1
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Saito T, Wang S, Ohkawa K, Ohara H, Kondo S. Deep learning with a small dataset predicts chromatin remodelling contribution to winter dormancy of apple axillary buds. TREE PHYSIOLOGY 2024; 44:tpae072. [PMID: 38905284 DOI: 10.1093/treephys/tpae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/31/2024] [Accepted: 06/20/2024] [Indexed: 06/23/2024]
Abstract
Epigenetic changes serve as a cellular memory for cumulative cold recognition in both herbaceous and tree species, including bud dormancy. However, most studies have discussed predicted chromatin structure with respect to histone marks. In the present study, we investigated the structural dynamics of bona fide chromatin to determine how plants recognize prolonged chilling during the initial stage of bud dormancy. The vegetative axillary buds of the 'Fuji' apple, which shows typical low temperature-dependent, but not photoperiod, dormancy induction, were used for the chromatin structure and transcriptional change analyses. The results were integrated using a deep-learning model and interpreted using statistical models, including Bayesian estimation. Although our model was constructed using a small dataset of two time points, chromatin remodelling due to random changes was excluded. The involvement of most nucleosome structural changes in transcriptional changes and the pivotal contribution of cold-driven circadian rhythm-dependent pathways regulated by the mobility of cis-regulatory elements were predicted. These findings may help to develop potential genetic targets for breeding species with less bud dormancy to overcome the effects of short winters during global warming. Our artificial intelligence concept can improve epigenetic analysis using a small dataset, especially in non-model plants with immature genome databases.
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Affiliation(s)
- Takanori Saito
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan
| | - Shanshan Wang
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan
| | - Katsuya Ohkawa
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan
| | - Hitoshi Ohara
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan
- Center for Environment, Health and Field Sciences, Chiba University, Kashiwa-no-ha 277-0882, Japan
| | - Satoru Kondo
- Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan
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2
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Muniesa-Vargas A, Davó-Martínez C, Ribeiro-Silva C, van der Woude M, Thijssen KL, Haspels B, Häckes D, Kaynak ÜU, Kanaar R, Marteijn JA, Theil AF, Kuijten MMP, Vermeulen W, Lans H. Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure. Nat Commun 2024; 15:3490. [PMID: 38664429 PMCID: PMC11045817 DOI: 10.1038/s41467-024-47935-9] [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] [Received: 04/22/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
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Affiliation(s)
- Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ben Haspels
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ülkem U Kaynak
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Maayke M P Kuijten
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
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3
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Hozhabrpour A, Mojbafan M, Palizban F, Vahidnezhad F, Talebi S, Amani M, Garshasbi M, Naghavi A, Khalesi R, Mansouri P, Sotoudeh S, Mahmoudi H, Varghaei A, Daneshpazhooh M, Karimi F, Zeinali S, Kalamati E, Uitto J, Youssefian L, Vahidnezhad H. DNA repair-related heritable photosensitivity syndromes: Mutation landscape in a multiethnic cohort of 17 multigenerational families with high degree of consanguinity. DNA Repair (Amst) 2024; 136:103633. [PMID: 38422792 DOI: 10.1016/j.dnarep.2024.103633] [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: 03/27/2023] [Revised: 12/30/2023] [Accepted: 01/19/2024] [Indexed: 03/02/2024]
Abstract
Inherited photosensitivity syndromes are a heterogeneous group of genetic skin disorders with tremendous phenotypic variability, characterized by photosensitivity and defective DNA repair, especially nucleotide excision repair. A cohort of 17 Iranian families with heritable photosensitivity syndromes was evaluated to identify their genetic defect. The patients' DNA was analyzed with either whole-exome sequencing or RNA sequencing (RNA-Seq). The interpretations of the genomic results were guided by genome-wide homozygosity mapping. Haplotype analysis was performed for cases with recurrent mutations. RNA-Seq, in addition to mutation detection, was also utilized to confirm the pathogenicity. Thirteen sequence variants, including six previously unreported pathogenic variants, were disclosed in 17 Iranian families, with XPC as the most common mutated gene in 10 families (59%). In one patient, RNA-Seq, as a first-tier diagnostic approach, revealed a non-canonical homozygous germline variant: XPC:c.413-9 T > A. The Sashimi plot showed skipping of exon 4 with dramatic XPC down-expression. Haplotype analysis of XPC:c.2251-1 G>C and XPC:1243 C>T in four families showed common haplotypes of 1.7 Mb and 2.6 Mb, respectively, denoting a founder effect. Lastly, two extremely rare cases were presented in this report: a homozygous UVSSA:c .1990 C>T was disclosed, and ERCC2-related cerebro-oculo-facio-skeletal (COFS) syndrome with an early childhood death. A direct comparison of our data with the results of previously reported cohorts demonstrates the international mutation landscape of DNA repair-related photosensitivity disorders, although population-specific differences were observed.
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Affiliation(s)
- Amir Hozhabrpour
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Marzieh Mojbafan
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Fahimeh Palizban
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Saeed Talebi
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Maliheh Amani
- Clinical Research Development Unit of Allameh Bohlool Gonabadi Hospital, Gonabad University of Medical Sciences, Gonabad, Iran; Department of Dermatology, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Anoosh Naghavi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Raziyeh Khalesi
- Department of Medical Genetics, DeNA Laboratory, Tehran, Iran
| | - Parvin Mansouri
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Sotoudeh
- Department of Dermatology, Children's Medical Center, Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Aida Varghaei
- Department of Dermatology, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Daneshpazhooh
- Department of Dermatology, Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | - Elnaz Kalamati
- Department of Obstetrics and Gynecology, Imam Zaman Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leila Youssefian
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA; Department of Dermatology and Cutaneous Biology, Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Theil AF, Häckes D, Lans H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst) 2023; 132:103568. [PMID: 37977600 DOI: 10.1016/j.dnarep.2023.103568] [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: 04/28/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/19/2023]
Abstract
The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands.
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5
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Jain A, Casanova D, Padilla AV, Paniagua Bojorges A, Kotla S, Ko KA, Samanthapudi VSK, Chau K, Nguyen MTH, Wen J, Hernandez Gonzalez SL, Rodgers SP, Olmsted-Davis EA, Hamilton DJ, Reyes-Gibby C, Yeung SCJ, Cooke JP, Herrmann J, Chini EN, Xu X, Yusuf SW, Yoshimoto M, Lorenzi PL, Hobbs B, Krishnan S, Koutroumpakis E, Palaskas NL, Wang G, Deswal A, Lin SH, Abe JI, Le NT. Premature senescence and cardiovascular disease following cancer treatments: mechanistic insights. Front Cardiovasc Med 2023; 10:1212174. [PMID: 37781317 PMCID: PMC10540075 DOI: 10.3389/fcvm.2023.1212174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/03/2023] [Indexed: 10/03/2023] Open
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality, especially among the aging population. The "response-to-injury" model proposed by Dr. Russell Ross in 1999 emphasizes inflammation as a critical factor in atherosclerosis development, with atherosclerotic plaques forming due to endothelial cell (EC) injury, followed by myeloid cell adhesion and invasion into the blood vessel walls. Recent evidence indicates that cancer and its treatments can lead to long-term complications, including CVD. Cellular senescence, a hallmark of aging, is implicated in CVD pathogenesis, particularly in cancer survivors. However, the precise mechanisms linking premature senescence to CVD in cancer survivors remain poorly understood. This article aims to provide mechanistic insights into this association and propose future directions to better comprehend this complex interplay.
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Affiliation(s)
- Ashita Jain
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Diego Casanova
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | | | - Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Khanh Chau
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Minh T. H. Nguyen
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Jake Wen
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Shaefali P. Rodgers
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | | | - Dale J. Hamilton
- Department of Medicine, Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, United States
| | - Cielito Reyes-Gibby
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Sai-Ching J. Yeung
- Department of Emergency Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John P. Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Joerg Herrmann
- Cardio Oncology Clinic, Division of Preventive Cardiology, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Eduardo N. Chini
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Jacksonville, FL, United States
| | - Xiaolei Xu
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, United States
| | - Syed Wamique Yusuf
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Momoko Yoshimoto
- Center for Stem Cell & Regenerative Medicine, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, Division of VP Research, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Brain Hobbs
- Department of Population Health, The University of Texas at Austin, Austin, TX, United States
| | - Sunil Krishnan
- Department of Neurosurgery, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Efstratios Koutroumpakis
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nicolas L. Palaskas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Guangyu Wang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
| | - Anita Deswal
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven H. Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jun-ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Nhat-Tu Le
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, United States
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6
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Zhu G, Khalid F, Zhang D, Cao Z, Maity P, Kestler HA, Orioli D, Scharffetter-Kochanek K, Iben S. Ribosomal Dysfunction Is a Common Pathomechanism in Different Forms of Trichothiodystrophy. Cells 2023; 12:1877. [PMID: 37508541 PMCID: PMC10377840 DOI: 10.3390/cells12141877] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Mutations in a broad variety of genes can provoke the severe childhood disorder trichothiodystrophy (TTD) that is classified as a DNA repair disease or a transcription syndrome of RNA polymerase II. In an attempt to identify the common underlying pathomechanism of TTD we performed a knockout/knockdown of the two unrelated TTD factors TTDN1 and RNF113A and investigated the consequences on ribosomal biogenesis and performance. Interestingly, interference with these TTD factors created a nearly uniform impact on RNA polymerase I transcription with downregulation of UBF, disturbed rRNA processing and reduction of the backbone of the small ribosomal subunit rRNA 18S. This was accompanied by a reduced quality of decoding in protein translation and the accumulation of misfolded and carbonylated proteins, indicating a loss of protein homeostasis (proteostasis). As the loss of proteostasis by the ribosome has been identified in the other forms of TTD, here we postulate that ribosomal dysfunction is a common underlying pathomechanism of TTD.
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Affiliation(s)
- Gaojie Zhu
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Fatima Khalid
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Danhui Zhang
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Zhouli Cao
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Pallab Maity
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
| | - Hans A Kestler
- Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Donata Orioli
- Istituto di Genetica Molecolare L.L. Cavalli-Sforza CNR, 27100 Pavia, Italy
| | | | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, 89081 Ulm, Germany
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Liu L, Cui J, Liu S, Pan E, Sun L. Case Report: Lung adenocarcinoma associated with germline ERCC2 frameshift mutation. Front Oncol 2023; 13:1177942. [PMID: 37223679 PMCID: PMC10200934 DOI: 10.3389/fonc.2023.1177942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Family history is an established risk factor for lung cancer. Previous studies have found that germline genetic alterations, such as those in EGFR, BRCA1, BRCA2, CHEK2, CDKN2A, HER2, MET, NBN, PARK2, RET, TERT, TP53, and YAP1, are associated with an increased risk of developing lung cancer. The study reports the first of a lung adenocarcinoma proband with germline ERCC2 frameshift mutation c.1849dup (p. A617Gfs*32). Her family cancer history review demonstrated that her two healthy sisters, a brother with lung cancer, and three healthy cousins were positive for ERCC2 frameshift mutation, which might contribute to increased cancer risk. Our study highlights the necessity of performing comprehensive genomic profiling in discovering rare genetic alterations, early cancer screening, and monitoring for patients with family cancer history.
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Affiliation(s)
- Lili Liu
- Department of Medical Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jia Cui
- Department of Medical Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Siye Liu
- Department of Medical, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Evenki Pan
- Department of Medical, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China
| | - Limin Sun
- Department of Medical Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
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8
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [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: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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9
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Maguina M, Kang PB, Tsai AC, Pacak CA. Peripheral neuropathies associated with DNA repair disorders. Muscle Nerve 2023; 67:101-110. [PMID: 36190439 PMCID: PMC10075233 DOI: 10.1002/mus.27721] [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: 12/13/2021] [Revised: 09/08/2022] [Accepted: 09/10/2022] [Indexed: 01/25/2023]
Abstract
Repair of genomic DNA is a fundamental housekeeping process that quietly maintains the health of our genomes. The consequences of a genetic defect affecting a component of this delicate mechanism are quite harmful, characterized by a cascade of premature aging that injures a variety of organs, including the nervous system. One part of the nervous system that is impaired in certain DNA repair disorders is the peripheral nerve. Chronic motor, sensory, and sensorimotor polyneuropathies have all been observed in affected individuals, with specific physiologies associated with different categories of DNA repair disorders. Cockayne syndrome has classically been linked to demyelinating polyneuropathies, whereas xeroderma pigmentosum has long been associated with axonal polyneuropathies. Three additional recessive DNA repair disorders are associated with neuropathies, including trichothiodystrophy, Werner syndrome, and ataxia-telangiectasia. Although plausible biological explanations exist for why the peripheral nerves are specifically vulnerable to impairments of DNA repair, specific mechanisms such as oxidative stress remain largely unexplored in this context, and bear further study. It is also unclear why different DNA repair disorders manifest with different types of neuropathy, and why neuropathy is not universally present in those diseases. Longitudinal physiological monitoring of these neuropathies with serial electrodiagnostic studies may provide valuable noninvasive outcome data in the context of future natural history studies, and thus the responses of these neuropathies may become sentinel outcome measures for future clinical trials of treatments currently in development such as adeno-associated virus gene replacement therapies.
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Affiliation(s)
- Melissa Maguina
- Medical Education Program, Nova Southeastern University, Fort Lauderdale, Florida
| | - Peter B Kang
- Department of Neurology, Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota.,Institute for Translational Neuroscience, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Ang-Chen Tsai
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida
| | - Christina A Pacak
- Department of Neurology, Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota Medical School, Minneapolis, Minnesota
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10
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Liang F, Li B, Xu Y, Gong J, Zheng S, Zhang Y, Wang Y. Identification and characterization of Necdin as a target for the Cockayne syndrome B protein in promoting neuronal differentiation and maintenance. Pharmacol Res 2023; 187:106637. [PMID: 36586641 DOI: 10.1016/j.phrs.2022.106637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/01/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
Cockayne syndrome (CS) is a devastating autosomal recessive genetic disorder, mainly characterized by photosensitivity, growth failure, neurological abnormalities, and premature aging. Mutations in CSB (ERCC6) are associated with almost all clinical phenotypes resembling classic CS. Using RNA-seq approach in multiple cell types, we identified Necdin (NDN) as a target of the CSB protein. Supportive of the RNA-seq results, CSB directly binds to NDN and manipulates the remodeling of active histone marks and DNA 5mC methylation on the regulatory elements of the NDN gene. Intriguingly, hyperactivation of NDN due to CSB deficiency does not interfere with nucleotide excision repair (1), but greatly affects neuronal cell differentiation. Inhibition of NDN can partially rescue the motor neuron defects in CSB mouse models. In addition to shedding light on cellular mechanisms underlying CS and pointing to future avenues for intervention, these data substantiate a reciprocal communication between CSB and NDN in the context of general transcription regulation.
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Affiliation(s)
- Fangkeng Liang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Bijuan Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yingying Xu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Junwei Gong
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shaohui Zheng
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yunlong Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yuming Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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11
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Ruszel KP, Zalewski DP, Stępniewski A, Gałkowski D, Bogucki J, Feldo M, Płachno BJ, Kocki J, Bogucka-Kocka A. Next-Generation Sequencing in the Assessment of the Transcriptomic Landscape of DNA Damage Repair Genes in Abdominal Aortic Aneurysm, Chronic Venous Disease and Lower Extremity Artery Disease. Int J Mol Sci 2022; 24:ijms24010551. [PMID: 36614026 PMCID: PMC9820637 DOI: 10.3390/ijms24010551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022] Open
Abstract
Vascular diseases are one of the most common causes of death and morbidity. Lower extremity artery disease (LEAD), abdominal aortic aneurysm (AAA) and chronic venous disease (CVD) belong to this group of conditions and exhibit various presentations and courses; thus, there is an urgent need for revealing new biomarkers for monitoring and potential treatment. Next-generation sequencing of mRNA allows rapid and detailed transcriptome analysis, allowing us to pinpoint the most pronounced differences between the mRNA expression profiles of vascular disease patients. Comparison of expression data of 519 DNA-repair-related genes obtained from mRNA next-generation sequencing revealed significant transcriptomic marks characterizing AAA, CVD and LEAD. Statistical, gene set enrichment analysis (GSEA), gene ontology (GO) and literature analyses were applied and highlighted many DNA repair and accompanying processes, such as cohesin functions, oxidative stress, homologous recombination, ubiquitin turnover, chromatin remodelling and DNA double-strand break repair. Surprisingly, obtained data suggest the contribution of genes engaged in the regulatory function of DNA repair as a key component that could be used to distinguish between analyzed conditions. DNA repair-related genes depicted in the presented study as dysregulated in AAA, CVD and LEAD could be utilized in the design of new biomarkers or therapies associated with these diseases.
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Affiliation(s)
- Karol P. Ruszel
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland
- Correspondence: ; Tel.: +48-81-448-6610
| | - Daniel P. Zalewski
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland
| | - Andrzej Stępniewski
- Ecotech Complex Analytical and Programme Centre for Advanced Environmentally Friendly Technologies, University of Marie Curie-Skłodowska, 39 Głęboka St., 20-612 Lublin, Poland
| | - Dariusz Gałkowski
- Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, One Robert Wood Johnson Place, New Brunswick, NJ 08903, USA
| | - Jacek Bogucki
- Chair and Department of Organic Chemistry, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland
| | - Marcin Feldo
- Chair and Department of Vascular Surgery and Angiology, Medical University of Lublin, 11 Staszica St., 20-081 Lublin, Poland
| | - Bartosz J. Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Kraków, Poland
| | - Janusz Kocki
- Department of Clinical Genetics, Chair of Medical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland
| | - Anna Bogucka-Kocka
- Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chodźki St., 20-093 Lublin, Poland
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12
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Lanzafame M, Nardo T, Ricotti R, Pantaleoni C, D'Arrigo S, Stanzial F, Benedicenti F, Thomas MA, Stefanini M, Orioli D, Botta E. TFIIH stabilization recovers the DNA repair and transcription dysfunctions in thermo-sensitive trichothiodystrophy. Hum Mutat 2022; 43:2222-2233. [PMID: 36259739 DOI: 10.1002/humu.24488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/19/2022] [Accepted: 10/17/2022] [Indexed: 01/25/2023]
Abstract
Trichothiodystrophy (TTD) is a rare hereditary disease whose prominent feature is brittle hair. Additional clinical signs are physical and neurodevelopmental abnormalities and in about half of the cases hypersensitivity to UV radiation. The photosensitive form of TTD (PS-TTD) is most commonly caused by mutations in the ERCC2/XPD gene encoding a subunit of the transcription/DNA repair complex TFIIH. Here we report novel ERCC2/XPD mutations affecting proper protein folding, which generate thermo-labile forms of XPD associated with thermo-sensitive phenotypes characterized by reversible aggravation of TTD clinical signs during episodes of fever. In patient cells, the newly identified XPD variants result in thermo-instability of the whole TFIIH complex and consequent temperature-dependent defects in DNA repair and transcription. Improving the protein folding process by exposing patient cells to low temperature or to the chemical chaperone glycerol allowed rescue of TFIIH thermo-instability and a concomitant recovery of the complex activities. Besides providing a rationale for the peculiar thermo-sensitive clinical features of these new cases, the present findings demonstrate how variations in the cellular concentration of mutated TFIIH impact the cellular functions of the complex and underlie how both quantitative and qualitative TFIIH alterations contribute to TTD clinical features.
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Affiliation(s)
- Manuela Lanzafame
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM) CNR, Pavia, Italy
| | - Tiziana Nardo
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM) CNR, Pavia, Italy
| | - Roberta Ricotti
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM) CNR, Pavia, Italy
| | - Chiara Pantaleoni
- Dipartimento Neuroscienze Pediatriche, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Stefano D'Arrigo
- Dipartimento Neuroscienze Pediatriche, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Mary A Thomas
- Department of Medical Genetics, Cumming, School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Miria Stefanini
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM) CNR, Pavia, Italy
| | - Donata Orioli
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM) CNR, Pavia, Italy
| | - Elena Botta
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM) CNR, Pavia, Italy
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13
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Savu DI, Moisoi N. Mitochondria - Nucleus communication in neurodegenerative disease. Who talks first, who talks louder? BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148588. [PMID: 35780856 DOI: 10.1016/j.bbabio.2022.148588] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/09/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Mitochondria - nuclear coadaptation has been central to eukaryotic evolution. The dynamic dialogue between the two compartments within the context of multiorganellar interactions is critical for maintaining cellular homeostasis and directing the balance survival-death in case of cellular stress. The conceptualisation of mitochondria - nucleus communication has so far been focused on the communication from the mitochondria under stress to the nucleus and the consequent signalling responses, as well as from the nucleus to mitochondria in the context of DNA damage and repair. During ageing processes this dialogue may be better viewed as an integrated bidirectional 'talk' with feedback loops that expand beyond these two organelles depending on physiological cues. Here we explore the current views on mitochondria - nucleus dialogue and its role in maintaining cellular health with a focus on brain cells and neurodegenerative disease. Thus, we detail the transcriptional responses initiated by mitochondrial dysfunction in order to protect itself and the general cellular homeostasis. Additionally, we are reviewing the knowledge of the stress pathways initiated by DNA damage which affect mitochondria homeostasis and we add the information provided by the study of combined mitochondrial and genotoxic damage. Finally, we reflect on how each organelle may take the lead in this dialogue in an ageing context where both compartments undergo accumulation of stress and damage and where, perhaps, even the communications' mechanisms may suffer interruptions.
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Affiliation(s)
- Diana Iulia Savu
- Department of Life and Environmental Physics, Horia Hulubei National Institute of Physics and Nuclear Engineering, Reactorului 30, P.O. Box MG-6, Magurele 077125, Romania
| | - Nicoleta Moisoi
- Leicester School of Pharmacy, Leicester Institute for Pharmaceutical Innovation, Faculty of Health Sciences, De Montfort University, The Gateway, Hawthorn Building 1.03, LE1 9BH Leicester, UK.
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14
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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: 9] [Impact Index Per Article: 4.5] [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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15
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Vanoli J, Nava M, Invernizzi C, Panizzuti F, Grassi G. Metronidazole-induced hepatotoxicity in a patient with xeroderma pigmentosum: A case report. Medicine (Baltimore) 2022; 101:e29416. [PMID: 35623073 PMCID: PMC9276075 DOI: 10.1097/md.0000000000029416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/18/2022] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Whereas metronidazole-induced hepatotoxicity is quite rare in the general population, in individuals carrying a nucleotide excision repair disorder, namely Cockayne syndrome, there is a high risk of developing this complication. PATIENT CONCERNS We report the case of a 44-year-old man, affected by xeroderma pigmentosum, who was admitted to the hospital presenting aspiration pneumoniae caused by worsening dysphagia and with severe hepatotoxicity during the hospitalization. DIAGNOSES Acute hepatitis, which was leading to acute liver failure, occurred during antibiotic treatment with metronidazole and ceftazidime with an elevation of liver enzymes consistent with hepatocellular damage pattern. INTERVENTIONS Hydration with glucose 5% solution, pantoprazole and vitamin K were administered, meanwhile other causes of hepatitis were ruled out and the ongoing antibiotic treatment was stopped suspecting a drug-induced liver injury. OUTCOMES Liver function nearly completely recovered 1 month later with a first rapid improvement, within few days, of aminotransferases and coagulation studies, and slower of cholestatic enzymes. LESSONS We describe the first case available in the literature of hepatotoxicity associated with metronidazole treatment in a xeroderma pigmentosum patient. Clinicians therefore, based on this report and according to the possible underlying mechanism shared by other genetic diseases characterized by alterations in the pathway of DNA-repair, should consider such adverse event also in patients affected by this rare disease.
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Affiliation(s)
| | - Miriam Nava
- University Milano-Bicocca, Milan, Italy
- Clinica Medica, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Chiara Invernizzi
- University Milano-Bicocca, Milan, Italy
- Clinica Medica, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Fabio Panizzuti
- Clinica Medica, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Guido Grassi
- University Milano-Bicocca, Milan, Italy
- Clinica Medica, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
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16
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Thijssen KL, van der Woude M, Davó-Martínez C, Dekkers DHW, Sabatella M, Demmers JAA, Vermeulen W, Lans H. C. elegans TFIIH subunit GTF-2H5/TTDA is a non-essential transcription factor indispensable for DNA repair. Commun Biol 2021; 4:1336. [PMID: 34824371 PMCID: PMC8617094 DOI: 10.1038/s42003-021-02875-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/09/2021] [Indexed: 11/08/2022] Open
Abstract
The 10-subunit TFIIH complex is vital to transcription and nucleotide excision repair. Hereditary mutations in its smallest subunit, TTDA/GTF2H5, cause a photosensitive form of the rare developmental disorder trichothiodystrophy. Some trichothiodystrophy features are thought to be caused by subtle transcription or gene expression defects. TTDA/GTF2H5 knockout mice are not viable, making it difficult to investigate TTDA/GTF2H5 in vivo function. Here we show that deficiency of C. elegans TTDA ortholog GTF-2H5 is, however, compatible with life, in contrast to depletion of other TFIIH subunits. GTF-2H5 promotes TFIIH stability in multiple tissues and is indispensable for nucleotide excision repair, in which it facilitates recruitment of TFIIH to DNA damage. Strikingly, when transcription is challenged, gtf-2H5 embryos die due to the intrinsic TFIIH fragility in absence of GTF-2H5. These results support the idea that TTDA/GTF2H5 mutations cause transcription impairment underlying trichothiodystrophy and establish C. elegans as model for studying pathogenesis of this disease.
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Affiliation(s)
- Karen L Thijssen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Dick H W Dekkers
- Proteomics Center, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Mariangela Sabatella
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Mariangela Sabatella, Princess Máxima Center for pediatric oncology, Heidelberglaan 25, 3584 CT, Utrecht, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands.
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17
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Ainsbury EA, Barnard SGR. Sensitivity and latency of ionising radiation-induced cataract. Exp Eye Res 2021; 212:108772. [PMID: 34562436 DOI: 10.1016/j.exer.2021.108772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/26/2021] [Accepted: 09/20/2021] [Indexed: 01/29/2023]
Abstract
When managed with appropriate radiation protection procedures, ionising radiation is of great benefit to society. Opacification of the lens, and vision impairing cataract, have recently been recognised at potential effects of relatively low dose radiation exposure, on the order of 1 Gy or below. Within the last 10 years, understanding of the effects of low dose ionising radiation on the lens has increased, particularly in terms of DNA damage and responses, and how multiple radiation or other events in the lens might contribute to the overall risk of cataract. However, gaps remain, not least in the understanding of how radiation interacts with other risk factors such as aging, as well as the relative radiosensitivity of the lens compared to tissues of the body. This paper reviews the current literature in the field of low dose radiation cataract, with a particular focus on sensitivity and latency.
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Affiliation(s)
- Elizabeth A Ainsbury
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot Oxford, OX11 ORQ, UK.
| | - Stephen G R Barnard
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot Oxford, OX11 ORQ, UK.
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18
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Martens MC, Emmert S, Boeckmann L. Xeroderma Pigmentosum: Gene Variants and Splice Variants. Genes (Basel) 2021; 12:1173. [PMID: 34440347 PMCID: PMC8391564 DOI: 10.3390/genes12081173] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/28/2022] Open
Abstract
The nucleotide excision repair (NER) is essential for the repair of ultraviolet (UV)-induced DNA damage, such as cyclobutane pyrimidine dimers (CPDs) and 6,4-pyrimidine-pyrimidone dimers (6,4-PPs). Alterations in genes of the NER can lead to DNA damage repair disorders such as Xeroderma pigmentosum (XP). XP is a rare autosomal recessive genetic disorder associated with UV-sensitivity and early onset of skin cancer. Recently, extensive research has been conducted on the functional relevance of splice variants and their relation to cancer. Here, we focus on the functional relevance of alternative splice variants of XP genes.
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Affiliation(s)
| | | | - Lars Boeckmann
- Clinic and Policlinic for Dermatology and Venerology, University Medical Center Rostock, 18057 Rostock, Germany; (M.C.M.); (S.E.)
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19
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Raina A, Sahu PK, Laskar RA, Rajora N, Sao R, Khan S, Ganai RA. Mechanisms of Genome Maintenance in Plants: Playing It Safe With Breaks and Bumps. Front Genet 2021; 12:675686. [PMID: 34239541 PMCID: PMC8258418 DOI: 10.3389/fgene.2021.675686] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/04/2021] [Indexed: 01/14/2023] Open
Abstract
Maintenance of genomic integrity is critical for the perpetuation of all forms of life including humans. Living organisms are constantly exposed to stress from internal metabolic processes and external environmental sources causing damage to the DNA, thereby promoting genomic instability. To counter the deleterious effects of genomic instability, organisms have evolved general and specific DNA damage repair (DDR) pathways that act either independently or mutually to repair the DNA damage. The mechanisms by which various DNA repair pathways are activated have been fairly investigated in model organisms including bacteria, fungi, and mammals; however, very little is known regarding how plants sense and repair DNA damage. Plants being sessile are innately exposed to a wide range of DNA-damaging agents both from biotic and abiotic sources such as ultraviolet rays or metabolic by-products. To escape their harmful effects, plants also harbor highly conserved DDR pathways that share several components with the DDR machinery of other organisms. Maintenance of genomic integrity is key for plant survival due to lack of reserve germline as the derivation of the new plant occurs from the meristem. Untowardly, the accumulation of mutations in the meristem will result in a wide range of genetic abnormalities in new plants affecting plant growth development and crop yield. In this review, we will discuss various DNA repair pathways in plants and describe how the deficiency of each repair pathway affects plant growth and development.
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Affiliation(s)
- Aamir Raina
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, India
- Botany Section, Women’s College, Aligarh Muslim University, Aligarh, India
| | - Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Agriculture University, Raipur, India
| | | | - Nitika Rajora
- National Agri-Food Biotechnology Institute, Mohali, India
| | - Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Agriculture University, Raipur, India
| | - Samiullah Khan
- Mutation Breeding Laboratory, Department of Botany, Aligarh Muslim University, Aligarh, India
| | - Rais A. Ganai
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, India
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20
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Reduced levels of prostaglandin I 2 synthase: a distinctive feature of the cancer-free trichothiodystrophy. Proc Natl Acad Sci U S A 2021; 118:2024502118. [PMID: 34155103 DOI: 10.1073/pnas.2024502118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cancer-free photosensitive trichothiodystrophy (PS-TTD) and the cancer-prone xeroderma pigmentosum (XP) are rare monogenic disorders that can arise from mutations in the same genes, namely ERCC2/XPD or ERCC3/XPB Both XPD and XPB proteins belong to the 10-subunit complex transcription factor IIH (TFIIH) that plays a key role in transcription and nucleotide excision repair, the DNA repair pathway devoted to the removal of ultraviolet-induced DNA lesions. Compelling evidence suggests that mutations affecting the DNA repair activity of TFIIH are responsible for the pathological features of XP, whereas those also impairing transcription give rise to TTD. By adopting a relatives-based whole transcriptome sequencing approach followed by specific gene expression profiling in primary fibroblasts from a large cohort of TTD or XP cases with mutations in ERCC2/XPD gene, we identify the expression alterations specific for TTD primary dermal fibroblasts. While most of these transcription deregulations do not impact on the protein level, very low amounts of prostaglandin I2 synthase (PTGIS) are found in TTD cells. PTGIS catalyzes the last step of prostaglandin I2 synthesis, a potent vasodilator and inhibitor of platelet aggregation. Its reduction characterizes all TTD cases so far investigated, both the PS-TTD with mutations in TFIIH coding genes as well as the nonphotosensitive (NPS)-TTD. A severe impairment of TFIIH and RNA polymerase II recruitment on the PTGIS promoter is found in TTD but not in XP cells. Thus, PTGIS represents a biomarker that combines all PS- and NPS-TTD cases and distinguishes them from XP.
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21
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Coppedè F. Mutations Involved in Premature-Ageing Syndromes. APPLICATION OF CLINICAL GENETICS 2021; 14:279-295. [PMID: 34103969 PMCID: PMC8180271 DOI: 10.2147/tacg.s273525] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/17/2021] [Indexed: 12/12/2022]
Abstract
Premature-ageing syndromes are a heterogeneous group of rare genetic disorders resembling features of accelerated ageing and resulting from mutations in genes coding for proteins required for nuclear lamina architecture, DNA repair and maintenance of genome stability, mitochondrial function and other cellular processes. Hutchinson–Gilford progeria syndrome (HGPS) and Werner syndrome (WS) are two of the best-characterized progeroid syndromes referred to as childhood- and adulthood-progeria, respectively. This article provides an updated overview of the mutations leading to HGPS, WS, and to the spectrum of premature-ageing laminopathies ranging in severity from congenital restrictive dermopathy (RD) to adult-onset atypical WS, including RD-like laminopathies, typical and atypical HGPS, more and less severe forms of mandibuloacral dysplasia (MAD), Néstor-Guillermo progeria syndrome (NGPS), atypical WS, and atypical progeroid syndromes resembling features of HGPS and/or MAD but resulting from impaired DNA repair or mitochondrial functions, including mandibular hypoplasia, deafness, progeroid features, and lipodystrophy (MDPL) syndrome and mandibuloacral dysplasia associated to MTX2 (MADaM). The overlapping signs and symptoms among different premature-ageing syndromes, resulting from both a large genetic heterogeneity and shared pathological pathways underlying these conditions, require an expert clinical evaluation in specialized centers paralleled by next-generation sequencing of panels of genes involved in these disorders in order to establish as early as possible an accurate clinical and molecular diagnosis for a proper patient management.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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22
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Nabouli I, Chikhaoui A, Othman H, Elouej S, Jones M, Lagarde A, Rekaya MB, Messaoud O, Zghal M, Delague V, Levy N, De Sandre-Giovannoli A, Abdelhak S, Yacoub-Youssef H. Case Report: Identification of Novel Variants in ERCC4 and DDB2 Genes in Two Tunisian Patients With Atypical Xeroderma Pigmentosum Phenotype. Front Genet 2021; 12:650639. [PMID: 34135938 PMCID: PMC8203331 DOI: 10.3389/fgene.2021.650639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Xeroderma Pigmentosum (XP) is a rare genetic disorder affecting the nucleotide excision repair system (NER). It is characterized by an extreme sensitivity to sunlight that induces cutaneous disorders such as severe sunburn, freckling and cancers. In Tunisia, six complementation groups have been already identified. However, the genetic etiology remains unknown for several patients. In this study, we investigated clinical characteristics and genetic defects in two families with atypical phenotypes originating from the central region in Tunisia. Clinical investigation revealed mild cutaneous features in two patients who develop multiple skin cancers at later ages, with no neurological disorders. Targeted gene sequencing revealed that they carried novel variants. A homozygous variation in the ERCC4 gene c.1762G>T, p.V588F, detected in patient XP21. As for patient XP134, he carried two homozygous mutations in the DDB2 gene c.613T>C, p.C205R and c.618C>A, p.S206R. Structural modeling of the protein predicted the identified ERCC4 variant to mildly affect protein stability without affecting its functional domains. As for the case of DDB2 double mutant, the second variation seems to cause a mild effect on the protein structure unlike the first variation which does not seem to have an effect on it. This study contributes to further characterize the mutation spectrum of XP in Tunisian families. Targeted gene sequencing accelerated the identification of rare unexpected genetic defects for diagnostic testing and genetic counseling.
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Affiliation(s)
- Imen Nabouli
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Asma Chikhaoui
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Houcemeddine Othman
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Sahar Elouej
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Meriem Jones
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia.,Service de dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | - Arnaud Lagarde
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - Meriem Ben Rekaya
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Mohamed Zghal
- Service de dermatologie, Hôpital Charles Nicolle, Tunis, Tunisia
| | | | - Nicolas Levy
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France.,Departement of Medical Genetics, Assistance Publique Hôpitaux de Marseille, La Timone Children's Hospital, Marseille, France
| | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France.,Biological Resource Center (CRB-TAC), Assistance Publique Hôpitaux de Marseille, La Timone Children's Hospital, Marseille, France
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, LR16IPT05, Université Tunis ElManar, Tunis, Tunisia
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23
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Niazi Y, Thomsen H, Smolkova B, Vodickova L, Vodenkova S, Kroupa M, Vymetalkova V, Kazimirova A, Barancokova M, Volkovova K, Staruchova M, Hoffmann P, Nöthen MM, Dusinska M, Musak L, Vodicka P, Försti A, Hemminki K. DNA repair gene polymorphisms and chromosomal aberrations in healthy, nonsmoking population. DNA Repair (Amst) 2021; 101:103079. [PMID: 33676360 DOI: 10.1016/j.dnarep.2021.103079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Nonspecific structural chromosomal aberrations (CAs) can be found at around 1% of circulating lymphocytes from healthy individuals but the frequency may be higher after exposure to carcinogenic chemicals or radiation. The frequency of CAs has been measured in occupational monitoring and an increased frequency of CAs has also been associated with cancer risk. Alterations in DNA damage repair and telomere maintenance are thought to contribute to the formation of CAs, which include chromosome type of aberrations and chromatid type of aberrations. In the present study, we used the result of our published genome-wide association studies to extract data on 153 DNA repair genes from 866 nonsmoking persons who had no known occupational exposure to genotoxic substances. Considering an arbitrary cut-off level of P< 5 × 10-3, single nucleotide polymorphisms (SNPs) tagging 22 DNA repair genes were significantly associated with CAs and they remained significant at P < 0.05 when adjustment for multiple comparisons was done by the Binomial Sequential Goodness of Fit test. Nucleotide excision repair pathway genes showed most associations with 6 genes. Among the associated genes were several in which mutations manifest CA phenotype, including Fanconi anemia, WRN, BLM and genes that are important in maintaining genome stability, as well as PARP2 and mismatch repair genes. RPA2 and RPA3 may participate in telomere maintenance through the synthesis of the C strand of telomeres. Errors in NHEJ1 function may lead to translocations. The present results show associations with some genes with known CA phenotype and suggest other pathways with mechanistic rationale for the formation of CAs in healthy nonsmoking population.
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Affiliation(s)
- Yasmeen Niazi
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
| | - Hauke Thomsen
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; GeneWerk GmbH, Im Neuenheimer Feld 582, 6910 Heidelberg, Germany
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 84505 Bratislava, Slovakia
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Soňa Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic
| | - Michal Kroupa
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Alena Kazimirova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Magdalena Barancokova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Katarina Volkovova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Marta Staruchova
- Department of Biology, Faculty of Medicine, Slovak Medical University, Limbova 12, 833 03 Bratislava, Slovakia
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany; Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003 Basel, Switzerland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Maria Dusinska
- Health Effects Laboratory, Department of Environmental Chemistry, NILU-Norwegian Institute for Air Research, Instituttveien 18, 2007 Kjeller, Norway
| | - Ludovit Musak
- Biomedical Center Martin, Comenius University in Bratislava, Jessenius Faculty of Medicine, Malá Hora 4D, 03601 Martin, Slovakia
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic
| | - Asta Försti
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, 30605 Pilsen, Czech Republic; Division of Cancer Epidemiology, German Cancer Research Centre (DKFZ), 69120 Heidelberg, Germany
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24
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Agolini E, Botta E, Lodi M, Digilio MC, Rinelli M, Bellacchio E, Alesi V, Nardo T, Zambruno G, Orioli D, Alessi I, Boccuto L, Rossi S, Carai A, Colafati GS, Cacchione A, Dallapiccola B, Novelli A, Mastronuzzi A. Expansion of the clinical and molecular spectrum of an XPD-related disorder linked to biallelic mutations in ERCC2 gene. Clin Genet 2021; 99:842-848. [PMID: 33733458 DOI: 10.1111/cge.13957] [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: 11/17/2020] [Revised: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/01/2022]
Abstract
Bi-allelic inactivation of XPD protein, a nucleotide excision repair (NER) signaling pathway component encoded by ERCC2 gene, has been associated with several defective DNA repair phenotypes, including xeroderma pigmentosum, photosensitive trichothiodystrophy, and cerebro-oculo-facio-skeletal syndrome. We report a pediatric patient harboring two compound heterozygous variants in ERCC2 gene, c.361-1G>A and c.2125A>C (p.Thr709Pro), affected by severe postnatal growth deficiency, microcephaly, facial dysmorphisms and pilocytic astrocytoma of the brainstem. Some of these features point to a DNA repair syndrome, and altogether delineate a phenotype differentiating from disorders known to be associated with ERCC2 mutations. The DNA repair efficiency following UV irradiation in the proband's skin fibroblasts was defective indicating that the new set of ERCC2 alleles impacts on NER efficiency. Sequencing analysis on tumor DNA did not reveal any somatic deleterious point variant in cancer-related genes, while SNP-array analysis disclosed a 2 Mb microduplication involving the 7q34 region, spanning from KIAA1549 to BRAF, and resulting in the KIAA1549:BRAF fusion protein, a marker of pilocytic astrocytoma. In conclusion, this report expands the clinical and mutational spectrum of ERCC2-related disorders.
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Affiliation(s)
- Emanuele Agolini
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Elena Botta
- Institute of Molecular Genetics LL Cavalli Sforza-CNR, Pavia, Italy
| | - Mariachiara Lodi
- Department of Hematology/Oncology, Gene and Cell Therapy, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Martina Rinelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Viola Alesi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Tiziana Nardo
- Institute of Molecular Genetics LL Cavalli Sforza-CNR, Pavia, Italy
| | - Giovanna Zambruno
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Donata Orioli
- Institute of Molecular Genetics LL Cavalli Sforza-CNR, Pavia, Italy
| | - Iside Alessi
- Department of Hematology/Oncology, Gene and Cell Therapy, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Luigi Boccuto
- College of Behavioral, Social and Health Sciences, Clemson University, Clemson, South Carolina, USA.,Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Sabrina Rossi
- Pathology Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Carai
- Neurosurgery Unit, Department of Neurosciences and Neurorehabilitation, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | | | - Antonella Cacchione
- Department of Hematology/Oncology, Gene and Cell Therapy, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Angela Mastronuzzi
- Department of Hematology/Oncology, Gene and Cell Therapy, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
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25
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Topka S, Steinsnyder Z, Ravichandran V, Tkachuk K, Kemel Y, Bandlamudi C, Winkel Madsen M, Furberg H, Ouerfelli O, Rudin CM, Iyer G, Lipkin SM, Mukherjee S, Solit DB, Berger MF, Bajorin DF, Rosenberg JE, Taylor BS, de Stanchina E, Vijai J, Offit K. Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer. Clin Cancer Res 2021; 27:1997-2010. [PMID: 33199492 DOI: 10.1158/1078-0432.ccr-20-3322] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/19/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities. EXPERIMENTAL DESIGN We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes. Gene-edited isogenic pairs of wild-type and mutant ERCC2 or ERCC3 cell lines were created and used to assess response to several candidate drugs. RESULTS We found that putative damaging germline and somatic alterations in NER genes were present with frequencies up to 10% across multiple cancer types. Both in vitro and in vivo studies showed significantly enhanced sensitivity to the sesquiterpene irofulven in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to a current standard-of-care agent, cisplatin. Hypomorphic ERCC2/3-mutant cells had impaired ability to repair irofulven-induced DNA damage. Transcriptomic profiling of tumor tissues suggested codependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies. CONCLUSIONS These findings provide novel insights into a synthetic lethal relationship between clinically observed NER gene deficiencies and sensitivity to irofulven and its potential synergistic combination with other drugs.See related commentary by Jiang and Greenberg, p. 1833.
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Affiliation(s)
- Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Helena Furberg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ouathek Ouerfelli
- Chemical Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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26
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Sirchia F, Fantasia I, Feresin A, Giorgio E, Faletra F, Mordeglia D, Barbieri M, Guida V, De Luca A, Stampalija T. Prenatal findings of cataract and arthrogryposis: recurrence of cerebro-oculo-facio-skeletal syndrome and review of differential diagnosis. BMC Med Genomics 2021; 14:89. [PMID: 33766032 PMCID: PMC7992958 DOI: 10.1186/s12920-021-00939-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cerebro-oculo-facio-skeletal syndrome (COFS) is a severe and progressive neurologic condition characterized by prenatal onset of arthrogryposis, cataract, microcephaly and growth failure. The aim of this study was to present a case of recurrence of the COFS syndrome and to propose a differential diagnosis flow-chart in case of prenatal findings of arthrogryposis and cataract. CASE PRESENTATION We report a case of recurrence of COFS3 syndrome within the same family, with similar diagnostic features. In the first case the COFS syndrome remained undiagnosed, while in the second case, due to prenatal findings of arthrogryposis and cataract, genetic investigation focusing on responsible genes of COFS (ERCC5, ERCC6 and FKTN genes) was carried out. The fetus was found to be compound heterozygous for two different ERCC5 mutations, confirming the clinical suspect of COFS syndrome. A review of the literature on possible causative genes of prenatal cataract and arthrogryposis was performed and we present a flow-chart to guide differential diagnosis and possible genetic testing in case of these findings. CONCLUSION COFS syndrome is a rare autosomic recessive condition. However, it can be suspected and diagnosed prenatally. The flow-chart illustrates a pathway to guide differential diagnosis according to the prenatal findings. Main syndromes, key testing and specific genes are included. Targeted molecular testing should be offered to the couple in order to reach a diagnosis and assess the recurrence risk for future pregnancies.
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Affiliation(s)
- Fabio Sirchia
- Department of Molecular Medicine, University of Pavia, Via Forlanini 14, 27100, Pavia, Italy.
| | - Ilaria Fantasia
- Unit of Fetal Medicine e Prenatal Diagnosis, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Agnese Feresin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Flavio Faletra
- Department of Medical Genetics, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Denise Mordeglia
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Moira Barbieri
- Unit of Fetal Medicine e Prenatal Diagnosis, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
| | - Valentina Guida
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Alessandro De Luca
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Tamara Stampalija
- Unit of Fetal Medicine e Prenatal Diagnosis, Institute for Maternal and Child Health IRCCS "Burlo Garofolo", Trieste, Italy
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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27
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Barnard SGR, McCarron R, Mancuso M, De Stefano I, Pazzaglia S, Pawliczek D, Dalke C, Ainsbury EA. Radiation-induced DNA Damage and Repair in Lens Epithelial Cells of both Ptch1(+/-) and Ercc2(+/-) Mutated Mice. Radiat Res 2021; 197:36-42. [PMID: 33652474 DOI: 10.1667/rade-20-00264.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/22/2021] [Indexed: 11/03/2022]
Abstract
Epidemiological studies suggest an increased incidence and risk of cataract after low-dose (<2 Gy) ionizing radiation exposures. However, the biological mechanism(s) of this process are not fully understood. DNA damage and repair are thought to have a contributing role in radiation-induced cataractogenesis. Recently we have reported an inverse dose-rate effect, as well as the low-dose response, of DNA damage and repair in lens epithelial cells (LECs). Here, we present further initial findings from two mutated strains (Ercc2+/- and Ptch1+/-) of mice, both reportedly susceptible to radiation-induced cataract, and their DNA damage and repair response to low-dose and low-dose-rate gamma rays. Our results support the hypothesis that the lens epithelium responds differently to radiation than other tissues, with reported radiation susceptibility to DNA damage not necessarily translating to the LECs. Genetic predisposition and strain(s) of mice have a significant role in radiation-induced cataract susceptibility.
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Affiliation(s)
- S G R Barnard
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot, Oxon, United Kingdom.,Department of Biosciences, University of Durham, Mountjoy Science Site, Durham DH13LE, United Kingdom
| | - R McCarron
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot, Oxon, United Kingdom
| | - M Mancuso
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Rome, Italy
| | - I De Stefano
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Rome, Italy
| | - S Pazzaglia
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Rome, Italy
| | - D Pawliczek
- Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany
| | - C Dalke
- Helmholtz Zentrum München GmbH - German Research Center for Environmental Health, Institute of Developmental Genetics, Neuherberg, Germany
| | - E A Ainsbury
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, Didcot, Oxon, United Kingdom
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28
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Zhou Q, Fu Y, Wen L, Deng Y, Chen J, Liu K. XPD Polymorphisms and Risk of Hepatocellular Carcinoma and Gastric Cancer: A Meta-Analysis. Technol Cancer Res Treat 2021; 20:1533033821990046. [PMID: 33517857 PMCID: PMC7871355 DOI: 10.1177/1533033821990046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background: Cancer is associated with genetic variants of DNA repair genes that alter DNA
repair capacity. The aim of this meta-analysis was to evaluate the relations
between the rs13181 and rs1799793 XPD gene polymorphisms and risk for
hepatocellular carcinoma (HCC) and gastric cancer. Methods: Relevant publications were systematically sought from Web of Science, Pubmed,
and China Academic Journals Full-text Database. The selection of eligible
studies was performed by 2 independent authors. A total of 32 case-control
studies were included. Meta-analyses were undertaken in all study
participants and each ethnic group. Results: The risk of HCC was significantly increased with the XPD rs13181 G allele (P
= 0.028, pooled odds ratio (OR) = 1.36, 95% confidence interval (CI) =
1.03-1.80) in all study participants. A subgroup analysis by ethnicity
showed that the association was significant in Chinese (P = 0.009, pooled OR
= 1.49, 95% CI = 1.11-2.02), but not in Caucasians (P = 0.619, pooled OR =
1.17, 95% CI = 0.64-2.13). Meta-analysis of the XPD rs1799793 polymorphism
and HCC showed an association between its variant T allele and increased HCC
risk in all study participants (P = 0.017, pooled OR = 1.23, 95% CI =
1.04-1.46, all Chinese). Our results showed no associations between the XPD
rs13181 G allele and rs1799793 T allele and gastric cancer risk (rs13181: P
= 0.298, pooled OR = 1.10, 95% CI = 0.92-1.31; rs1799793: P = 0.068, pooled
OR = 1.31, 95% CI = 0.98-1.74). Conclusions: This meta-analysis demonstrated that the XPD rs13181 G allele and rs1799793 T
allele have significant associations with HCC and may be risk factors for
HCC in the Chinese population. Current evidence indicated that they are not
related to gastric cancer risk.
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Affiliation(s)
- Qiang Zhou
- Department of Hepatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yu Fu
- Department of Hepatopancreatobiliary Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Lijia Wen
- Department of Hepatopancreatobiliary Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yu Deng
- Department of Hepatopancreatobiliary Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Junhong Chen
- Department of Hepatopancreatobiliary Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Kai Liu
- Department of Hepatopancreatobiliary Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
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29
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Bermisheva MA, Gilyazova IR, Zinnatullina GF, Khusnutdinova EK. Analysis of Rare Variant c.2395C>T (p.Arg799Trp) in Gene ERCC4 in Breast Cancer Patients from Bashkortostan. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420050026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Le Van Quyen P, Calmels N, Bonnière M, Chartier S, Razavi F, Chelly J, El Chehadeh S, Baer S, Boutaud L, Bacrot S, Obringer C, Favre R, Attié-Bitach T, Laugel V, Antal MC. Prenatal diagnosis of cerebro-oculo-facio-skeletal syndrome: Report of three fetuses and review of the literature. Am J Med Genet A 2020; 182:1236-1242. [PMID: 32052936 DOI: 10.1002/ajmg.a.61520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 11/22/2019] [Accepted: 01/29/2020] [Indexed: 12/15/2022]
Abstract
Cerebro-oculo-facio-skeletal syndrome (COFS) is a rare autosomal recessive neurodegenerative disease belonging to the family of DNA repair disorders, characterized by microcephaly, congenital cataracts, facial dysmorphism and arthrogryposis. Here, we describe the detailed morphological and microscopic phenotype of three fetuses from two families harboring ERCC5/XPG likely pathogenic variants, and review the five previously reported fetal cases. In addition to the classical features of COFS, the fetuses display thymus hyperplasia, splenomegaly and increased hematopoiesis. Microencephaly is present in the three fetuses with delayed development of the gyri, but normal microscopic anatomy at the supratentorial level. Microscopic anomalies reminiscent of pontocerebellar hypoplasia are present at the infratentorial level. In conclusion, COFS syndrome should be considered in fetuses when intrauterine growth retardation is associated with microcephaly, arthrogryposis and ocular anomalies. Further studies are needed to better understand XPG functions during human development.
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Affiliation(s)
- Pauline Le Van Quyen
- Unité de Fœtopathologie, Service de Pathologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nadège Calmels
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Laboratoire de Génétique Médicale-INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Maryse Bonnière
- Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris Cedex 15, France
| | - Suzanne Chartier
- Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris Cedex 15, France
| | - Féréchté Razavi
- Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris Cedex 15, France
| | - Jamel Chelly
- Laboratoires de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sarah Baer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Lucile Boutaud
- Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris Cedex 15, France.,Inserm U1163, Institut Imagine, Université Paris Descartes, Paris Cedex 15, France
| | - Séverine Bacrot
- Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris Cedex 15, France
| | - Cathy Obringer
- Laboratoire de Génétique Médicale-INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Romain Favre
- Service de Gynécologie-Obstétrique, Centre Médico-Chirurgical et Obstétrical (CMCO), Hôpitaux Universitaires de Strasbourg, Schiltigheim Cedex, France
| | - Tania Attié-Bitach
- Unité d'Embryofœtopathologie, Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris Cedex 15, France.,Inserm U1163, Institut Imagine, Université Paris Descartes, Paris Cedex 15, France
| | - Vincent Laugel
- Laboratoire de Génétique Médicale-INSERM U1112, Institut de Génétique Médicale d'Alsace (IGMA), Faculté de Médecine, Université de Strasbourg, Strasbourg, France.,Service de Pédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Maria C Antal
- Unité de Fœtopathologie, Service de Pathologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut d'Histologie, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
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31
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Lans H, Hoeijmakers JHJ, Vermeulen W, Marteijn JA. The DNA damage response to transcription stress. Nat Rev Mol Cell Biol 2019; 20:766-784. [DOI: 10.1038/s41580-019-0169-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/30/2022]
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32
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Tiwari V, Wilson DM. DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging. Am J Hum Genet 2019; 105:237-257. [PMID: 31374202 PMCID: PMC6693886 DOI: 10.1016/j.ajhg.2019.06.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic information is constantly being attacked by intrinsic and extrinsic damaging agents, such as reactive oxygen species, atmospheric radiation, environmental chemicals, and chemotherapeutics. If DNA modifications persist, they can adversely affect the polymerization of DNA or RNA, leading to replication fork collapse or transcription arrest, or can serve as mutagenic templates during nucleic acid synthesis reactions. To combat the deleterious consequences of DNA damage, organisms have developed complex repair networks that remove chemical modifications or aberrant base arrangements and restore the genome to its original state. Not surprisingly, inherited or sporadic defects in DNA repair mechanisms can give rise to cellular outcomes that underlie disease and aging, such as transformation, apoptosis, and senescence. In the review here, we discuss several genetic disorders linked to DNA repair defects, attempting to draw correlations between the nature of the accumulating DNA damage and the pathological endpoints, namely cancer, neurological disease, and premature aging.
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Affiliation(s)
- Vinod Tiwari
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA.
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33
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Phan T, Khalid F, Iben S. Nucleolar and Ribosomal Dysfunction-A Common Pathomechanism in Childhood Progerias? Cells 2019; 8:E534. [PMID: 31167386 PMCID: PMC6627804 DOI: 10.3390/cells8060534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/21/2019] [Accepted: 06/02/2019] [Indexed: 01/03/2023] Open
Abstract
The nucleolus organizes around the sites of transcription by RNA polymerase I (RNA Pol I). rDNA transcription by this enzyme is the key step of ribosome biogenesis and most of the assembly and maturation processes of the ribosome occur co-transcriptionally. Therefore, disturbances in rRNA transcription and processing translate to ribosomal malfunction. Nucleolar malfunction has recently been described in the classical progeria of childhood, Hutchinson-Gilford syndrome (HGPS), which is characterized by severe signs of premature aging, including atherosclerosis, alopecia, and osteoporosis. A deregulated ribosomal biogenesis with enlarged nucleoli is not only characteristic for HGPS patients, but it is also found in the fibroblasts of "normal" aging individuals. Cockayne syndrome (CS) is also characterized by signs of premature aging, including the loss of subcutaneous fat, alopecia, and cataracts. It has been shown that all genes in which a mutation causes CS, are involved in rDNA transcription by RNA Pol I. A disturbed ribosomal biogenesis affects mitochondria and translates into ribosomes with a reduced translational fidelity that causes endoplasmic reticulum (ER) stress and apoptosis. Therefore, it is speculated that disease-causing disturbances in the process of ribosomal biogenesis may be more common than hitherto anticipated.
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Affiliation(s)
- Tamara Phan
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
| | - Fatima Khalid
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
| | - Sebastian Iben
- Department of Dermatology, Ulm University, James-Franck Ring N27, 89081 Ulm, Germany.
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