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Seidizadeh O, Cairo A, Mancini I, George JN, Peyvandi F. Global prevalence of hereditary thrombotic thrombocytopenic purpura determined by genetic analysis. Blood Adv 2024; 8:4386-4396. [PMID: 38935915 DOI: 10.1182/bloodadvances.2024013421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024] Open
Abstract
ABSTRACT Hereditary thrombotic thrombocytopenic purpura (hTTP) is a rare autosomal recessive, life-threatening disorder caused by a severe deficiency of the plasma enzyme, ADAMTS13. The current estimated prevalence of hTTP in different regions of the world, 0.5 to 2.0 patients per million, is determined by the frequency of diagnosed patients. To evaluate more accurately the worldwide prevalence of hTTP, and also the prevalence within distinct ethnic groups, we used data available in exome and genome sequencing of 807 162 (730 947 exomes, 76 215 genomes) subjects reported recently by the Genome Aggregation Database (gnomAD-v4.1). Among 1 614 324 analyzed alleles in the gnomAD population we identified 6321 distinct ADAMTS13 variants. Of these, 758 were defined as pathogenic; 140 (18%) variants had been previously reported and 618 (82%) were novel (predicted as pathogenic). In total 10 154 alleles (0.6%) were carrying the reported or predicted pathogenic variants; 7759 (77%) with previously reported variants. Considering all 758 pathogenic variants and also only the 140 previously reported variants, we estimated a global hTTP prevalence of 40 and 23 cases per 106, respectively. Considering only the 140 previously reported variants, the highest estimated prevalence was in East Asians (42 per 106). The estimated prevalences of other populations were: Finnish, 32 per 106; non-Finnish Europeans, 28 per 106; Admixed Americans, 19 per 106; Africans/African Americans, 6 per 106; and South Asians, 4 per 106. The lowest prevalences were Middle Eastern, 1 per 106 and Ashkenazi Jews, 0.7 per 106. This population-based genetic epidemiology study reports that hTTP prevalence is substantially higher than the currently estimated prevalence based on diagnosed patients. Many patients with hTTP may not be diagnosed or may have died during the neonatal period.
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Affiliation(s)
- Omid Seidizadeh
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Andrea Cairo
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - Ilaria Mancini
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - James N George
- Departments of Medicine, Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK
| | - Flora Peyvandi
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
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2
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Garcia-Moreno H, Langbehn DR, Abiona A, Garrood I, Fleszar Z, Manes MA, Morley AMS, Craythorne E, Mohammed S, Henshaw T, Turner S, Naik H, Bodi I, Sarkany RPE, Fassihi H, Lehmann AR, Giunti P. Neurological disease in xeroderma pigmentosum: prospective cohort study of its features and progression. Brain 2023; 146:5044-5059. [PMID: 38040034 PMCID: PMC10690019 DOI: 10.1093/brain/awad266] [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: 02/21/2023] [Revised: 06/22/2023] [Accepted: 07/16/2023] [Indexed: 12/03/2023] Open
Abstract
Xeroderma pigmentosum (XP) results from biallelic mutations in any of eight genes involved in DNA repair systems, thus defining eight different genotypes (XPA, XPB, XPC, XPD, XPE, XPF, XPG and XP variant or XPV). In addition to cutaneous and ophthalmological features, some patients present with XP neurological disease. It is unknown whether the different neurological signs and their progression differ among groups. Therefore, we aim to characterize the XP neurological disease and its evolution in the heterogeneous UK XP cohort. Patients with XP were followed in the UK National XP Service, from 2009 to 2021. Age of onset for different events was recorded. Cerebellar ataxia and additional neurological signs and symptoms were rated with the Scale for the Assessment and Rating of Ataxia (SARA), the Inventory of Non-Ataxia Signs (INAS) and the Activities of Daily Living questionnaire (ADL). Patients' mutations received scores based on their predicted effects. Data from available ancillary tests were collected. Ninety-three XP patients were recruited. Thirty-six (38.7%) reported neurological symptoms, especially in the XPA, XPD and XPG groups, with early-onset and late-onset forms, and typically appearing after cutaneous and ophthalmological symptoms. XPA, XPD and XPG patients showed higher SARA scores compared to XPC, XPE and XPV. SARA total scores significantly increased over time in XPD (0.91 points/year, 95% confidence interval: 0.61, 1.21) and XPA (0.63 points/year, 95% confidence interval: 0.38, 0.89). Hyporeflexia, hypopallesthaesia, upper motor neuron signs, chorea, dystonia, oculomotor signs and cognitive impairment were frequent findings in XPA, XPD and XPG. Cerebellar and global brain atrophy, axonal sensory and sensorimotor neuropathies, and sensorineural hearing loss were common findings in patients. Some XPC, XPE and XPV cases presented with abnormalities on examination and/or ancillary tests, suggesting underlying neurological involvement. More severe mutations were associated with a faster progression in SARA total score in XPA (0.40 points/year per 1-unit increase in severity score) and XPD (0.60 points/year per 1-unit increase), and in ADL total score in XPA (0.35 points/year per 1-unit increase). Symptomatic and asymptomatic forms of neurological disease are frequent in XP patients, and neurological symptoms can be an important cause of disability. Typically, the neurological disease will be preceded by cutaneous and ophthalmological features, and these should be actively searched in patients with idiopathic late-onset neurological syndromes. Scales assessing cerebellar function, especially walking and speech, and disability can show progression in some of the groups. Mutation severity can be used as a prognostic biomarker for stratification purposes in clinical trials.
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Affiliation(s)
- Hector Garcia-Moreno
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Douglas R Langbehn
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Adesoji Abiona
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Isabel Garrood
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Zofia Fleszar
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Marta Antonia Manes
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ana M Susana Morley
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
- Department of Ophthalmology, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Emma Craythorne
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Shehla Mohammed
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Tanya Henshaw
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Sally Turner
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Harsha Naik
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Istvan Bodi
- Clinical Neuropathology, Academic Neuroscience Building, King’s College Hospital, London SE5 9RS, UK
| | - Robert P E Sarkany
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Hiva Fassihi
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
| | - Alan R Lehmann
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Paola Giunti
- Ataxia Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UK National Xeroderma Pigmentosum Service, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK
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Seidizadeh O, Cairo A, Baronciani L, Valenti L, Peyvandi F. Population-based prevalence and mutational landscape of von Willebrand disease using large-scale genetic databases. NPJ Genom Med 2023; 8:31. [PMID: 37845247 PMCID: PMC10579253 DOI: 10.1038/s41525-023-00375-8] [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: 03/13/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023] Open
Abstract
Von Willebrand disease (VWD) is a common bleeding disorder caused by mutations in the von Willebrand factor gene (VWF). The true global prevalence of VWD has not been accurately established. We estimated the worldwide and within-population prevalence of inherited VWD by analyzing exome and genome data of 141,456 individuals gathered by the genome Aggregation Database (gnomAD). We also extended our data deepening by mining the main databases containing VWF variants i.e., the Leiden Open Variation Database (LOVD) and the Human Gene Mutation Database (HGMD) with the goal to explore the global mutational spectrum of VWD. A total of 4,313 VWF variants were identified in the gnomAD population, of which 505 were predicted to be pathogenic or already reported to be associated with VWD. Among the 282,912 alleles analyzed, 31,785 were affected by the aforementioned variants. The global prevalence of dominant VWD in 1000 individuals was established to be 74 for type 1, 3 for 2A, 3 for 2B and 6 for 2M. The global prevalences for recessive VWD forms (type 2N and type 3) were 0.31 and 0.7 in 1000 individuals, respectively. This comprehensive analysis provided a global mutational landscape of VWF by means of 927 already reported variants in the HGMD and LOVD datasets and 287 novel pathogenic variants identified in the gnomAD. Our results reveal that there is a considerably higher than expected prevalence of putative disease alleles and variants associated with VWD and suggest that a large number of VWD patients are undiagnosed.
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Affiliation(s)
- Omid Seidizadeh
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Andrea Cairo
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - Luciano Baronciani
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Precision Medicine Lab, Biological Resource Center, Department of Transfusion Medicine, Milan, Italy
| | - Flora Peyvandi
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Milan, Italy.
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
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Yu J, Yan C, Dodd T, Tsai CL, Tainer JA, Tsutakawa SE, Ivanov I. Dynamic conformational switching underlies TFIIH function in transcription and DNA repair and impacts genetic diseases. Nat Commun 2023; 14:2758. [PMID: 37179334 PMCID: PMC10183003 DOI: 10.1038/s41467-023-38416-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH's global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.
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Affiliation(s)
- Jina Yu
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Thomas Dodd
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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5
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Le J, Min JH. Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein. J Biomol Struct Dyn 2023; 41:13535-13562. [PMID: 36890638 PMCID: PMC10485178 DOI: 10.1080/07391102.2023.2177349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/27/2023] [Indexed: 03/10/2023]
Abstract
Xeroderma pigmentosum C (XPC) is a key initiator in the global genome nucleotide excision repair pathway in mammalian cells. Inherited mutations in the XPC gene can cause xeroderma pigmentosum (XP) cancer predisposition syndrome that dramatically increases the susceptibility to sunlight-induced cancers. Various genetic variants and mutations of the protein have been reported in cancer databases and literature. The current lack of a high-resolution 3-D structure of human XPC makes it difficult to assess the structural impact of the mutations/genetic variations. Using the available high-resolution crystal structure of its yeast ortholog, Rad4, we built a homology model of human XPC protein and compared it with a model generated by AlphaFold. The two models are largely consistent with each other in the structured domains. We have also assessed the degree of conservation for each residue using 966 sequences of XPC orthologs. Our structure- and sequence conservation-based assessments largely agree with the variant's impact on the protein's structural stability, computed by FoldX and SDM. Known XP missense mutations such as Y585C, W690S, and C771Y are consistently predicted to destabilize the protein's structure. Our analyses also reveal several highly conserved hydrophobic regions that are surface-exposed, which may indicate novel intermolecular interfaces that are yet to be characterized.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jennifer Le
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Jung-Hyun Min
- Department of Chemistry & Biochemistry, Baylor University, Waco, TX 76798, USA
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6
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Cordts I, Önder D, Traschütz A, Kobeleva X, Karin I, Minnerop M, Koertvelyessy P, Biskup S, Forchhammer S, Binder J, Tzschach A, Meiss F, Schmidt A, Kreiß M, Cremer K, Mensah MA, Park J, Rautenberg M, Deininger N, Sturm M, Lingor P, Klopstock T, Weiler M, Marxreiter F, Synofzik M, Posch C, Sirokay J, Klockgether T, Haack TB, Deschauer M. Adult-Onset Neurodegeneration in Nucleotide Excision Repair Disorders (NERD ND ): Time to Move Beyond the Skin. Mov Disord 2022; 37:1707-1718. [PMID: 35699229 DOI: 10.1002/mds.29071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/06/2022] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Variants in genes of the nucleotide excision repair (NER) pathway have been associated with heterogeneous clinical presentations ranging from xeroderma pigmentosum to Cockayne syndrome and trichothiodystrophy. NER deficiencies manifest with photosensitivity and skin cancer, but also developmental delay and early-onset neurological degeneration. Adult-onset neurological features have been reported in only a few xeroderma pigmentosum cases, all showing at least mild skin manifestations. OBJECTIVE The aim of this multicenter study was to investigate the frequency and clinical features of patients with biallelic variants in NER genes who are predominantly presenting with neurological signs. METHODS In-house exome and genome datasets of 14,303 patients, including 3543 neurological cases, were screened for deleterious variants in NER-related genes. Clinical workup included in-depth neurological and dermatological assessments. RESULTS We identified 13 patients with variants in ERCC4 (n = 8), ERCC2 (n = 4), or XPA (n = 1), mostly proven biallelic, including five different recurrent and six novel variants. All individuals had adult-onset progressive neurological deterioration with ataxia, dementia, and frequently chorea, neuropathy, and spasticity. Brain magnetic resonance imaging showed profound global brain atrophy in all patients. Dermatological examination did not show any skin cancer or pronounced ultraviolet damage. CONCLUSIONS We introduce NERDND as adult-onset neurodegeneration (ND ) within the spectrum of autosomal recessive NER disorders (NERD). Our study demonstrates that NERDND is probably an underdiagnosed cause of neurodegeneration in adulthood and should be considered in patients with overlapping cognitive and movement abnormalities. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Isabell Cordts
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Demet Önder
- Department of Neurology, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Andreas Traschütz
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Xenia Kobeleva
- Department of Neurology, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Ivan Karin
- Friedrich-Baur-Institute, Department of Neurology, University Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Martina Minnerop
- Institute of Neuroscience and Medicine, Research Centre Jülich, Jülich, Germany.,Department of Neurology, Center for Movement Disorders and Neuromodulation, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Koertvelyessy
- Department of Neurology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Saskia Biskup
- CeGaT GmbH und Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Stephan Forchhammer
- Division of Dermatooncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | | | - Andreas Tzschach
- Institute of Human Genetics, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Meiss
- Department of Dermatology and Venereology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Martina Kreiß
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Martin A Mensah
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.,BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Maren Rautenberg
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Natalie Deininger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Paul Lingor
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Thomas Klopstock
- Friedrich-Baur-Institute, Department of Neurology, University Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,German Center for Neurodegenerative Diseases, Munich, Germany
| | - Markus Weiler
- Department of Neurology, Heidelberg University Hospital, Heidelberg, Germany
| | - Franz Marxreiter
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Center for Rare Diseases (ZSEER), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Christian Posch
- Department of Dermatology and Allergy, School of Medicine, German Cancer Consortium, Technical University of Munich, Munich, Germany.,Faculty of Medicine, Sigmund Freud University Vienna, Vienna, Austria
| | - Judith Sirokay
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Thomas Klockgether
- Department of Neurology, University Hospital Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marcus Deschauer
- Department of Neurology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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Tsutakawa SE, Bacolla A, Katsonis P, Bralić A, Hamdan SM, Lichtarge O, Tainer JA, Tsai CL. Decoding Cancer Variants of Unknown Significance for Helicase-Nuclease-RPA Complexes Orchestrating DNA Repair During Transcription and Replication. Front Mol Biosci 2021; 8:791792. [PMID: 34966786 PMCID: PMC8710748 DOI: 10.3389/fmolb.2021.791792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
All tumors have DNA mutations, and a predictive understanding of those mutations could inform clinical treatments. However, 40% of the mutations are variants of unknown significance (VUS), with the challenge being to objectively predict whether a VUS is pathogenic and supports the tumor or whether it is benign. To objectively decode VUS, we mapped cancer sequence data and evolutionary trace (ET) scores onto crystallography and cryo-electron microscopy structures with variant impacts quantitated by evolutionary action (EA) measures. As tumors depend on helicases and nucleases to deal with transcription/replication stress, we targeted helicase–nuclease–RPA complexes: (1) XPB-XPD (within TFIIH), XPF-ERCC1, XPG, and RPA for transcription and nucleotide excision repair pathways and (2) BLM, EXO5, and RPA plus DNA2 for stalled replication fork restart. As validation, EA scoring predicts severe effects for most disease mutations, but disease mutants with low ET scores not only are likely destabilizing but also disrupt sophisticated allosteric mechanisms. For sites of disease mutations and VUS predicted to be severe, we found strong co-localization to ordered regions. Rare discrepancies highlighted the different survival requirements between disease and tumor mutations, as well as the value of examining proteins within complexes. In a genome-wide analysis of 33 cancer types, we found correlation between the number of mutations in each tumor and which pathways or functional processes in which the mutations occur, revealing different mutagenic routes to tumorigenesis. We also found upregulation of ancient genes including BLM, which supports a non-random and concerted cancer process: reversion to a unicellular, proliferation-uncontrolled, status by breaking multicellular constraints on cell division. Together, these genes and global analyses challenge the binary “driver” and “passenger” mutation paradigm, support a gradient impact as revealed by EA scoring from moderate to severe at a single gene level, and indicate reduced regulation as well as activity. The objective quantitative assessment of VUS scoring and gene overexpression in the context of functional interactions and pathways provides insights for biology, oncology, and precision medicine.
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Affiliation(s)
- Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Panagiotis Katsonis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Amer Bralić
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Samir M Hamdan
- Laboratory of DNA Replication and Recombination, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivier Lichtarge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - John A Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States.,Department of Cancer Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
| | - Chi-Lin Tsai
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX, United States
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8
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Yan C, Dodd T, Yu J, Leung B, Xu J, Oh J, Wang D, Ivanov I. Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair. Nat Commun 2021; 12:7001. [PMID: 34853308 PMCID: PMC8636621 DOI: 10.1038/s41467-021-27295-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/10/2021] [Indexed: 12/22/2022] Open
Abstract
Transcription-coupled repair is essential for the removal of DNA lesions from the transcribed genome. The pathway is initiated by CSB protein binding to stalled RNA polymerase II. Mutations impairing CSB function cause severe genetic disease. Yet, the ATP-dependent mechanism by which CSB powers RNA polymerase to bypass certain lesions while triggering excision of others is incompletely understood. Here we build structural models of RNA polymerase II bound to the yeast CSB ortholog Rad26 in nucleotide-free and bound states. This enables simulations and graph-theoretical analyses to define partitioning of this complex into dynamic communities and delineate how its structural elements function together to remodel DNA. We identify an allosteric pathway coupling motions of the Rad26 ATPase modules to changes in RNA polymerase and DNA to unveil a structural mechanism for CSB-assisted progression past less bulky lesions. Our models allow functional interpretation of the effects of Cockayne syndrome disease mutations.
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Affiliation(s)
- Chunli Yan
- grid.256304.60000 0004 1936 7400Department of Chemistry, Georgia State University, Atlanta, GA USA ,grid.256304.60000 0004 1936 7400Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA USA
| | - Thomas Dodd
- grid.256304.60000 0004 1936 7400Department of Chemistry, Georgia State University, Atlanta, GA USA ,grid.256304.60000 0004 1936 7400Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA USA
| | - Jina Yu
- grid.256304.60000 0004 1936 7400Department of Chemistry, Georgia State University, Atlanta, GA USA ,grid.256304.60000 0004 1936 7400Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA USA
| | - Bernice Leung
- grid.266100.30000 0001 2107 4242Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Jun Xu
- grid.266100.30000 0001 2107 4242Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Juntaek Oh
- grid.266100.30000 0001 2107 4242Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093 USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA. .,Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA. .,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA, USA. .,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA.
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9
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Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations. Proc Natl Acad Sci U S A 2020; 117:14127-14138. [PMID: 32522879 PMCID: PMC7321962 DOI: 10.1073/pnas.1921311117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA repair is essential to life and to avoidance of genome instability and cancer. Xeroderma pigmentosum group G (XPG) protein acts in multiple DNA repair pathways, both as an active enzyme and as a scaffold for coordinating with other repair proteins. We present here the structure of the catalytic domain responsible for its DNA binding and nuclease activity. Our analysis provides structure-based hypotheses for how XPG recognizes its bubble DNA substrate and predictions of the structural impacts of XPG disease mutations associated with two phenotypically distinct diseases: xeroderma pigmentosum (XP, skin cancer prone) or Cockayne syndrome (XP/CS, severe progressive developmental defects). Xeroderma pigmentosum group G (XPG) protein is both a functional partner in multiple DNA damage responses (DDR) and a pathway coordinator and structure-specific endonuclease in nucleotide excision repair (NER). Different mutations in the XPG gene ERCC5 lead to either of two distinct human diseases: Cancer-prone xeroderma pigmentosum (XP-G) or the fatal neurodevelopmental disorder Cockayne syndrome (XP-G/CS). To address the enigmatic structural mechanism for these differing disease phenotypes and for XPG’s role in multiple DDRs, here we determined the crystal structure of human XPG catalytic domain (XPGcat), revealing XPG-specific features for its activities and regulation. Furthermore, XPG DNA binding elements conserved with FEN1 superfamily members enable insights on DNA interactions. Notably, all but one of the known pathogenic point mutations map to XPGcat, and both XP-G and XP-G/CS mutations destabilize XPG and reduce its cellular protein levels. Mapping the distinct mutation classes provides structure-based predictions for disease phenotypes: Residues mutated in XP-G are positioned to reduce local stability and NER activity, whereas residues mutated in XP-G/CS have implied long-range structural defects that would likely disrupt stability of the whole protein, and thus interfere with its functional interactions. Combined data from crystallography, biochemistry, small angle X-ray scattering, and electron microscopy unveil an XPG homodimer that binds, unstacks, and sculpts duplex DNA at internal unpaired regions (bubbles) into strongly bent structures, and suggest how XPG complexes may bind both NER bubble junctions and replication forks. Collective results support XPG scaffolding and DNA sculpting functions in multiple DDR processes to maintain genome stability.
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10
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Lee JW, Ratnakumar K, Hung KF, Rokunohe D, Kawasumi M. Deciphering UV-induced DNA Damage Responses to Prevent and Treat Skin Cancer. Photochem Photobiol 2020; 96:478-499. [PMID: 32119110 DOI: 10.1111/php.13245] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/11/2020] [Indexed: 12/11/2022]
Abstract
Ultraviolet (UV) radiation is among the most prevalent environmental factors that influence human health and disease. Even 1 h of UV irradiation extensively damages the genome. To cope with resulting deleterious DNA lesions, cells activate a multitude of DNA damage response pathways, including DNA repair. Strikingly, UV-induced DNA damage formation and repair are affected by chromatin state. When cells enter S phase with these lesions, a distinct mutation signature is created via error-prone translesion synthesis. Chronic UV exposure leads to high mutation burden in skin and consequently the development of skin cancer, the most common cancer in the United States. Intriguingly, UV-induced oxidative stress has opposing effects on carcinogenesis. Elucidating the molecular mechanisms of UV-induced DNA damage responses will be useful for preventing and treating skin cancer with greater precision. Excitingly, recent studies have uncovered substantial depth of novel findings regarding the molecular and cellular consequences of UV irradiation. In this review, we will discuss updated mechanisms of UV-induced DNA damage responses including the ATR pathway, which maintains genome integrity following UV irradiation. We will also present current strategies for preventing and treating nonmelanoma skin cancer, including ATR pathway inhibition for prevention and photodynamic therapy for treatment.
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Affiliation(s)
- Jihoon W Lee
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Kajan Ratnakumar
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Kai-Feng Hung
- Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Daiki Rokunohe
- Department of Dermatology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Masaoki Kawasumi
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
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