1
|
Shender VO, Anufrieva KS, Shnaider PV, Arapidi GP, Pavlyukov MS, Ivanova OM, Malyants IK, Stepanov GA, Zhuravlev E, Ziganshin RH, Butenko IO, Bukato ON, Klimina KM, Veselovsky VA, Grigorieva TV, Malanin SY, Aleshikova OI, Slonov AV, Babaeva NA, Ashrafyan LA, Khomyakova E, Evtushenko EG, Lukina MM, Wang Z, Silantiev AS, Nushtaeva AA, Kharlampieva DD, Lazarev VN, Lashkin AI, Arzumanyan LK, Petrushanko IY, Makarov AA, Lebedeva OS, Bogomazova AN, Lagarkova MA, Govorun VM. Therapy-induced secretion of spliceosomal components mediates pro-survival crosstalk between ovarian cancer cells. Nat Commun 2024; 15:5237. [PMID: 38898005 PMCID: PMC11187153 DOI: 10.1038/s41467-024-49512-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Ovarian cancer often develops resistance to conventional therapies, hampering their effectiveness. Here, using ex vivo paired ovarian cancer ascites obtained before and after chemotherapy and in vitro therapy-induced secretomes, we show that molecules secreted by ovarian cancer cells upon therapy promote cisplatin resistance and enhance DNA damage repair in recipient cancer cells. Even a short-term incubation of chemonaive ovarian cancer cells with therapy-induced secretomes induces changes resembling those that are observed in chemoresistant patient-derived tumor cells after long-term therapy. Using integrative omics techniques, we find that both ex vivo and in vitro therapy-induced secretomes are enriched with spliceosomal components, which relocalize from the nucleus to the cytoplasm and subsequently into the extracellular vesicles upon treatment. We demonstrate that these molecules substantially contribute to the phenotypic effects of therapy-induced secretomes. Thus, SNU13 and SYNCRIP spliceosomal proteins promote therapy resistance, while the exogenous U12 and U6atac snRNAs stimulate tumor growth. These findings demonstrate the significance of spliceosomal network perturbation during therapy and further highlight that extracellular signaling might be a key factor contributing to the emergence of ovarian cancer therapy resistance.
Collapse
Affiliation(s)
- Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology; Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Georgij P Arapidi
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Irina K Malyants
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Evgenii Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Ivan O Butenko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Olga N Bukato
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Ksenia M Klimina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Vladimir A Veselovsky
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | | | | | - Olga I Aleshikova
- National Medical Scientific Centre of Obstetrics, Gynaecology and Perinatal Medicine named after V.I. Kulakov, Moscow, 117198, Russian Federation
- Russian Research Center of Roentgenology and Radiology, Moscow, 117997, Russian Federation
| | - Andrey V Slonov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Nataliya A Babaeva
- National Medical Scientific Centre of Obstetrics, Gynaecology and Perinatal Medicine named after V.I. Kulakov, Moscow, 117198, Russian Federation
- Russian Research Center of Roentgenology and Radiology, Moscow, 117997, Russian Federation
| | - Lev A Ashrafyan
- National Medical Scientific Centre of Obstetrics, Gynaecology and Perinatal Medicine named after V.I. Kulakov, Moscow, 117198, Russian Federation
- Russian Research Center of Roentgenology and Radiology, Moscow, 117997, Russian Federation
| | | | - Evgeniy G Evtushenko
- Faculty of Chemistry; Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Zixiang Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University; Jinan, 250012, Shandong, China
| | - Artemiy S Silantiev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anna A Nushtaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russian Federation
| | - Daria D Kharlampieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Vassili N Lazarev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Arseniy I Lashkin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Lorine K Arzumanyan
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Irina Yu Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Olga S Lebedeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Alexandra N Bogomazova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Maria A Lagarkova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Vadim M Govorun
- Research Institute for Systems Biology and Medicine, Moscow, 117246, Russian Federation
| |
Collapse
|
2
|
Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024; 43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [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: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024] Open
Abstract
TDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis.
Collapse
Affiliation(s)
- Mathéa Geraud
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Simona Salimbeni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Nicolas Bery
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Virginie Jouffret
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France; BigA Core Facility, Centre de Biologie Intégrative (CBI), Université de Toulouse, 31062 Toulouse, France
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Andrea Carla Ajello
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Pierre Cordelier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France.
| |
Collapse
|
3
|
Siametis A, Stratigi K, Giamaki D, Chatzinikolaou G, Akalestou-Clocher A, Goulielmaki E, Luke B, Schumacher B, Garinis GA. Transcription stress at telomeres leads to cytosolic DNA release and paracrine senescence. Nat Commun 2024; 15:4061. [PMID: 38744897 PMCID: PMC11094137 DOI: 10.1038/s41467-024-48443-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription stress has been linked to DNA damage -driven aging, yet the underlying mechanism remains unclear. Here, we demonstrate that Tcea1-/- cells, which harbor a TFIIS defect in transcription elongation, exhibit RNAPII stalling at oxidative DNA damage sites, impaired transcription, accumulation of R-loops, telomere uncapping, chromatin bridges, and genome instability, ultimately resulting in cellular senescence. We found that R-loops at telomeres causally contribute to the release of telomeric DNA fragments in the cytoplasm of Tcea1-/- cells and primary cells derived from naturally aged animals triggering a viral-like immune response. TFIIS-defective cells release extracellular vesicles laden with telomeric DNA fragments that target neighboring cells, which consequently undergo cellular senescence. Thus, transcription stress elicits paracrine signals leading to cellular senescence, promoting aging.
Collapse
Affiliation(s)
- Athanasios Siametis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Despoina Giamaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology (IMB), Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Alexia Akalestou-Clocher
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Evi Goulielmaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Brian Luke
- Institute of Molecular Biology (IMB), Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece.
- Department of Biology, University of Crete, Heraklion, Crete, Greece.
| |
Collapse
|
4
|
Stanković D, Tain LS, Uhlirova M. Xrp1 governs the stress response program to spliceosome dysfunction. Nucleic Acids Res 2024; 52:2093-2111. [PMID: 38303573 PMCID: PMC10954486 DOI: 10.1093/nar/gkae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Co-transcriptional processing of nascent pre-mRNAs by the spliceosome is vital to regulating gene expression and maintaining genome integrity. Here, we show that the deficiency of functional U5 small nuclear ribonucleoprotein particles (snRNPs) in Drosophila imaginal cells causes extensive transcriptome remodeling and accumulation of highly mutagenic R-loops, triggering a robust stress response and cell cycle arrest. Despite compromised proliferative capacity, the U5 snRNP-deficient cells increased protein translation and cell size, causing intra-organ growth disbalance before being gradually eliminated via apoptosis. We identify the Xrp1-Irbp18 heterodimer as the primary driver of transcriptional and cellular stress program downstream of U5 snRNP malfunction. Knockdown of Xrp1 or Irbp18 in U5 snRNP-deficient cells attenuated JNK and p53 activity, restored normal cell cycle progression and growth, and inhibited cell death. Reducing Xrp1-Irbp18, however, did not rescue the splicing defects, highlighting the requirement of accurate splicing for cellular and tissue homeostasis. Our work provides novel insights into the crosstalk between splicing and the DNA damage response and defines the Xrp1-Irbp18 heterodimer as a critical sensor of spliceosome malfunction and mediator of the stress-induced cellular senescence program.
Collapse
Affiliation(s)
- Dimitrije Stanković
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Luke S Tain
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| |
Collapse
|
5
|
Valenzisi P, Marabitti V, Pichierri P, Franchitto A. WRNIP1 prevents transcription-associated genomic instability. eLife 2024; 12:RP89981. [PMID: 38488661 PMCID: PMC10942783 DOI: 10.7554/elife.89981] [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] [Indexed: 03/17/2024] Open
Abstract
R-loops are non-canonical DNA structures that form during transcription and play diverse roles in various physiological processes. Disruption of R-loop homeostasis can lead to genomic instability and replication impairment, contributing to several human diseases, including cancer. Although the molecular mechanisms that protect cells against such events are not fully understood, recent research has identified fork protection factors and DNA damage response proteins as regulators of R-loop dynamics. In this study, we identify the Werner helicase-interacting protein 1 (WRNIP1) as a novel factor that counteracts transcription-associated DNA damage upon replication perturbation. Loss of WRNIP1 leads to R-loop accumulation, resulting in collisions between the replisome and transcription machinery. We observe co-localization of WRNIP1 with transcription/replication complexes and R-loops after replication perturbation, suggesting its involvement in resolving transcription-replication conflicts. Moreover, WRNIP1-deficient cells show impaired replication restart from transcription-induced fork stalling. Notably, transcription inhibition and RNase H1 overexpression rescue all the defects caused by loss of WRNIP1. Importantly, our findings highlight the critical role of WRNIP1 ubiquitin-binding zinc finger (UBZ) domain in preventing pathological persistence of R-loops and limiting DNA damage, thereby safeguarding genome integrity.
Collapse
Affiliation(s)
- Pasquale Valenzisi
- Section of Mechanisms Biomarkers and Models, Department of Environment and Health, Istituto Superiore di SanitaRomeItaly
| | - Veronica Marabitti
- Section of Mechanisms Biomarkers and Models, Department of Environment and Health, Istituto Superiore di SanitaRomeItaly
| | - Pietro Pichierri
- Section of Mechanisms Biomarkers and Models, Department of Environment and Health, Istituto Superiore di SanitaRomeItaly
| | - Annapaola Franchitto
- Section of Mechanisms Biomarkers and Models, Department of Environment and Health, Istituto Superiore di SanitaRomeItaly
| |
Collapse
|
6
|
Paull TT, Woolley PR. A-T neurodegeneration and DNA damage-induced transcriptional stress. DNA Repair (Amst) 2024; 135:103647. [PMID: 38377644 DOI: 10.1016/j.dnarep.2024.103647] [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: 12/20/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
Loss of the ATM protein kinase in humans results in Ataxia-telangiectasia, a disorder characterized by childhood-onset neurodegeneration of the cerebellum as well as cancer predisposition and immunodeficiency. Although many aspects of ATM function are well-understood, the mechanistic basis of the progressive cerebellar ataxia that occurs in patients is not. Here we review recent progress related to the role of ATM in neurons and the cerebellum that comes from many sources: animal models, post-mortem brain tissue samples, and human neurons in culture. These observations have revealed new insights into the consequences of ATM loss on DNA damage, gene expression, and immune signaling in the brain. Many results point to the importance of reactive oxygen species as well as single-strand DNA breaks in the progression of molecular events leading to neuronal dysfunction. In addition, innate immunity signaling pathways appear to play a critical role in ATM functions in microglia, responding to various forms of nucleic acid sensors and regulating survival of neurons and other cell types. Overall, the results lead to an updated view of transcriptional stress and DNA damage resulting from ATM loss that results in changes in gene expression as well as neuroinflammation that contribute to the cerebellar neurodegeneration observed in patients.
Collapse
Affiliation(s)
- Tanya T Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA.
| | - Phillip R Woolley
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX 78712, USA
| |
Collapse
|
7
|
Atkinson J, Bezak E, Le H, Kempson I. DNA Double Strand Break and Response Fluorescent Assays: Choices and Interpretation. Int J Mol Sci 2024; 25:2227. [PMID: 38396904 PMCID: PMC10889524 DOI: 10.3390/ijms25042227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Accurately characterizing DNA double-stranded breaks (DSBs) and understanding the DNA damage response (DDR) is crucial for assessing cellular genotoxicity, maintaining genomic integrity, and advancing gene editing technologies. Immunofluorescence-based techniques have proven to be invaluable for quantifying and visualizing DSB repair, providing valuable insights into cellular repair processes. However, the selection of appropriate markers for analysis can be challenging due to the intricate nature of DSB repair mechanisms, often leading to ambiguous interpretations. This comprehensively summarizes the significance of immunofluorescence-based techniques, with their capacity for spatiotemporal visualization, in elucidating complex DDR processes. By evaluating the strengths and limitations of different markers, we identify where they are most relevant chronologically from DSB detection to repair, better contextualizing what each assay represents at a molecular level. This is valuable for identifying biases associated with each assay and facilitates accurate data interpretation. This review aims to improve the precision of DSB quantification, deepen the understanding of DDR processes, assay biases, and pathway choices, and provide practical guidance on marker selection. Each assay offers a unique perspective of the underlying processes, underscoring the need to select markers that are best suited to specific research objectives.
Collapse
Affiliation(s)
- Jake Atkinson
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia;
| | - Eva Bezak
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5095, Australia; (E.B.)
- Department of Physics, University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Hien Le
- UniSA Allied Health and Human Performance, University of South Australia, Adelaide, SA 5095, Australia; (E.B.)
- Department of Radiation Oncology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Ivan Kempson
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia;
| |
Collapse
|
8
|
Zhou X, Liu X, Wan X, Xu M, Wang R, Yang D, Peng M, Jin T, Tang R, Liu M, Hou Y. Oxidized ATM governs stemness of breast cancer stem cell through regulating ubiquitylation and acetylation switch. Biochem Biophys Res Commun 2024; 691:149243. [PMID: 38016338 DOI: 10.1016/j.bbrc.2023.149243] [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: 08/21/2023] [Revised: 11/05/2023] [Accepted: 11/09/2023] [Indexed: 11/30/2023]
Abstract
Cancer stem cells (CSCs), as parts of tumor initiation cells, play a crucial role to tumorigenesis, development and recurrence. However, the complicated mechanisms of CSCs to adapt to tumor microenvironment and its stemness maintenance remains unclear. Here, we show that oxidized ATM, a hypoxia-activated cytoplasm ATM, acts a novel function to maintain CSC stemness in triple-negative breast cancer cells (BCSCs) via regulating histone H4 acetylation. Mechanistically, oxidized ATM phosphorylates TRIM21 (a E3 ubiquitin ligase) serine 80 and serine 469. Serine 80 phosphorylation of TRIM21 is essential for the ubiquitination activity of TRIM21. TRIM21 binds with SIRT1 (one of deacetylase), resulting in ubiquitylation-mediated degradation of SIRT1. The reduced SIRT1 leads to increase of histone H4 acetylation, thus facilitating CSC-related gene expression. Clinical data verify that high level of ATM in breast tumors is positively correlated with malignant grade, and is closely related with low SIRT1, high p-TRIM21, and high CD44 expression. In conclusion, our study provides a novel mechanism by which oxidized ATM governing BCSCs stemness and reveals an important link among oxidized ATM, histone acetylation, and BCSCs maintenance.
Collapse
Affiliation(s)
- Xinyue Zhou
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaoqi Liu
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, 400014, China
| | - Xueying Wan
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Ming Xu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Rui Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Dan Yang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Meixi Peng
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Ting Jin
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Rui Tang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Manran Liu
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, China
| | - Yixuan Hou
- Experimental Teaching Center of Basic Medicine Science, Chongqing Medical University, Chongqing, 400016, China.
| |
Collapse
|
9
|
Kumar C, Remus D. Looping out of control: R-loops in transcription-replication conflict. Chromosoma 2024; 133:37-56. [PMID: 37419963 PMCID: PMC10771546 DOI: 10.1007/s00412-023-00804-8] [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: 04/18/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Transcription-replication conflict is a major cause of replication stress that arises when replication forks collide with the transcription machinery. Replication fork stalling at sites of transcription compromises chromosome replication fidelity and can induce DNA damage with potentially deleterious consequences for genome stability and organismal health. The block to DNA replication by the transcription machinery is complex and can involve stalled or elongating RNA polymerases, promoter-bound transcription factor complexes, or DNA topology constraints. In addition, studies over the past two decades have identified co-transcriptional R-loops as a major source for impairment of DNA replication forks at active genes. However, how R-loops impede DNA replication at the molecular level is incompletely understood. Current evidence suggests that RNA:DNA hybrids, DNA secondary structures, stalled RNA polymerases, and condensed chromatin states associated with R-loops contribute to the of fork progression. Moreover, since both R-loops and replication forks are intrinsically asymmetric structures, the outcome of R-loop-replisome collisions is influenced by collision orientation. Collectively, the data suggest that the impact of R-loops on DNA replication is highly dependent on their specific structural composition. Here, we will summarize our current understanding of the molecular basis for R-loop-induced replication fork progression defects.
Collapse
Affiliation(s)
- Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA.
| |
Collapse
|
10
|
McGrail DJ, Li Y, Smith RS, Feng B, Dai H, Hu L, Dennehey B, Awasthi S, Mendillo ML, Sood AK, Mills GB, Lin SY, Yi SS, Sahni N. Widespread BRCA1/2-independent homologous recombination defects are caused by alterations in RNA-binding proteins. Cell Rep Med 2023; 4:101255. [PMID: 37909041 PMCID: PMC10694618 DOI: 10.1016/j.xcrm.2023.101255] [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: 06/29/2020] [Revised: 10/02/2022] [Accepted: 09/29/2023] [Indexed: 11/02/2023]
Abstract
Defects in homologous recombination DNA repair (HRD) both predispose to cancer development and produce therapeutic vulnerabilities, making it critical to define the spectrum of genetic events that cause HRD. However, we found that mutations in BRCA1/2 and other canonical HR genes only identified 10%-20% of tumors that display genomic evidence of HRD. Using a networks-based approach, we discovered that over half of putative genes causing HRD originated outside of canonical DNA damage response genes, with a particular enrichment for RNA-binding protein (RBP)-encoding genes. These putative drivers of HRD were experimentally validated, cross-validated in an independent cohort, and enriched in cancer-associated genome-wide association study loci. Mechanistic studies indicate that some RBPs are recruited to sites of DNA damage to facilitate repair, whereas others control the expression of canonical HR genes. Overall, this study greatly expands the repertoire of known drivers of HRD, with implications for basic biology, genetic screening, and therapy stratification.
Collapse
Affiliation(s)
- Daniel J McGrail
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44106, USA; Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA.
| | - Yang Li
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roger S Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Bin Feng
- GSK Oncology Experimental Medicine Unit, Waltham, MA 02451, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Briana Dennehey
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sharad Awasthi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Knight Cancer Institute, Oregon Health and Sciences University, Portland, OR 97201, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
11
|
Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [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: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
Collapse
Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| |
Collapse
|
12
|
Reichlmeir M, Canet-Pons J, Koepf G, Nurieva W, Duecker RP, Doering C, Abell K, Key J, Stokes MP, Zielen S, Schubert R, Ivics Z, Auburger G. In Cerebellar Atrophy of 12-Month-Old ATM-Null Mice, Transcriptome Upregulations Concern Most Neurotransmission and Neuropeptide Pathways, While Downregulations Affect Prominently Itpr1, Usp2 and Non-Coding RNA. Cells 2023; 12:2399. [PMID: 37830614 PMCID: PMC10572167 DOI: 10.3390/cells12192399] [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: 09/14/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/14/2023] Open
Abstract
The autosomal recessive disorder Ataxia-Telangiectasia is caused by a dysfunction of the stress response protein, ATM. In the nucleus of proliferating cells, ATM senses DNA double-strand breaks and coordinates their repair. This role explains T-cell dysfunction and tumour risk. However, it remains unclear whether this function is relevant for postmitotic neurons and underlies cerebellar atrophy, since ATM is cytoplasmic in postmitotic neurons. Here, we used ATM-null mice that survived early immune deficits via bone-marrow transplantation, and that reached initial neurodegeneration stages at 12 months of age. Global cerebellar transcriptomics demonstrated that ATM depletion triggered upregulations in most neurotransmission and neuropeptide systems. Downregulated transcripts were found for the ATM interactome component Usp2, many non-coding RNAs, ataxia genes Itpr1, Grid2, immediate early genes and immunity factors. Allelic splice changes affected prominently the neuropeptide machinery, e.g., Oprm1. Validation experiments with stressors were performed in human neuroblastoma cells, where ATM was localised only to cytoplasm, similar to the brain. Effect confirmation in SH-SY5Y cells occurred after ATM depletion and osmotic stress better than nutrient/oxidative stress, but not after ATM kinase inhibition or DNA stressor bleomycin. Overall, we provide pioneer observations from a faithful A-T mouse model, which suggest general changes in synaptic and dense-core vesicle stress adaptation.
Collapse
Affiliation(s)
- Marina Reichlmeir
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (M.R.); (J.C.-P.); (J.K.)
| | - Júlia Canet-Pons
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (M.R.); (J.C.-P.); (J.K.)
| | - Gabriele Koepf
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (M.R.); (J.C.-P.); (J.K.)
| | - Wasifa Nurieva
- Transposition and Genome Engineering, Research Centre of the Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, 63225 Langen, Germany; (W.N.); (Z.I.)
| | - Ruth Pia Duecker
- Division of Pediatrics, Pulmonology, Allergology, Infectious Diseases and Gastroenterology, Children’s Hospital, University Hospital, Goethe-University, 60590 Frankfurt am Main, Germany; (R.P.D.); (S.Z.); (R.S.)
| | - Claudia Doering
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Kathryn Abell
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA; (K.A.); (M.P.S.)
| | - Jana Key
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (M.R.); (J.C.-P.); (J.K.)
| | - Matthew P. Stokes
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA; (K.A.); (M.P.S.)
| | - Stefan Zielen
- Division of Pediatrics, Pulmonology, Allergology, Infectious Diseases and Gastroenterology, Children’s Hospital, University Hospital, Goethe-University, 60590 Frankfurt am Main, Germany; (R.P.D.); (S.Z.); (R.S.)
- Respiratory Research Institute, Medaimun GmbH, 60596 Frankfurt am Main, Germany
| | - Ralf Schubert
- Division of Pediatrics, Pulmonology, Allergology, Infectious Diseases and Gastroenterology, Children’s Hospital, University Hospital, Goethe-University, 60590 Frankfurt am Main, Germany; (R.P.D.); (S.Z.); (R.S.)
| | - Zoltán Ivics
- Transposition and Genome Engineering, Research Centre of the Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, 63225 Langen, Germany; (W.N.); (Z.I.)
| | - Georg Auburger
- Goethe University Frankfurt, University Hospital, Clinic of Neurology, Exp. Neurology, Heinrich Hoffmann Str. 7, 60590 Frankfurt am Main, Germany; (M.R.); (J.C.-P.); (J.K.)
| |
Collapse
|
13
|
Liakos A, Synacheri AC, Konstantopoulos D, Stefos G, Lavigne M, Fousteri M. Enhanced frequency of transcription pre-initiation complexes assembly after exposure to UV irradiation results in increased repair activity and reduced probabilities for mutagenesis. Nucleic Acids Res 2023; 51:8575-8586. [PMID: 37470822 PMCID: PMC10484669 DOI: 10.1093/nar/gkad593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/24/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
In addition to being essential for gene expression, transcription is crucial for the maintenance of genome integrity. Here, we undertook a systematic approach, to monitor the assembly kinetics of the pre-initiating RNA Polymerase (Pol) II at promoters at steady state and different stages during recovery from UV irradiation-stress, when pre-initiation and initiation steps have been suggested to be transiently shut down. Taking advantage of the reversible dissociation of pre-initiating Pol II after high salt treatment, we found that de novo recruitment of the available Pol II molecules at active promoters not only persists upon UV at all times tested but occurs significantly faster in the early phase of recovery (2 h) than in unexposed human fibroblasts at the majority of active genes. Our method unveiled groups of genes with significantly different pre-initiation complex (PIC) assembly dynamics after UV that present distinct rates of UV-related mutational signatures in melanoma tumours, providing functional relevance to the importance of keeping transcription initiation active during UV recovery. Our findings uncover novel mechanistic insights further detailing the multilayered transcriptional response to genotoxic stress and link PIC assembly dynamics after exposure to genotoxins with cancer mutational landscapes.
Collapse
Affiliation(s)
- Anastasios Liakos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Anna-Chloe Synacheri
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Dimitris Konstantopoulos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Georgios C Stefos
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Matthieu D Lavigne
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| | - Maria Fousteri
- Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming”, 34 Fleming st., Vari 16672, Greece
| |
Collapse
|
14
|
Cusan M, Shen H, Zhang B, Liao A, Yang L, Jin M, Fernandez M, Iyer P, Wu Y, Hart K, Gutierrez C, Nik S, Pruett-Miller SM, Stark J, Obeng EA, Bowman TV, Wu CJ, Lin RJ, Wang L. SF3B1 mutation and ATM deletion codrive leukemogenesis via centromeric R-loop dysregulation. J Clin Invest 2023; 133:e163325. [PMID: 37463047 PMCID: PMC10471171 DOI: 10.1172/jci163325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
RNA splicing factor SF3B1 is recurrently mutated in various cancers, particularly in hematologic malignancies. We previously reported that coexpression of Sf3b1 mutation and Atm deletion in B cells, but not either lesion alone, leads to the onset of chronic lymphocytic leukemia (CLL) with CLL cells harboring chromosome amplification. However, the exact role of Sf3b1 mutation and Atm deletion in chromosomal instability (CIN) remains unclear. Here, we demonstrated that SF3B1 mutation promotes centromeric R-loop (cen-R-loop) accumulation, leading to increased chromosome oscillation, impaired chromosome segregation, altered spindle architecture, and aneuploidy, which could be alleviated by removal of cen-R-loop and exaggerated by deletion of ATM. Aberrant splicing of key genes involved in R-loop processing underlay augmentation of cen-R-loop, as overexpression of the normal isoform, but not the altered form, mitigated mitotic stress in SF3B1-mutant cells. Our study identifies a critical role of splice variants in linking RNA splicing dysregulation and CIN and highlights cen-R-loop augmentation as a key mechanism for leukemogenesis.
Collapse
Affiliation(s)
- Martina Cusan
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Haifeng Shen
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Bo Zhang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Department of Hematology, Union Hospital Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aijun Liao
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Department of Hematology, Affiliated Shengjing Hospital of China Medical University, Shenyang, China
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Meiling Jin
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Mike Fernandez
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Prajish Iyer
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Yiming Wu
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Kevyn Hart
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| | - Catherine Gutierrez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sara Nik
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Jeremy Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Esther A. Obeng
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Teresa V. Bowman
- Gottesman Institute for Stem Cell Biology and Regenerative Medicine and
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ren-Jang Lin
- Center for RNA Biology and Therapeutics, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, California, USA
| |
Collapse
|
15
|
Jin B, Zhu J, Pan T, Yang Y, Liang L, Zhou Y, Zhang T, Teng Y, Wang Z, Wang X, Tian Q, Guo B, Li H, Chen T. MEN1 is a regulator of alternative splicing and prevents R-loop-induced genome instability through suppression of RNA polymerase II elongation. Nucleic Acids Res 2023; 51:7951-7971. [PMID: 37395406 PMCID: PMC10450199 DOI: 10.1093/nar/gkad548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
The fidelity of alternative splicing (AS) patterns is essential for growth development and cell fate determination. However, the scope of the molecular switches that regulate AS remains largely unexplored. Here we show that MEN1 is a previously unknown splicing regulatory factor. MEN1 deletion resulted in reprogramming of AS patterns in mouse lung tissue and human lung cancer cells, suggesting that MEN1 has a general function in regulating alternative precursor mRNA splicing. MEN1 altered exon skipping and the abundance of mRNA splicing isoforms of certain genes with suboptimal splice sites. Chromatin immunoprecipitation and chromosome walking assays revealed that MEN1 favored the accumulation of RNA polymerase II (Pol II) in regions encoding variant exons. Our data suggest that MEN1 regulates AS by slowing the Pol II elongation rate and that defects in these processes trigger R-loop formation, DNA damage accumulation and genome instability. Furthermore, we identified 28 MEN1-regulated exon-skipping events in lung cancer cells that were closely correlated with survival in patients with lung adenocarcinoma, and MEN1 deficiency sensitized lung cancer cells to splicing inhibitors. Collectively, these findings led to the identification of a novel biological role for menin in maintaining AS homeostasis and link this role to the regulation of cancer cell behavior.
Collapse
Affiliation(s)
- Bangming Jin
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Jiamei Zhu
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Ting Pan
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yunqiao Yang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Li Liang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yuxia Zhou
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Tuo Zhang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Yin Teng
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Ziming Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Xuyan Wang
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Qianting Tian
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Bing Guo
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| | - Haiyang Li
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Guizhou Institute of Precision Medicine, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
| | - Tengxiang Chen
- Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, 550025 Guiyang, China
- Department of Surgery, Affiliated Hospital of Guizhou Medical University, 550025 Guiyang, China
- Transformation Engineering Research Center of Chronic Disease Diagnosis and Treatment, Guizhou Medical University, Guiyang, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, 550025 Guiyang, China
| |
Collapse
|
16
|
Einig E, Jin C, Andrioletti V, Macek B, Popov N. RNAPII-dependent ATM signaling at collisions with replication forks. Nat Commun 2023; 14:5147. [PMID: 37620345 PMCID: PMC10449895 DOI: 10.1038/s41467-023-40924-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Deregulation of RNA Polymerase II (RNAPII) by oncogenic signaling leads to collisions of RNAPII with DNA synthesis machinery (transcription-replication conflicts, TRCs). TRCs can result in DNA damage and are thought to underlie genomic instability in tumor cells. Here we provide evidence that elongating RNAPII nucleates activation of the ATM kinase at TRCs to stimulate DNA repair. We show the ATPase WRNIP1 associates with RNAPII and limits ATM activation during unperturbed cell cycle. WRNIP1 binding to elongating RNAPII requires catalytic activity of the ubiquitin ligase HUWE1. Mutation of HUWE1 induces TRCs, promotes WRNIP1 dissociation from RNAPII and binding to the replisome, stimulating ATM recruitment and activation at RNAPII. TRCs and translocation of WRNIP1 are rapidly induced in response to hydroxyurea treatment to activate ATM and facilitate subsequent DNA repair. We propose that TRCs can provide a controlled mechanism for stalling of replication forks and ATM activation, instrumental in cellular response to replicative stress.
Collapse
Affiliation(s)
- Elias Einig
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany
| | - Chao Jin
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany
| | - Valentina Andrioletti
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany
- enGenome S.R.L., Via Fratelli Cuzio 42, 27100, Pavia, Italy
| | - Boris Macek
- Interfaculty Institute of Cell Biology, Eberhard Karls University of Tübingen, Auf d. Morgenstelle 15, 72076, Tübingen, Germany
| | - Nikita Popov
- Department of Medical Oncology and Pulmonology, University Hospital Tübingen, Otfried-Mueller-Str 14, 72076, Tübingen, Germany.
| |
Collapse
|
17
|
McCann JJ, Fleenor DE, Chen J, Lai CH, Bass TE, Kastan MB. Participation of ATM, SMG1, and DDX5 in a DNA Damage-Induced Alternative Splicing Pathway. Radiat Res 2023; 199:406-421. [PMID: 36921295 PMCID: PMC10162594 DOI: 10.1667/rade-22-00219.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Altered cellular responses to DNA damage can contribute to cancer development, progression, and therapeutic resistance. Mutations in key DNA damage response factors occur across many cancer types, and the DNA damage-responsive gene, TP53, is frequently mutated in a high percentage of cancers. We recently reported that an alternative splicing pathway induced by DNA damage regulates alternative splicing of TP53 RNA and further modulates cellular stress responses. Through damage-induced inhibition of the SMG1 kinase, TP53 pre-mRNA is alternatively spliced to generate TP53b mRNA and p53b protein is required for optimal induction of cellular senescence after ionizing radiation-induced DNA damage. Herein, we confirmed and extended these observations by demonstrating that the ATM protein kinase is required for repression of SMG1 kinase activity after ionizing radiation. We found that the RNA helicase and splicing factor, DDX5, interacts with SMG1, is required for alternative splicing of TP53 pre-mRNA to TP53b and TP53c mRNAs after DNA damage, and contributes to radiation-induced cellular senescence. Interestingly, the role of SMG1 in alternative splicing of p53 appears to be distinguishable from its role in regulating nonsense-mediated RNA decay. Thus, ATM, SMG1, and DDX5 participate in a DNA damage-induced alternative splicing pathway that regulates TP53 splicing and modulates radiation-induced cellular senescence.
Collapse
Affiliation(s)
- Jennifer J. McCann
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Donald E. Fleenor
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Jing Chen
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Chun-Hsiang Lai
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Thomas E. Bass
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| | - Michael B. Kastan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina 27710
| |
Collapse
|
18
|
Braunstein EM, Imada E, Pasca S, Wang S, Chen H, Alba C, Hupalo DN, Wilkerson M, Dalgard CL, Ghannam J, Liu Y, Marchionni L, Moliterno A, Hourigan CS, Gondek LP. Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms. Leukemia 2023; 37:627-635. [PMID: 36543879 DOI: 10.1038/s41375-022-01797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Genetic predisposition (familial risk) in the myeloproliferative neoplasms (MPNs) is more common than the risk observed in most other cancers, including breast, prostate, and colon. Up to 10% of MPNs are considered to be familial. Recent genome-wide association studies have identified genomic loci associated with an MPN diagnosis. However, the identification of variants with functional contributions to the development of MPN remains limited. In this study, we have included 630 MPN patients and whole genome sequencing was performed in 64 individuals with familial MPN to uncover recurrent germline predisposition variants. Both targeted and unbiased filtering of single nucleotide variants (SNVs) was performed, with a comparison to 218 individuals with MPN unselected for familial status. This approach identified an ATM L2307F SNV occurring in nearly 8% of individuals with familial MPN. Structural protein modeling of this variant suggested stabilization of inactive ATM dimer, and alteration of the endogenous ATM locus in a human myeloid cell line resulted in decreased phosphorylation of the downstream tumor suppressor CHEK2. These results implicate ATM, and the DNA-damage response pathway, in predisposition to MPN.
Collapse
Affiliation(s)
- Evan M Braunstein
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Eddie Imada
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Shiyu Wang
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hang Chen
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA.,Committee on Genetics, Genomics and Systems Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Camille Alba
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Dan N Hupalo
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew Wilkerson
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yujia Liu
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Luigi Marchionni
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
| |
Collapse
|
19
|
Saha S, Pommier Y. R-loops, type I topoisomerases and cancer. NAR Cancer 2023; 5:zcad013. [PMID: 37600974 PMCID: PMC9984992 DOI: 10.1093/narcan/zcad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
R-loops are abundant and dynamic structures ubiquitously present in human cells both in the nuclear and mitochondrial genomes. They form in cis in the wake of transcription complexes and in trans apart from transcription complexes. In this review, we focus on the relationship between R-loops and topoisomerases, and cancer genomics and therapies. We summarize the topological parameters associated with the formation and resolution of R-loops, which absorb and release high levels of genomic negative supercoiling (Sc-). We review the deleterious consequences of excessive R-loops and rationalize how human type IA (TOP3B) and type IB (TOP1) topoisomerases regulate and resolve R-loops in coordination with helicase and RNase H enzymes. We also review the drugs (topoisomerase inhibitors, splicing inhibitors, G4 stabilizing ligands) and cancer predisposing genes (BRCA1/2, transcription, and splicing genes) known to induce R-loops, and whether stabilizing R-loops and thereby inducing genomic damage can be viewed as a strategy for cancer treatment.
Collapse
Affiliation(s)
- Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| |
Collapse
|
20
|
Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
Collapse
Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
| |
Collapse
|
21
|
Mistry H, Gupta GD. Transcription coupled DNA repair protein UVSSA binds to DNA and RNA: Mapping of nucleic acid interaction sites on human UVSSA. Arch Biochem Biophys 2023; 735:109515. [PMID: 36623745 DOI: 10.1016/j.abb.2023.109515] [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: 10/06/2022] [Revised: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Transcription-coupled repair (TCR) is a dedicated pathway for the preferential repair of bulky transcription-blocking DNA lesions. These lesions stall the elongating RNA-polymerase II (RNAPII) triggering the recruitment of TCR proteins at the damaged site. UV-stimulated scaffold protein A (UVSSA) is a recently identified cofactor which is involved in stabilization of the TCR complex, recruitment of DNA-repair machinery and removal/restoration of RNAPII from the lesion site. Mutations in UVSSA render the cells TCR-deficient and have been linked to UV-sensitive syndrome. Human UVSSA is a 709-residue long protein with two short conserved domains; an N-terminal (residues 1-150) and a C-terminal (residues 495-605) domain, while the rest of the protein is predicted to be intrinsically disordered. The protein is well conserved in eukaryotes, however; none of its homologs have been characterized yet. Here, we have purified the recombinant human UVSSA and have characterized it using bioinformatics, biophysical and biochemical techniques. Using EMSA, SPR and fluorescence-based methods, we have shown that human UVSSA interacts with DNA and RNA. Furthermore, we have mapped the nucleic acid binding regions using several recombinant protein fragments containing either the N-terminal or the C-terminal domains. Our data indicate that UVSSA possesses at least two nucleic acid binding regions; the N-terminal domain and a C-terminal tail region (residues 606-662). These regions, far apart in sequence space, are predicted to be in close proximity in structure-space suggesting a coherent interaction with target DNA/RNA. The study may provide functional clues about the novel family of UVSSA proteins.
Collapse
Affiliation(s)
- Hiral Mistry
- Radiation Biology & Health Science Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
| | - Gagan Deep Gupta
- Radiation Biology & Health Science Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, India.
| |
Collapse
|
22
|
Gyenis A, Chang J, Demmers JJPG, Bruens ST, Barnhoorn S, Brandt RMC, Baar MP, Raseta M, Derks KWJ, Hoeijmakers JHJ, Pothof J. Genome-wide RNA polymerase stalling shapes the transcriptome during aging. Nat Genet 2023; 55:268-279. [PMID: 36658433 PMCID: PMC9925383 DOI: 10.1038/s41588-022-01279-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/07/2022] [Indexed: 01/21/2023]
Abstract
Gene expression profiling has identified numerous processes altered in aging, but how these changes arise is largely unknown. Here we combined nascent RNA sequencing and RNA polymerase II chromatin immunoprecipitation followed by sequencing to elucidate the underlying mechanisms triggering gene expression changes in wild-type aged mice. We found that in 2-year-old liver, 40% of elongating RNA polymerases are stalled, lowering productive transcription and skewing transcriptional output in a gene-length-dependent fashion. We demonstrate that this transcriptional stress is caused by endogenous DNA damage and explains the majority of gene expression changes in aging in most mainly postmitotic organs, specifically affecting aging hallmark pathways such as nutrient sensing, autophagy, proteostasis, energy metabolism, immune function and cellular stress resilience. Age-related transcriptional stress is evolutionary conserved from nematodes to humans. Thus, accumulation of stochastic endogenous DNA damage during aging deteriorates basal transcription, which establishes the age-related transcriptome and causes dysfunction of key aging hallmark pathways, disclosing how DNA damage functionally underlies major aspects of normal aging.
Collapse
Affiliation(s)
- Akos Gyenis
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany
| | - Jiang Chang
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serena T Bruens
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marjolein P Baar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marko Raseta
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics and School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany
- Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
23
|
MDC1 maintains active elongation complexes of RNA polymerase II. Cell Rep 2023; 42:111979. [PMID: 36640322 DOI: 10.1016/j.celrep.2022.111979] [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: 12/14/2021] [Revised: 10/04/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
The role of MDC1 in the DNA damage response has been extensively studied; however, its impact on other cellular processes is not well understood. Here, we describe the role of MDC1 in transcription as a regulator of RNA polymerase II (RNAPII). Depletion of MDC1 causes a genome-wide reduction in the abundance of actively engaged RNAPII elongation complexes throughout the gene body of protein-encoding genes under unperturbed conditions. Decreased engaged RNAPII subsequently alters the assembly of the spliceosome complex on chromatin, leading to changes in pre-mRNA splicing. Mechanistically, the S/TQ domain of MDC1 modulates RNAPII-mediated transcription. Upon genotoxic stress, MDC1 promotes the abundance of engaged RNAPII complexes at DNA breaks, thereby stimulating nascent transcription at the damaged sites. Of clinical relevance, cancer cells lacking MDC1 display hypersensitivity to RNAPII inhibitors. Overall, we unveil a role of MDC1 in RNAPII-mediated transcription with potential implications for cancer treatment.
Collapse
|
24
|
Sarker AH, Cooper PK. Slot Blot Assay for Detection of R Loops. Methods Mol Biol 2023; 2701:149-156. [PMID: 37574480 DOI: 10.1007/978-1-0716-3373-1_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] [Indexed: 08/15/2023]
Abstract
R loops (DNA-RNA hybrid) are three-stranded nucleic acid structures that comprise of template DNA strand hybridized with the nascent RNA leaving the displaced non-template strand. Although a programmed R loop formation can serve as powerful regulators of gene expression, these structures can also turn into major sources of genomic instability and contribute to the development of diseases. Therefore, understanding how cells prevent the deleterious consequences of R loops yet allow R loop formation to participate in various physiological processes will help to understand how their homeostasis is maintained. Detection and quantitative measurements of R loops are critical that largely relied on S9.6 antibody. Immunofluorescence methods are frequently used to localize and quantify R loops in the cell but they require specialized tools for analysis and relatively expensive; therefore, they are not always useful for initial assessments of R loop accumulation. Here, we describe an improved slot blot protocol to detect and estimate R loops and show its sensitivity and specificity using the S9.6 antibody. Since specific factors protecting cells from harmful R loop accumulation are expanding, this protocol can be used to determine R loop accumulation in research and clinical settings.
Collapse
Affiliation(s)
- Altaf H Sarker
- Department of BioEngineering and BioMedical Sciences, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Priscilla K Cooper
- Department of BioEngineering and BioMedical Sciences, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| |
Collapse
|
25
|
Liu J, Jin T, Ran L, Zhao Z, Zhu R, Xie G, Bi X. Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation. Hereditas 2022; 159:41. [PMID: 36271387 PMCID: PMC9587650 DOI: 10.1186/s41065-022-00254-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Background ATM (ataxia-telangiectasia mutated) protein kinase is highly conserved in metazoan, and plays a critical role at DNA damage response, oxidative stress, metabolic stress, immunity, RNA biogenesis etc. Systemic profiling of ATM regulated genes, including protein-coding genes, miRNAs, and long non-coding RNAs, will greatly improve our understanding of ATM functions and its regulation. Results 1) differentially expressed protein-coding genes, miRNAs, and long non-coding RNAs in atm mutated flies were identified at physiological condition and after X-ray irradiation. 2) functions of differentially expressed genes in atm mutated flies, regardless of protein-coding genes or non-coding RNAs, are closely related with metabolic process, immune response, DNA damage response or oxidative stress. 3) these phenomena are persistent after irradiation. 4) there is a cross-talk regulation towards miRNAs by ATM, E2f1, and p53 during development and after irradiation. 5) knock-out flies or knock-down flies of most irradiation-induced miRNAs were sensitive to ionizing radiation. Conclusions We provide a valuable resource of protein-coding genes, miRNAs, and long non-coding RNAs, for understanding ATM functions and regulations. Our work provides the new evidence of inter-dependence among ATM-E2F1-p53 for the regulation of miRNAs. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00254-9.
Collapse
Affiliation(s)
- Jun Liu
- School of Medicine, Nantong University, Nantong, 226001, China
| | - Tianyu Jin
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Lanxi Ran
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Ze Zhao
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Rui Zhu
- College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China
| | - Gangcai Xie
- School of Medicine, Nantong University, Nantong, 226001, China.
| | - Xiaolin Bi
- School of Medicine, Nantong University, Nantong, 226001, China. .,College of Basic Medical Medicine, Dalian Medical University, Dalian, 116044, China.
| |
Collapse
|
26
|
Patitaki E, Schivre G, Zioutopoulou A, Perrella G, Bourbousse C, Barneche F, Kaiserli E. Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:333-349. [PMID: 35949052 PMCID: PMC9826491 DOI: 10.1111/nph.18424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/26/2022] [Indexed: 05/31/2023]
Abstract
The plant nucleus provides a major hub for environmental signal integration at the chromatin level. Multiple light signaling pathways operate and exchange information by regulating a large repertoire of gene targets that shape plant responses to a changing environment. In addition to the established role of transcription factors in triggering photoregulated changes in gene expression, there are eminent reports on the significance of chromatin regulators and nuclear scaffold dynamics in promoting light-induced plant responses. Here, we report and discuss recent advances in chromatin-regulatory mechanisms modulating plant architecture and development in response to light, including the molecular and physiological roles of key modifications such as DNA, RNA and histone methylation, and/or acetylation. The significance of the formation of biomolecular condensates of key light signaling components is discussed and potential applications to agricultural practices overviewed.
Collapse
Affiliation(s)
- Eirini Patitaki
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Geoffrey Schivre
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
- Université Paris‐SaclayOrsay91400France
| | - Anna Zioutopoulou
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Giorgio Perrella
- Department of BiosciencesUniversity of MilanVia Giovanni Celoria, 2620133MilanItaly
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| |
Collapse
|
27
|
Safeguarding DNA Replication: A Golden Touch of MiDAS and Other Mechanisms. Int J Mol Sci 2022; 23:ijms231911331. [PMID: 36232633 PMCID: PMC9570362 DOI: 10.3390/ijms231911331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
DNA replication is a tightly regulated fundamental process allowing the correct duplication and transfer of the genetic information from the parental cell to the progeny. It involves the coordinated assembly of several proteins and protein complexes resulting in replication fork licensing, firing and progression. However, the DNA replication pathway is strewn with hurdles that affect replication fork progression during S phase. As a result, cells have adapted several mechanisms ensuring replication completion before entry into mitosis and segregating chromosomes with minimal, if any, abnormalities. In this review, we describe the possible obstacles that a replication fork might encounter and how the cell manages to protect DNA replication from S to the next G1.
Collapse
|
28
|
Nazlamova L, Villa Vasquez SS, Lord J, Karthik V, Cheung MK, Lakowski J, Wheway G. Microtubule modification defects underlie cilium degeneration in cell models of retinitis pigmentosa associated with pre-mRNA splicing factor mutations. Front Genet 2022; 13:1009430. [PMID: 36176300 PMCID: PMC9513239 DOI: 10.3389/fgene.2022.1009430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding pre-mRNA splicing factors are associated with non-syndromic RP. The molecular mechanism of disease remains incompletely understood, limiting opportunities for targeted treatment. Here we use CRISPR and base edited PRPF6 and PRPF31 mutant cell lines, and publicly-available data from human PRPF31+/− patient derived retinal organoids and PRPF31 siRNA-treated organotypic retinal cultures to confirm an enrichment of differential splicing of microtubule, centrosomal, cilium and DNA damage response pathway genes in these cells. We show that genes with microtubule/centrosome/centriole/cilium gene ontology terms are enriched for weak 3′ and 5′ splice sites, and that subtle defects in spliceosome activity predominantly affect efficiency of splicing of these exons. We suggest that the primary defect in PRPF6 or PRPF31 mutant cells is microtubule and centrosomal defects, leading to defects in cilium and mitotic spindle stability, with the latter leading to DNA damage, triggering differential splicing of DNA damage response genes to activate this pathway. Finally, we expand understanding of “splicing factor RP” by investigating the function of TTLL3, one of the most statistically differentially expressed genes in PRPF6 and PRPF31 mutant cells. We identify that TTLL3 is the only tubulin glycylase expressed in the human retina, essential for monoglycylation of microtubules of the cilium, including the retinal photoreceptor cilium, to prevent cilium degeneration and retinal degeneration. Our preliminary data suggest that rescue of tubulin glycylation through overexpression of TTLL3 is sufficient to rescue cilium number in PRPF6 and PRPF31 mutant cells, suggesting that this defect underlies the cellular defect and may represent a potential target for therapeutic intervention in this group of disorders.
Collapse
Affiliation(s)
- Liliya Nazlamova
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Suly Saray Villa Vasquez
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Varshini Karthik
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Man-Kim Cheung
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Jörn Lakowski
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- *Correspondence: Gabrielle Wheway,
| |
Collapse
|
29
|
Shinriki S, Matsui H. Unique role of DDX41, a DEAD-box type RNA helicase, in hematopoiesis and leukemogenesis. Front Oncol 2022; 12:992340. [PMID: 36119490 PMCID: PMC9478608 DOI: 10.3389/fonc.2022.992340] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
In myeloid malignancies including acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), patient selection and therapeutic strategies are increasingly based on tumor-specific genetic mutations. Among these, mutations in DDX41, which encodes a DEAD-box type RNA helicase, are present in approximately 2–5% of AML and MDS patients; this disease subtype exhibits a distinctive disease phenotype characterized by late age of onset, tendency toward cytopenia in the peripheral blood and bone marrow, a relatively favorable prognosis, and a high frequency of normal karyotypes. Typically, individuals with a loss-of-function germline DDX41 variant in one allele later acquire the p.R525H mutation in the other allele before overt disease manifestation, suggesting that the progressive decrease in DDX41 expression and/or function is involved in myeloid leukemogenesis.RNA helicases play roles in many processes involving RNA metabolism by altering RNA structure and RNA-protein interactions through ATP-dependent helicase activity. A single RNA helicase can play multiple cellular roles, making it difficult to elucidate the mechanisms by which mutations in DDX41 are involved in leukemogenesis. Nevertheless, multiple DDX41 functions have been associated with disease development. The enzyme has been implicated in the regulation of RNA splicing, nucleic acid sensing in the cytoplasm, R-loop resolution, and snoRNA processing.Most of the mutated RNA splicing-related factors in MDS are involved in the recognition and determination of 3’ splice sites (SS), although their individual roles are distinct. On the other hand, DDX41 is likely incorporated into the C complex of the spliceosome, which may define a distinctive disease phenotype. This review summarizes the current understanding of how DDX41 is involved in this unique myeloid malignancy.
Collapse
|
30
|
Hluchý M, Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Kluge M, Berger BT, Slabá Z, Potěšil D, Weiß E, Ule J, Zdráhal Z, Knapp S, Paruch K, Friedel CC, Blazek D. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature 2022; 609:829-834. [PMID: 36104565 DOI: 10.1038/s41586-022-05204-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA-protein complex that assembles de novo on each pre-mRNA intron through an ordered assembly of intermediate complexes1,2. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex1-5. Splicing factor 3B subunit 1 (SF3B1) protein-a subunit of the U2 small nuclear ribonucleoprotein6-is phosphorylated during spliceosome activation7-10, but the kinase that is responsible has not been identified. Here we show that cyclin-dependent kinase 11 (CDK11) associates with SF3B1 and phosphorylates threonine residues at its N terminus during spliceosome activation. The phosphorylation is important for the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, termed the Bact complex, and the phosphorylation can be blocked by OTS964, a potent and selective inhibitor of CDK11. Inhibition of CDK11 prevents spliceosomal transition from the precatalytic complex B to the activated complex Bact and leads to widespread intron retention and accumulation of non-functional spliceosomes on pre-mRNAs and chromatin. We demonstrate a central role of CDK11 in spliceosome assembly and splicing regulation and characterize OTS964 as a highly selective CDK11 inhibitor that suppresses spliceosome activation and splicing.
Collapse
Affiliation(s)
- Milan Hluchý
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavla Gajdušková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK
- Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Michael Kluge
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Benedict-Tilman Berger
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Zuzana Slabá
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Elena Weiß
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Jernej Ule
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute, King's College London, London, UK
| | - Zbyněk Zdráhal
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Stefan Knapp
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences (BMLS), Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Institut für Pharmazeutische Chemie, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Kamil Paruch
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St Anne's University Hospital in Brno, Brno, Czech Republic
| | - Caroline C Friedel
- Institut für Informatik, Ludwig-Maximilians-Universität München, München, Germany
| | - Dalibor Blazek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
| |
Collapse
|
31
|
R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage. EPIGENOMES 2022; 6:epigenomes6030026. [PMID: 36135313 PMCID: PMC9498298 DOI: 10.3390/epigenomes6030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/24/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is thought to employ a strategy of exclusively transcribing meiotic or post-meiotic genes before their use. Recent studies have shown that R-loops, three-stranded DNA/RNA hybrid nucleotide structures formed during transcription, play a crucial role in transcription and genome integrity. Although our knowledge about the function of R-loops during meiosis is limited, recent findings in mouse models have suggested that they play crucial roles in meiosis. Given that defective formation of an R-loop can cause abnormal transcription and transcription-coupled DNA damage, the precise regulatory network of R-loops may be essential in vivo for the faithful progression of mammalian meiosis and gametogenesis.
Collapse
|
32
|
DNA Damage Regulates the Functions of the RNA Binding Protein Sam68 through ATM-Dependent Phosphorylation. Cancers (Basel) 2022; 14:cancers14163847. [PMID: 36010841 PMCID: PMC9405969 DOI: 10.3390/cancers14163847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/26/2022] [Accepted: 08/05/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Alterations of the complex network of interactions between the DNA damage response pathway and RNA metabolism have been described in several tumors, and increasing efforts are devoted to the elucidation of the molecular mechanisms involved in this network. Previous large-scale proteomic studies identified the RNA binding protein Sam68 as a putative target of the ATM kinase. Herein, we demonstrate that ATM phosphorylates Sam68 upon DNA damage induction, and this post-translational modification regulates both the signaling function of Sam68 in the initial phase of the DNA damage response and its RNA processing activity. Thus, our study uncovers anew crosstalk between ATM and Sam68, which may represent a paradigm for the functional interaction between the DDR pathway and RNA binding proteins, and a possible actionabletarget in human cancers. Abstract Cancer cells frequently exhibit dysregulation of the DNA damage response (DDR), genomic instability, and altered RNA metabolism. Recent genome-wide studies have strongly suggested an interaction between the pathways involved in the cellular response to DDR and in the regulation of RNA metabolism, but the molecular mechanism(s) involved in this crosstalk are largely unknown. Herein, we found that activation of the DDR kinase ATM promotes its interaction with Sam68, leading to phosphorylation of this multifunctional RNA binding protein (RBP) on three residues: threonine 61, serine 388 and serine 390. Moreover, we demonstrate that ATM-dependent phosphorylation of threonine 61 promotes the function of Sam68 in the DDR pathway and enhances its RNA processing activity. Importantly, ATM-mediated phosphorylation of Sam68 in prostate cancer cells modulates alternative polyadenylation of transcripts that are targets of Sam68, supporting the notion that the ATM–Sam68 axis exerts a multifaceted role in the response to DNA damage. Thus, our work validates Sam68 as an ATM kinase substrate and uncovers an unexpected bidirectional interplay between ATM and Sam68, which couples the DDR pathway to modulation of RNA metabolism in response to genotoxic stress.
Collapse
|
33
|
Donnio LM, Cerutti E, Magnani C, Neuillet D, Mari PO, Giglia-Mari G. XAB2 dynamics during DNA damage-dependent transcription inhibition. eLife 2022; 11:77094. [PMID: 35880862 PMCID: PMC9436415 DOI: 10.7554/elife.77094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Xeroderma Pigmentosum group A-binding protein 2 (XAB2) is a multifunctional protein playing a critical role in distinct cellular processes including transcription, splicing, DNA repair, and messenger RNA export. In this study, we demonstrate that XAB2 is involved specifically and exclusively in Transcription-Coupled Nucleotide Excision Repair (TC-NER) reactions and solely for RNA polymerase 2 (RNAP2)-transcribed genes. Surprisingly, contrary to all the other NER proteins studied so far, XAB2 does not accumulate on the local UV-C damage; on the contrary, it becomes more mobile after damage induction. XAB2 mobility is restored when DNA repair reactions are completed. By scrutinizing from which cellular complex/partner/structure XAB2 is released, we have identified that XAB2 is detached after DNA damage induction from DNA:RNA hybrids, commonly known as R-loops, and from the CSA and XPG proteins. This release contributes to the DNA damage recognition step during TC-NER, as in the absence of XAB2, RNAP2 is blocked longer on UV lesions. Moreover, we also demonstrate that XAB2 has a role in retaining RNAP2 on its substrate without any DNA damage.
Collapse
Affiliation(s)
- Lise-Marie Donnio
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Elena Cerutti
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Charlene Magnani
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Neuillet
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Pierre-Olivier Mari
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Giuseppina Giglia-Mari
- Institut NeuroMyogène (INMG), CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| |
Collapse
|
34
|
Ljungman M. Transcription and genome integrity. DNA Repair (Amst) 2022; 118:103373. [PMID: 35914488 DOI: 10.1016/j.dnarep.2022.103373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/16/2022] [Accepted: 07/17/2022] [Indexed: 11/03/2022]
Abstract
Transcription can cause genome instability by promoting R-loop formation but also act as a mutation-suppressing machinery by sensing of DNA lesions leading to the activation of DNA damage signaling and transcription-coupled repair. Recovery of RNA synthesis following the resolution of repair of transcription-blocking lesions is critical to avoid apoptosis and several new factors involved in this process have recently been identified. Some DNA repair proteins are recruited to initiating RNA polymerases and this may expediate the recruitment of other factors that participate in the repair of transcription-blocking DNA lesions. Recent studies have shown that transcription of protein-coding genes does not always give rise to spliced transcripts, opening the possibility that cells may use the transcription machinery in a splicing-uncoupled manner for other purposes including surveillance of the transcribed genome.
Collapse
Affiliation(s)
- Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, Rogel Cancer Center and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
35
|
Ortiz-Sánchez C, Encarnación-Medina J, Park JY, Moreno N, Ruiz-Deya G, Matta J. Reduced DNA Repair Capacity in Prostate Cancer Patients: A Phenotypic Approach Using the CometChip. Cancers (Basel) 2022; 14:3117. [PMID: 35804887 PMCID: PMC9264934 DOI: 10.3390/cancers14133117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/17/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Prostate cancer (PCa) accounts for 22% of the new cases diagnosed in Hispanic men in the US. Among Hispanics, Puerto Rican (PR) men show the highest PCa-specific mortality. Epidemiological studies using functional assays in lymphocytes have demonstrated that having low DRC is a significant risk factor for cancer development. The aim of this study was to evaluate variations in DRC in PR men with PCa. Lymphocytes were isolated from blood samples from PCa cases (n = 41) and controls (n = 14) recruited at a hospital setting. DRC levels through the nucleotide excision repair (NER) pathway were measured with the CometChip using UVC as a NER inductor. The mean DRC for controls and PCa cases were 20.66% (±7.96) and 8.41 (±4.88), respectively (p < 0.001). The relationship between DRC and tumor aggressiveness was also evaluated. Additional comparisons were performed to evaluate the contributions of age, anthropometric measurements, and prostate-specific antigen levels to the DRC. This is the first study to apply the CometChip in a clinical cancer study. Our results represent an innovative step in the development of a blood-based screening test for PCa based on DRC levels. Our data also suggest that DRC levels may have the potential to discriminate between aggressive and indolent cases.
Collapse
Affiliation(s)
- Carmen Ortiz-Sánchez
- Department of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00716-2347, Puerto Rico; (J.E.-M.); (J.M.)
| | - Jarline Encarnación-Medina
- Department of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00716-2347, Puerto Rico; (J.E.-M.); (J.M.)
| | - Jong Y. Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Natasha Moreno
- St. Luke’s Episcopal Hospital, Ponce, PR 00733, Puerto Rico; (N.M.); (G.R.-D.)
| | - Gilberto Ruiz-Deya
- St. Luke’s Episcopal Hospital, Ponce, PR 00733, Puerto Rico; (N.M.); (G.R.-D.)
- Department of Surgery, Ponce Health Sciences University, Ponce, PR 00716-2347, Puerto Rico
| | - Jaime Matta
- Department of Basic Sciences, Ponce Research Institute, Ponce Health Sciences University, Ponce, PR 00716-2347, Puerto Rico; (J.E.-M.); (J.M.)
| |
Collapse
|
36
|
Steurer B, Janssens RC, Geijer ME, Aprile-Garcia F, Geverts B, Theil AF, Hummel B, van Royen ME, Evers B, Bernards R, Houtsmuller AB, Sawarkar R, Marteijn J. DNA damage-induced transcription stress triggers the genome-wide degradation of promoter-bound Pol II. Nat Commun 2022; 13:3624. [PMID: 35750669 PMCID: PMC9232492 DOI: 10.1038/s41467-022-31329-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/10/2022] [Indexed: 01/22/2023] Open
Abstract
The precise regulation of RNA Polymerase II (Pol II) transcription after genotoxic stress is crucial for proper execution of the DNA damage-induced stress response. While stalling of Pol II on transcription-blocking lesions (TBLs) blocks transcript elongation and initiates DNA repair in cis, TBLs additionally elicit a response in trans that regulates transcription genome-wide. Here we uncover that, after an initial elongation block in cis, TBLs trigger the genome-wide VCP-mediated proteasomal degradation of promoter-bound, P-Ser5-modified Pol II in trans. This degradation is mechanistically distinct from processing of TBL-stalled Pol II, is signaled via GSK3, and contributes to the TBL-induced transcription block, even in transcription-coupled repair-deficient cells. Thus, our data reveal the targeted degradation of promoter-bound Pol II as a critical pathway that allows cells to cope with DNA damage-induced transcription stress and enables the genome-wide adaptation of transcription to genotoxic stress.
Collapse
Affiliation(s)
- Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Bart Geverts
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Martin E van Royen
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- MRC, University of Cambridge, Cambridge, UK
| | - Jurgen Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| |
Collapse
|
37
|
Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
Collapse
|
38
|
The UVSSA protein is part of a genome integrity homeostasis network with links to transcription-coupled DNA repair and ATM signaling. Proc Natl Acad Sci U S A 2022; 119:e2116254119. [PMID: 35254895 PMCID: PMC8931232 DOI: 10.1073/pnas.2116254119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Significance
Transcription-coupled repair (TCR) involves four core proteins: CSA, CSB, USP7, and UVSSA. CSA and CSB are mutated in the severe human neurocutaneous disease Cockayne syndrome. In contrast UVSSA is a mild photosensitive disease in which a mutated protein sequence prevents recruitment of USP7 protease to deubiquitinate and stabilize CSB. We deleted the UVSSA protein using CRISPR-Cas9 in an aneuploid cell line, HEK293, and determined the functional consequences. The knockout cell line was sensitive to transcription-blocking lesions but not sensitive to oxidative agents or PARP inhibitors, unlike CSB. Knockout of UVSSA also activated ATM, like CSB, in transcription-arrested cells. The phenotype of UVSSA, especially its rarity, suggests that many TCR-deficient patients and tumors fail to be recognized clinically.
Collapse
|
39
|
Abstract
The XPG/ERCC5 endonuclease was originally identified as the causative gene for Xeroderma Pigmentosum complementation group G. Ever since its discovery, in depth biochemical, structural and cell biological studies have provided detailed mechanistic insight into its function in excising DNA damage in nucleotide excision repair, together with the ERCC1–XPF endonuclease. In recent years, it has become evident that XPG has additional important roles in genome maintenance that are independent of its function in NER, as XPG has been implicated in protecting replication forks by promoting homologous recombination as well as in resolving R-loops. Here, we provide an overview of the multitasking of XPG in genome maintenance, by describing in detail how its activity in NER is regulated and the evidence that points to important functions outside of NER. Furthermore, we present the various disease phenotypes associated with inherited XPG deficiency and discuss current ideas on how XPG deficiency leads to these different types of disease.
Collapse
|
40
|
Marabitti V, Valenzisi P, Lillo G, Malacaria E, Palermo V, Pichierri P, Franchitto A. R-Loop-Associated Genomic Instability and Implication of WRN and WRNIP1. Int J Mol Sci 2022; 23:ijms23031547. [PMID: 35163467 PMCID: PMC8836129 DOI: 10.3390/ijms23031547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/05/2023] Open
Abstract
Maintenance of genome stability is crucial for cell survival and relies on accurate DNA replication. However, replication fork progression is under constant attack from different exogenous and endogenous factors that can give rise to replication stress, a source of genomic instability and a notable hallmark of pre-cancerous and cancerous cells. Notably, one of the major natural threats for DNA replication is transcription. Encounters or conflicts between replication and transcription are unavoidable, as they compete for the same DNA template, so that collisions occur quite frequently. The main harmful transcription-associated structures are R-loops. These are DNA structures consisting of a DNA–RNA hybrid and a displaced single-stranded DNA, which play important physiological roles. However, if their homeostasis is altered, they become a potent source of replication stress and genome instability giving rise to several human diseases, including cancer. To combat the deleterious consequences of pathological R-loop persistence, cells have evolved multiple mechanisms, and an ever growing number of replication fork protection factors have been implicated in preventing/removing these harmful structures; however, many others are perhaps still unknown. In this review, we report the current knowledge on how aberrant R-loops affect genome integrity and how they are handled, and we discuss our recent findings on the role played by two fork protection factors, the Werner syndrome protein (WRN) and the Werner helicase-interacting protein 1 (WRNIP1) in response to R-loop-induced genome instability.
Collapse
|
41
|
Abstract
RNase H1 has become an essential tool to uncover the physiological and pathological roles of R-loops, three-stranded structures consisting of and RNA-DNA hybrid opposite to a single DNA strand (ssDNA). RNase H1 degrades the RNA portion of the R-loops returning the two DNA strands to double-stranded form (dsDNA). Overexpression of RNase H1 in different systems has helped to address the questions of where R-loops are located, their abundance, and mechanisms of formation, stability, and degradation. In this chapter we review multiple studies that used RNase H1 as an instrument to investigate R-loops multiple functions and their relevance in health and diseases.
Collapse
Affiliation(s)
- Susana M Cerritelli
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kiran Sakhuja
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
42
|
Böttcher R, Schmidts I, Nitschko V, Duric P, Förstemann K. RNA polymerase II is recruited to DNA double-strand breaks for dilncRNA transcription in Drosophila. RNA Biol 2021; 19:68-77. [PMID: 34965182 PMCID: PMC8786327 DOI: 10.1080/15476286.2021.2014694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
DNA double-strand breaks are among the most toxic lesions that can occur in a genome and their faithful repair is thus of great importance. Recent findings have uncovered local transcription that initiates at the break and forms a non-coding transcript, called damage-induced long non-coding RNA (dilncRNA), which helps to coordinate the DNA transactions necessary for repair. We provide nascent RNA sequencing-based evidence that RNA polymerase II transcribes the dilncRNA in Drosophila and that this is more efficient for DNA breaks in an intron-containing gene, consistent with the higher damage-induced siRNA levels downstream of an intron. The spliceosome thus stimulates recruitment of RNA polymerase II to the break, rather than merely promoting the annealing of sense and antisense RNA to form the siRNA precursor. In contrast, RNA polymerase III nascent RNA libraries did not contain reads corresponding to the cleaved loci and selective inhibition of RNA polymerase III did not reduce the yield of damage-induced siRNAs. Finally, the damage-induced siRNA density was unchanged downstream of a T8 sequence, which terminates RNA polymerase III transcription. We thus found no evidence for a participation of RNA polymerase III in dilncRNA transcription in cultured Drosophila cells.
Collapse
Affiliation(s)
- Romy Böttcher
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Ines Schmidts
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Volker Nitschko
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Petar Duric
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Klaus Förstemann
- Department. Of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| |
Collapse
|
43
|
Kwak YD, Shaw TI, Downing SM, Tewari A, Jin H, Li Y, Dumitrache LC, Katyal S, Khodakhah K, Russell HR, McKinnon PJ. Chromatin architecture at susceptible gene loci in cerebellar Purkinje cells characterizes DNA damage-induced neurodegeneration. SCIENCE ADVANCES 2021; 7:eabg6363. [PMID: 34910524 DOI: 10.1126/sciadv.abg6363] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The pathogenesis of inherited genome instability neurodegenerative syndromes remains largely unknown. Here, we report new disease-relevant murine models of genome instability–driven neurodegeneration involving disabled ATM and APTX that develop debilitating ataxia. We show that neurodegeneration and ataxia result from transcriptional interference in the cerebellum via aberrant messenger RNA splicing. Unexpectedly, these splicing defects were restricted to only Purkinje cells, disrupting the expression of critical homeostatic regulators including ITPR1, GRID2, and CA8. Abundant genotoxic R loops were also found at these Purkinje cell gene loci, further exacerbating DNA damage and transcriptional disruption. Using ATAC-seq to profile global chromatin accessibility in the cerebellum, we found a notably unique chromatin conformation specifically in Purkinje chromatin at the affected gene loci, thereby promoting susceptibility to DNA damage. These data reveal the pathogenic basis of DNA damage in the nervous system and suggest chromatin conformation as a feature in directing genome instability–associated neuropathology.
Collapse
Affiliation(s)
- Young Don Kwak
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | | | - Susanna M Downing
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Ambika Tewari
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yang Li
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Lavinia C Dumitrache
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Sachin Katyal
- CancerCare Manitoba Research Institute, CancerCare Manitoba and Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB R3E OV9, Canada
| | - Kamran Khodakhah
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Helen R Russell
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Departments of Genetics and Cell Molecular Biology, Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Memphis, TN 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN 38105, USA
| |
Collapse
|
44
|
Macaeva E, Tabury K, Michaux A, Janssen A, Averbeck N, Moreels M, De Vos WH, Baatout S, Quintens R. High-LET Carbon and Iron Ions Elicit a Prolonged and Amplified p53 Signaling and Inflammatory Response Compared to low-LET X-Rays in Human Peripheral Blood Mononuclear Cells. Front Oncol 2021; 11:768493. [PMID: 34888245 PMCID: PMC8649625 DOI: 10.3389/fonc.2021.768493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/01/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding the differences in biological response to photon and particle radiation is important for optimal exploitation of particle therapy for cancer patients, as well as for the adequate application of radiation protection measures for astronauts. To address this need, we compared the transcriptional profiles of isolated peripheral blood mononuclear cells 8 h after exposure to 1 Gy of X-rays, carbon ions or iron ions with those of non-irradiated cells using microarray technology. All genes that were found differentially expressed in response to either radiation type were up-regulated and predominantly controlled by p53. Quantitative PCR of selected genes revealed a significantly higher up-regulation 24 h after exposure to heavy ions as compared to X-rays, indicating their prolonged activation. This coincided with increased residual DNA damage as evidenced by quantitative γH2AX foci analysis. Furthermore, despite the converging p53 signature between radiation types, specific gene sets related to the immune response were significantly enriched in up-regulated genes following irradiation with heavy ions. In addition, irradiation, and in particular exposure to carbon ions, promoted transcript variation. Differences in basal and iron ion exposure-induced expression of DNA repair genes allowed the identification of a donor with distinct DNA repair profile. This suggests that gene signatures may serve as a sensitive indicator of individual DNA damage repair capacity. In conclusion, we have shown that photon and particle irradiation induce similar transcriptional pathways, albeit with variable amplitude and timing, but also elicit radiation type-specific responses that may have implications for cancer progression and treatment
Collapse
Affiliation(s)
- Ellina Macaeva
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium.,Department of Molecular Biotechnology, Ghent University, Ghent, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Kevin Tabury
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium.,Department of Biomedical Engineering, University of South Carolina, Columbia, SC, United States
| | - Arlette Michaux
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium
| | - Ann Janssen
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium
| | - Nicole Averbeck
- Department of Biophysics, GSI Helmholtzzentrum für Schwerionenforschung, Darmstadt, Germany
| | - Marjan Moreels
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium
| | - Winnok H De Vos
- Department of Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium.,Department of Molecular Biotechnology, Ghent University, Ghent, Belgium
| | - Roel Quintens
- Radiobiology Unit, Studiecentrum voor kernenergie - Centre d'étude de l'énergie nucléaire (SCK CEN), Mol, Belgium
| |
Collapse
|
45
|
Wang M, Chen S, Ao D. Targeting DNA repair pathway in cancer: Mechanisms and clinical application. MedComm (Beijing) 2021; 2:654-691. [PMID: 34977872 PMCID: PMC8706759 DOI: 10.1002/mco2.103] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Over the last decades, the growing understanding on DNA damage response (DDR) pathways has broadened the therapeutic landscape in oncology. It is becoming increasingly clear that the genomic instability of cells resulted from deficient DNA damage response contributes to the occurrence of cancer. One the other hand, these defects could also be exploited as a therapeutic opportunity, which is preferentially more deleterious in tumor cells than in normal cells. An expanding repertoire of DDR-targeting agents has rapidly expanded to inhibitors of multiple members involved in DDR pathways, including PARP, ATM, ATR, CHK1, WEE1, and DNA-PK. In this review, we sought to summarize the complex network of DNA repair machinery in cancer cells and discuss the underlying mechanism for the application of DDR inhibitors in cancer. With the past preclinical evidence and ongoing clinical trials, we also provide an overview of the history and current landscape of DDR inhibitors in cancer treatment, with special focus on the combination of DDR-targeted therapies with other cancer treatment strategies.
Collapse
Affiliation(s)
- Manni Wang
- Department of BiotherapyCancer CenterWest China HospitalSichuan UniversityChengduChina
| | - Siyuan Chen
- Department of BiotherapyCancer CenterWest China HospitalSichuan UniversityChengduChina
| | - Danyi Ao
- Department of BiotherapyCancer CenterWest China HospitalSichuan UniversityChengduChina
| |
Collapse
|
46
|
Ruta V, Pagliarini V, Sette C. Coordination of RNA Processing Regulation by Signal Transduction Pathways. Biomolecules 2021; 11:biom11101475. [PMID: 34680108 PMCID: PMC8533259 DOI: 10.3390/biom11101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 02/06/2023] Open
Abstract
Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.
Collapse
Affiliation(s)
- Veronica Ruta
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Organoids Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (V.R.); (V.P.)
- Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Correspondence:
| |
Collapse
|
47
|
Cellular functions of the protein kinase ATM and their relevance to human disease. Nat Rev Mol Cell Biol 2021; 22:796-814. [PMID: 34429537 DOI: 10.1038/s41580-021-00394-2] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
The protein kinase ataxia telangiectasia mutated (ATM) is a master regulator of double-strand DNA break (DSB) signalling and stress responses. For three decades, ATM has been investigated extensively to elucidate its roles in the DNA damage response (DDR) and in the pathogenesis of ataxia telangiectasia (A-T), a human neurodegenerative disease caused by loss of ATM. Although hundreds of proteins have been identified as ATM phosphorylation targets and many important roles for this kinase have been identified, it is still unclear how ATM deficiency leads to the early-onset cerebellar degeneration that is common in all individuals with A-T. Recent studies suggest the existence of links between ATM deficiency and other cerebellum-specific neurological disorders, as well as the existence of broader similarities with more common neurodegenerative disorders. In this Review, we discuss recent structural insights into ATM regulation, and possible aetiologies of A-T phenotypes, including reactive oxygen species, mitochondrial dysfunction, alterations in transcription, R-loop metabolism and alternative splicing, defects in cellular proteostasis and metabolism, and potential pathogenic roles for hyper-poly(ADP-ribosyl)ation.
Collapse
|
48
|
Fedrizzi T, Ciani Y, Lorenzin F, Cantore T, Gasperini P, Demichelis F. Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations. Comput Struct Biotechnol J 2021; 19:4394-4403. [PMID: 34429855 PMCID: PMC8369001 DOI: 10.1016/j.csbj.2021.08.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Mutual Exclusivity analysis of genomic aberrations contributes to the exploration of potential synthetic lethal (SL) relationships thus guiding the nomination of specific cancer cells vulnerabilities. When multiple classes of genomic aberrations and large cohorts of patients are interrogated, exhaustive genome-wide analyses are not computationally feasible with commonly used approaches. Here we present Fast Mutual Exclusivity (FaME), an algorithm based on matrix multiplication that employs a logarithm-based implementation of the Fisher's exact test to achieve fast computation of genome-wide mutual exclusivity tests; we show that brute force testing for mutual exclusivity of hundreds of millions of aberrations combinations can be performed in few minutes. We applied FaME to allele-specific data from whole exome experiments of 27 TCGA studies cohorts, detecting both mutual exclusivity of point mutations, as well as allele-specific copy number signals that span sets of contiguous cytobands. We next focused on a case study involving the loss of tumor suppressors and druggable genes while exploiting an integrated analysis of both public cell lines loss of function screens data and patients' transcriptomic profiles. FaME algorithm implementation as well as allele-specific analysis output are publicly available at https://github.com/demichelislab/FaME.
Collapse
Affiliation(s)
- Tarcisio Fedrizzi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Lorenzin
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Thomas Cantore
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Paola Gasperini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Al-Saud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10021, USA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| |
Collapse
|
49
|
Jia N, Guo C, Nakazawa Y, van den Heuvel D, Luijsterburg MS, Ogi T. Dealing with transcription-blocking DNA damage: Repair mechanisms, RNA polymerase II processing and human disorders. DNA Repair (Amst) 2021; 106:103192. [PMID: 34358806 DOI: 10.1016/j.dnarep.2021.103192] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 12/15/2022]
Abstract
Transcription-blocking DNA lesions (TBLs) in genomic DNA are triggered by a wide variety of DNA-damaging agents. Such lesions cause stalling of elongating RNA polymerase II (RNA Pol II) enzymes and fully block transcription when unresolved. The toxic impact of DNA damage on transcription progression is commonly referred to as transcription stress. In response to RNA Pol II stalling, cells activate and employ transcription-coupled repair (TCR) machineries to repair cytotoxic TBLs and resume transcription. Increasing evidence indicates that the modification and processing of stalled RNA Pol II is an integral component of the cellular response to and the repair of TBLs. If TCR pathways fail, the prolonged stalling of RNA Pol II will impede global replication and transcription as well as block the access of other DNA repair pathways that may act upon the TBL. Consequently, such prolonged stalling will trigger profound genome instability and devastating clinical features. In this review, we will discuss the mechanisms by which various types of TBLs are repaired by distinct TCR pathways and how RNA Pol II processing is regulated during these processes. We will also discuss the clinical consequences of transcription stress and genotype-phenotype correlations of related TCR-deficiency disorders.
Collapse
Affiliation(s)
- Nan Jia
- Department of Allergy and Clinical Immunology, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Chaowan Guo
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yuka Nakazawa
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
| |
Collapse
|
50
|
Ramachandran S, Ma TS, Griffin J, Ng N, Foskolou IP, Hwang MS, Victori P, Cheng WC, Buffa FM, Leszczynska KB, El-Khamisy SF, Gromak N, Hammond EM. Hypoxia-induced SETX links replication stress with the unfolded protein response. Nat Commun 2021; 12:3686. [PMID: 34140498 PMCID: PMC8211819 DOI: 10.1038/s41467-021-24066-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023] Open
Abstract
Tumour hypoxia is associated with poor patient prognosis and therapy resistance. A unique transcriptional response is initiated by hypoxia which includes the rapid activation of numerous transcription factors in a background of reduced global transcription. Here, we show that the biological response to hypoxia includes the accumulation of R-loops and the induction of the RNA/DNA helicase SETX. In the absence of hypoxia-induced SETX, R-loop levels increase, DNA damage accumulates, and DNA replication rates decrease. Therefore, suggesting that, SETX plays a role in protecting cells from DNA damage induced during transcription in hypoxia. Importantly, we propose that the mechanism of SETX induction in hypoxia is reliant on the PERK/ATF4 arm of the unfolded protein response. These data not only highlight the unique cellular response to hypoxia, which includes both a replication stress-dependent DNA damage response and an unfolded protein response but uncover a novel link between these two distinct pathways.
Collapse
Affiliation(s)
- Shaliny Ramachandran
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Tiffany S Ma
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Jon Griffin
- Department of Molecular Biology and Biotechnology, Healthy Lifespan and Neuroscience Institute, Firth Court, University of Sheffield, Sheffield, UK
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Natalie Ng
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Iosifina P Foskolou
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Ming-Shih Hwang
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Pedro Victori
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Wei-Chen Cheng
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Katarzyna B Leszczynska
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Healthy Lifespan and Neuroscience Institute, Firth Court, University of Sheffield, Sheffield, UK
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ester M Hammond
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK.
| |
Collapse
|