not cause VEODS and support the hypothesis of very early embryonic lethality in males with POLA1 nullisomy.
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Affiliation(s)
- Anaïs Begemann
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Beatrice Oneda
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Alessandra Baumer
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Marina Guldimann
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Boris Tutschek
- Prenatal Zürich, Zurich, Switzerland; Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Anita Rauch
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland; University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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15
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Salami Ghaleh S, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Mollapour Sisakht M, Farhadi A, Mousakhan Bakhtiari M, Lee Kuehu D, Deng Y. SARS-CoV-2 Non-Structural Protein 1(NSP1) Mutation Virulence and Natural Selection: Evolutionary Trends in the Six Continents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.22.501212. [PMID: 35923310 PMCID: PMC9347281 DOI: 10.1101/2022.07.22.501212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unsegmented positivesense single-stranded RNA virus that belongs to the β-coronavirus . This virus was the cause of a novel severe acute respiratory syndrome in 2019 (COVID-19) that emerged in Wuhan, China at the early stage of the pandemic and rapidly spread around the world. Rapid transmission and reproduction of SARS-CoV-2 threaten worldwide health with a high mortality rate from the virus. According to the significant role of non-structural protein 1 (NSP1) in inhibiting host mRNA translation, this study focuses on the link between amino acid sequences of NSP1 and alterations of them spreading around the world. The SARS-CoV-2 NSP1 protein sequences were analyzed and FASTA files were processed by Python language programming libraries. Reference sequences compared with each NSP1 sample to identify every mutation and categorize them were based on continents and frequencies. NSP1 mutations rate divided into continents were different. Based on continental studies, E87D in global vision and also in Europe notably increased. The E87D mutation has significantly risen especially in the last months of the study as the first frequent mutation observed. The remarkable mutations, H110Y and R24C, have the second and third frequencies, respectively. Based on this mutational information, despite NSP1 being a conserved sequence occurrence, these mutations change the rate of flexibility and stability of the NSP1 protein, which can eventually affect inhibiting the host translation. IMPORTANCE In this study, we analyzed 6,510,947 sequences of non-structural protein 1 as a conserved region of SARS-CoV-2. According to the obtained results, 93.4819% of samples had no mutant regions on their amino acid sequences. Heat map data of mutational samples demonstrated high percentages of mutations that occurred in the region of 72 to 126 amino acids indicating a hot spot region of the protein. Increased rates of E87D, H110Y, and R24C mutations in the timeline of our study were reported as significant compared to available mutant samples. Analyzing the details of replacing amino acids in the most frequent E87D mutation reveals the role of this alteration in increasing molecule flexibility and destabilizing the structure of the protein.
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16
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Kilkenny ML, Veale CE, Guppy A, Hardwick SW, Chirgadze DY, Rzechorzek NJ, Maman JD, Pellegrini L. Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase α-primase. Protein Sci 2022; 31:333-344. [PMID: 34719824 PMCID: PMC8661717 DOI: 10.1002/pro.4220] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/21/2022]
Abstract
The molecular mechanisms that drive the infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the causative agent of coronavirus disease 2019 (COVID-19)-are under intense current scrutiny to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated. Recent proteomic screens of the interactions between viral and host proteins have identified the human proteins targeted by SARS-CoV-2. The DNA polymerase α (Pol α)-primase complex or primosome-responsible for initiating DNA synthesis during genomic duplication-was identified as a target of nonstructural protein 1 (nsp1), a major virulence factor in the SARS-CoV-2 infection. Here, we validate the published reports of the interaction of nsp1 with the primosome by demonstrating direct binding with purified recombinant components and providing a biochemical characterization of their interaction. Furthermore, we provide a structural basis for the interaction by elucidating the cryo-electron microscopy structure of nsp1 bound to the primosome. Our findings provide biochemical evidence for the reported targeting of Pol α by the virulence factor nsp1 and suggest that SARS-CoV-2 interferes with Pol α's putative role in the immune response during the viral infection.
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Affiliation(s)
| | | | - Amir Guppy
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
| | | | | | - Neil J. Rzechorzek
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
- Present address:
The Francis Crick InstituteLondonNW1 1ATUK
| | - Joseph D. Maman
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
| | - Luca Pellegrini
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
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17
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Bainbridge LJ, Teague R, Doherty AJ. Repriming DNA synthesis: an intrinsic restart pathway that maintains efficient genome replication. Nucleic Acids Res 2021; 49:4831-4847. [PMID: 33744934 PMCID: PMC8136793 DOI: 10.1093/nar/gkab176] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
To bypass a diverse range of fork stalling impediments encountered during genome replication, cells possess a variety of DNA damage tolerance (DDT) mechanisms including translesion synthesis, template switching, and fork reversal. These pathways function to bypass obstacles and allow efficient DNA synthesis to be maintained. In addition, lagging strand obstacles can also be circumvented by downstream priming during Okazaki fragment generation, leaving gaps to be filled post-replication. Whether repriming occurs on the leading strand has been intensely debated over the past half-century. Early studies indicated that both DNA strands were synthesised discontinuously. Although later studies suggested that leading strand synthesis was continuous, leading to the preferred semi-discontinuous replication model. However, more recently it has been established that replicative primases can perform leading strand repriming in prokaryotes. An analogous fork restart mechanism has also been identified in most eukaryotes, which possess a specialist primase called PrimPol that conducts repriming downstream of stalling lesions and structures. PrimPol also plays a more general role in maintaining efficient fork progression. Here, we review and discuss the historical evidence and recent discoveries that substantiate repriming as an intrinsic replication restart pathway for maintaining efficient genome duplication across all domains of life.
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Affiliation(s)
- Lewis J Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Rebecca Teague
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
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18
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A patient with POLA1 splice variant expands the yet evolving phenotype of Van Esch O'Driscoll syndrome. Eur J Med Genet 2021; 64:104261. [PMID: 34119699 DOI: 10.1016/j.ejmg.2021.104261] [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: 02/07/2021] [Revised: 05/24/2021] [Accepted: 06/08/2021] [Indexed: 11/23/2022]
Abstract
Van Esch-O'Driscoll syndrome (VEODS) is a rare cause of syndromic X-linked intellectual disability characterised by short stature, microcephaly, variable degree of intellectual disability, and hypogonadotropic hypogonadism. To date, heterozygous hypomorphic variants in the gene encoding the DNA Polymerase α subunit, POLA1, have been observed in nine patients from five unrelated families with VEODS. We report a three-year-old child with VEODS having borderline intellectual disability due to a novel splice site variant causing exon 6 skipping and reduced POLA1 expression.
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19
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Zhu M, Wu M, Bian S, Song Q, Xiao M, Huang H, You L, Zhang J, Zhang J, Cheng C, Ni W, Zheng W. DNA primase subunit 1 deteriorated progression of hepatocellular carcinoma by activating AKT/mTOR signaling and UBE2C-mediated P53 ubiquitination. Cell Biosci 2021; 11:42. [PMID: 33622397 PMCID: PMC7903777 DOI: 10.1186/s13578-021-00555-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Background DNA primase subunit 1 (PRIM1) has been reported as a novel oncogene in several cancer types. However, its roles in hepatocellular carcinoma (HCC) remain unclear. This study aimed to investigate underlying mechanisms of PRIM1 and identify it as a potential molecular target for HCC. Methods Hub genes were screened between HCC tissues and normal liver tissues in 3 gene expression omnibus (GEO) datasets and the cancer genome atlas (TCGA). The expression features and prognostic value of one of the hub genes PRIM1 were analyzed by bioinformatic analyses and immunohistochemistry. Loss-of-function and gain-of-function studies were used to investigate the regulatory role of PRIM1 in HCC cells. Real-time (RT)-qPCR, western blotting, and ubiquitin immunoprecipitation assays were performed to explore the underlying mechanisms. The xenograft model was employed to detect the roles of PRIM1 in tumor growth in vivo. Finally, the 3D spheroid model was conducted to validate the role of PRIM1 in tumor growth and sorafenib resistance. Results The hub genes of HCC were screened in multiple bioinformatic datasets. PRIM1, as one of the hub genes, was significantly overexpressed in HCC tissues in mRNA and protein levels. In addition, high expression of PRIM1 indicated poor prognosis of HCC patients in TCGA, ICGC, and Nantong cohorts. Overexpression of PRIM1 promoted the proliferation, migration/invasion, and sorafenib resistance of HCC cells, with the decrease in apoptosis and cell cycle arrest. Mechanically, PRIM1 facilitated epithelial-mesenchymal transition (EMT) process and the activity of PI3K/AKT/mTOR signaling of HCC cells. Additionally, PRIM1 could cause the ubiquitination and degradation of P53 by upregulating Ubiquitin Conjugating Enzyme E2 C (UBE2C). Furthermore, knockdown of PRIM1 significantly inhibited the growth of xenograft tumors and HCC cells-derived spheroids with enhanced sorafenib resistance. Conclusion This study implies that PRIM1 may play a key role in the progression of HCC and may serve as a potential target for HCC treatment.
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Affiliation(s)
- Mengqi Zhu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.,School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Mengna Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Saiyan Bian
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.,School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Qianqian Song
- Department of Radiology, Wake Forest School of Medicine, One Medical Center Boulevard, Winston-Salem, 27157 NC, USA
| | - Mingbing Xiao
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Hua Huang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Li You
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Jianping Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Jie Zhang
- Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Chun Cheng
- School of Medicine, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
| | - Wenkai Ni
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China. .,Department of Oncology, Affiliated Hospital of Nantong University, 20 Xisi Road, Nantong, 226001, Jiangsu, China.
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20
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Schmit M, Bielinsky AK. Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms. Int J Mol Sci 2021; 22:E911. [PMID: 33477564 PMCID: PMC7831139 DOI: 10.3390/ijms22020911] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/19/2022] Open
Abstract
Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations or larger chromosomal anomalies such as rearrangements. While cancer is the most common class of disease associated with genomic instability, several congenital diseases with dysfunctional DNA replication give rise to similar DNA alterations. In this review, we discuss all congenital diseases that arise from pathogenic variants in essential replication genes across the spectrum of aberrant replisome assembly, origin activation and DNA synthesis. For each of these conditions, we describe their clinical phenotypes as well as molecular studies aimed at determining the functional mechanisms of disease, including the assessment of genomic stability. By comparing and contrasting these diseases, we hope to illuminate how the disruption of DNA replication at distinct steps affects human health in a surprisingly cell-type-specific manner.
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Affiliation(s)
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
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21
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Starokadomskyy P, Escala Perez-Reyes A, Burstein E. Immune Dysfunction in Mendelian Disorders of POLA1 Deficiency. J Clin Immunol 2021; 41:285-293. [PMID: 33392852 DOI: 10.1007/s10875-020-00953-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
POLA1 encodes the catalytic unit of DNA polymerase α, which together with the Primase complex launches the DNA replication process. While complete deficiency of this essential gene is presumed to be lethal, at least two conditions due to partial POLA1 deficiency have been described. The first genetic syndrome to be mapped to POLA1 was X-linked reticulate pigmentary disorder (XLPDR, MIM #301220), a rare syndrome characterized by skin hyperpigmentation, sterile multiorgan inflammation, recurrent infections, and distinct facial features. XLPDR has been shown to be accompanied by profound activation of type I interferon signaling, but unlike other interferonopathies, it is not associated with autoantibodies or classical autoimmunity. Rather, it is accompanied by marked Natural Killer (NK) cell dysfunction, which may explain the recurrent infections seen in this syndrome. To date, all XLPDR cases are caused by the same recurrent intronic mutation, which results in gene missplicing. Several hypomorphic mutations in POLA1, distinct from the XLPDR intronic mutation, have been recently reported and these mutations associate with a separate condition, van Esch-O'Driscoll syndrome (VEODS, MIM #301030). This condition results in growth retardation, microcephaly, hypogonadism, and in some cases, overlapping immunological features to those seen in XLPDR. This review summarizes our current understanding of the clinical manifestations of POLA1 gene mutations with an emphasis on its immunological consequences, as well as recent advances in understanding of its pathophysiologic basis and potential therapeutic options.
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Affiliation(s)
- Petro Starokadomskyy
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA.
| | - Andrea Escala Perez-Reyes
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - Ezra Burstein
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA. .,Department of Molecular Biology, UT Southwestern Medical Center, 5323 Harry Hines blvd, Dallas, TX, 75390-9151, USA.
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