1
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Li J, Ma X, Wang X, Hu X, Fang S, Jin G, Liu K, Dong Z. Mutations found in cancer patients compromise DNA binding of the winged helix protein STK19. Sci Rep 2024; 14:14098. [PMID: 38890355 PMCID: PMC11189558 DOI: 10.1038/s41598-024-64840-9] [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: 02/23/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Serine/threonine protein kinase 19 (STK19) has been reported to phosphorylate and activate oncogenic NRAS to promote melanomagenesis. However, concerns have been raised about whether STK19 is a kinase. STK19 has also been identified as a putative factor involved in the transcription-coupled nucleotide excision repair (TC-NER) pathway. In this study, we determined the 1.32 Å crystal structure of human STK19. The structure reveals that STK19 is a winged helix (WH) protein consisting of three tandem WH domains. STK19 binds more strongly to double-stranded DNA and RNA (dsDNA/dsRNA) than to ssDNA. A positively charged patch centered on helix WH3-H1 contributes to dsDNA binding, which is unusual because the WH domain typically uses helix H3 as the recognition helix. Importantly, mutations of the conserved residues in the basic patch, K186N, R200W, and R215W, are found in cancer patients, and these mutations compromise STK19 DNA binding. Other mutations have been predicted to produce a similar effect, including two mutations that disrupt the nuclear localization signal (NLS) motif. These mutations may indirectly impact the DNA binding capacity of STK19 by interfering with its nuclear localization.
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Affiliation(s)
- Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
| | - Xinli Ma
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
| | - Xiaoyu Wang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Xiaotong Hu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Shaobo Fang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
| | - Guoguo Jin
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
- Henan Key Laboratory of Chronic Disease Management, Fuwai Central China Cardiovascular Hospital, Zhengzhou, 450000, Henan, China
| | - Kangdong Liu
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zigang Dong
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450003, Henan, China.
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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2
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Luo Y, Li J, Li X, Lin H, Mao Z, Xu Z, Li S, Nie C, Zhou XA, Liao J, Xiong Y, Xu X, Wang J. The ARK2N-CK2 complex initiates transcription-coupled repair through enhancing the interaction of CSB with lesion-stalled RNAPII. Proc Natl Acad Sci U S A 2024; 121:e2404383121. [PMID: 38843184 PMCID: PMC11181095 DOI: 10.1073/pnas.2404383121] [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: 03/04/2024] [Accepted: 05/08/2024] [Indexed: 06/19/2024] Open
Abstract
Transcription is extremely important for cellular processes but can be hindered by RNA polymerase II (RNAPII) pausing and stalling. Cockayne syndrome protein B (CSB) promotes the progression of paused RNAPII or initiates transcription-coupled nucleotide excision repair (TC-NER) to remove stalled RNAPII. However, the specific mechanism by which CSB initiates TC-NER upon damage remains unclear. In this study, we identified the indispensable role of the ARK2N-CK2 complex in the CSB-mediated initiation of TC-NER. The ARK2N-CK2 complex is recruited to damage sites through CSB and then phosphorylates CSB. Phosphorylation of CSB enhances its binding to stalled RNAPII, prolonging the association of CSB with chromatin and promoting CSA-mediated ubiquitination of stalled RNAPII. Consistent with this finding, Ark2n-/- mice exhibit a phenotype resembling Cockayne syndrome. These findings shed light on the pivotal role of the ARK2N-CK2 complex in governing the fate of RNAPII through CSB, bridging a critical gap necessary for initiating TC-NER.
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Affiliation(s)
- Yefei Luo
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Jia Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xiaoman Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Haodong Lin
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Zuchao Mao
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Chen Nie
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Junwei Liao
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen518055, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Institute of Advanced Clinical Medicine, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing100191, China
- Department of Gastrointestinal Translational Research, Peking University Cancer Hospital, Beijing100142, China
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3
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Kulkarni A, Zhou J, Biyani N, Kathad U, Banerjee PP, Srivastava S, Prucsi Z, Solarczyk K, Bhatia K, Ewesuedo RB, Sharma P. LP-184, a Novel Acylfulvene Molecule, Exhibits Anticancer Activity against Diverse Solid Tumors with Homologous Recombination Deficiency. CANCER RESEARCH COMMUNICATIONS 2024; 4:1199-1210. [PMID: 38630886 PMCID: PMC11072798 DOI: 10.1158/2767-9764.crc-23-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Homologous recombination (HR)-related gene alterations are present in a significant subset of prostate, breast, ovarian, pancreatic, lung, and colon cancers rendering these tumors as potential responders to specific DNA damaging agents. A small molecule acylfulvene prodrug, LP-184, metabolizes to an active compound by the oxidoreductase activity of enzyme prostaglandin reductase 1 (PTGR1), which is frequently elevated in multiple solid tumor types. Prior work demonstrated that cancer cell lines deficient in a spectrum of DNA damage repair (DDR) pathway genes show increased susceptibility to LP-184. Here, we investigated the potential of LP-184 in targeting multiple tumors with impaired HR function and its mechanism of action as a DNA damaging agent. LP-184 induced elevated DNA double-strand breaks in HR deficient (HRD) cancer cells. Depletion of key HR components BRCA2 or ataxia telangiectasia mutated (ATM) in cancer cells conferred up to 12-fold increased sensitivity to the LP-184. LP-184 showed nanomolar potency in a diverse range of HRD cancer models, including prostate cancer organoids, leiomyosarcoma cell lines, and patient-derived tumor graft models of lung, pancreatic, and prostate cancers. LP-184 demonstrated complete, durable tumor regression in 10 patient-derived xenograft (PDX) models of HRD triple-negative breast cancer (TNBC) including those resistant to PARP inhibitors (PARPi). LP-184 further displayed strong synergy with PARPi in ovarian and prostate cancer cell lines as well as in TNBC PDX models. These preclinical findings illustrate the potential of LP-184 as a pan-HRD cancer therapeutic. Taken together, our results support continued clinical evaluation of LP-184 in a large subset of HRD solid tumors. SIGNIFICANCE New agents with activity against DDR-deficient solid tumors refractory to standard-of-care therapies are needed. We report multiple findings supporting the potential for LP-184, a novel alkylating agent with three FDA orphan drug designations, to fill this void clinically: strong nanomolar potency; sustained, durable regression of solid tumor xenografts; synthetic lethality with HR defects. LP-184 adult phase IA trial to assess safety in advanced solid tumors is ongoing.
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Affiliation(s)
| | | | | | | | - Partha P. Banerjee
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Shiv Srivastava
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
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4
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Carnie CJ, Acampora AC, Bader AS, Erdenebat C, Zhao S, Bitensky E, van den Heuvel D, Parnas A, Gupta V, D'Alessandro G, Sczaniecka-Clift M, Weickert P, Aygenli F, Götz MJ, Cordes J, Esain-Garcia I, Melidis L, Wondergem AP, Lam S, Robles MS, Balasubramanian S, Adar S, Luijsterburg MS, Jackson SP, Stingele J. Transcription-coupled repair of DNA-protein cross-links depends on CSA and CSB. Nat Cell Biol 2024; 26:797-810. [PMID: 38600235 PMCID: PMC11098753 DOI: 10.1038/s41556-024-01391-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 02/29/2024] [Indexed: 04/12/2024]
Abstract
Covalent DNA-protein cross-links (DPCs) are toxic DNA lesions that block replication and require repair by multiple pathways. Whether transcription blockage contributes to the toxicity of DPCs and how cells respond when RNA polymerases stall at DPCs is unknown. Here we find that DPC formation arrests transcription and induces ubiquitylation and degradation of RNA polymerase II. Using genetic screens and a method for the genome-wide mapping of DNA-protein adducts, DPC sequencing, we discover that Cockayne syndrome (CS) proteins CSB and CSA provide resistance to DPC-inducing agents by promoting DPC repair in actively transcribed genes. Consequently, CSB- or CSA-deficient cells fail to efficiently restart transcription after induction of DPCs. In contrast, nucleotide excision repair factors that act downstream of CSB and CSA at ultraviolet light-induced DNA lesions are dispensable. Our study describes a transcription-coupled DPC repair pathway and suggests that defects in this pathway may contribute to the unique neurological features of CS.
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Affiliation(s)
- Christopher J Carnie
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Aleida C Acampora
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Aldo S Bader
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chimeg Erdenebat
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elnatan Bitensky
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Avital Parnas
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Giuseppina D'Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Pedro Weickert
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fatih Aygenli
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian J Götz
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Isabel Esain-Garcia
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Larry Melidis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Annelotte P Wondergem
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simon Lam
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Maria S Robles
- Institute of Medical Psychology and Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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5
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Muniesa-Vargas A, Davó-Martínez C, Ribeiro-Silva C, van der Woude M, Thijssen KL, Haspels B, Häckes D, Kaynak ÜU, Kanaar R, Marteijn JA, Theil AF, Kuijten MMP, Vermeulen W, Lans H. Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure. Nat Commun 2024; 15:3490. [PMID: 38664429 PMCID: PMC11045817 DOI: 10.1038/s41467-024-47935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
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Affiliation(s)
- Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ben Haspels
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ülkem U Kaynak
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Maayke M P Kuijten
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
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6
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Son K, Takhaveev V, Mor V, Yu H, Dillier E, Zilio N, Püllen NJL, Ivanov D, Ulrich HD, Sturla SJ, Schärer OD. Trabectedin derails transcription-coupled nucleotide excision repair to induce DNA breaks in highly transcribed genes. Nat Commun 2024; 15:1388. [PMID: 38360910 PMCID: PMC10869700 DOI: 10.1038/s41467-024-45664-7] [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: 08/04/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Most genotoxic anticancer agents fail in tumors with intact DNA repair. Therefore, trabectedin, anagent more toxic to cells with active DNA repair, specifically transcription-coupled nucleotide excision repair (TC-NER), provides therapeutic opportunities. To unlock the potential of trabectedin and inform its application in precision oncology, an understanding of the mechanism of the drug's TC-NER-dependent toxicity is needed. Here, we determine that abortive TC-NER of trabectedin-DNA adducts forms persistent single-strand breaks (SSBs) as the adducts block the second of the two sequential NER incisions. We map the 3'-hydroxyl groups of SSBs originating from the first NER incision at trabectedin lesions, recording TC-NER on a genome-wide scale. Trabectedin-induced SSBs primarily occur in transcribed strands of active genes and peak near transcription start sites. Frequent SSBs are also found outside gene bodies, connecting TC-NER to divergent transcription from promoters. This work advances the use of trabectedin for precision oncology and for studying TC-NER and transcription.
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Affiliation(s)
- Kook Son
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Vakil Takhaveev
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Visesato Mor
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Hobin Yu
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea
| | - Emma Dillier
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Nicola Zilio
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Nikolai J L Püllen
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland
| | - Dmitri Ivanov
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, 8092, Zürich, Switzerland.
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science (IBS), 44919, Ulsan, Republic of Korea.
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), 44919, Ulsan, Republic of Korea.
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7
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Zhou D, Yu Q, Janssens RC, Marteijn JA. Live-cell imaging of endogenous CSB-mScarletI as a sensitive marker for DNA-damage-induced transcription stress. CELL REPORTS METHODS 2024; 4:100674. [PMID: 38176411 PMCID: PMC10831951 DOI: 10.1016/j.crmeth.2023.100674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/06/2024]
Abstract
Transcription by RNA polymerase II (RNA Pol II) is crucial for cellular function, but DNA damage severely impedes this process. Thus far, transcription-blocking DNA lesions (TBLs) and their repair have been difficult to quantify in living cells. To overcome this, we generated, using CRISPR-Cas9-mediated gene editing, mScarletI-tagged Cockayne syndrome group B protein (CSB) and UV-stimulated scaffold protein A (UVSSA) knockin cells. These cells allowed us to study the binding dynamics of CSB and UVSSA to lesion-stalled RNA Pol II using fluorescence recovery after photobleaching (FRAP). We show that especially CSB mobility is a sensitive transcription stress marker at physiologically relevant DNA damage levels. Transcription-coupled nucleotide excision repair (TC-NER)-mediated repair can be assessed by studying CSB immobilization over time. Additionally, flow cytometry reveals the regulation of CSB protein levels by CRL4CSA-mediated ubiquitylation and deubiquitylation by USP7. This approach allows the sensitive detection of TBLs and their repair and the study of TC-NER complex assembly and stability in living cells.
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Affiliation(s)
- Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qing Yu
- 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
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands.
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8
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Jayakumar S, Patel M, Boulet F, Aziz H, Brooke GN, Tummala H, Pradeepa MM. PSIP1/LEDGF reduces R-loops at transcription sites to maintain genome integrity. Nat Commun 2024; 15:361. [PMID: 38191578 PMCID: PMC10774266 DOI: 10.1038/s41467-023-44544-w] [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: 02/23/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
R-loops that accumulate at transcription sites pose a persistent threat to genome integrity. PSIP1 is a chromatin protein associated with transcriptional elongation complex, possesses histone chaperone activity, and is implicated in recruiting RNA processing and DNA repair factors to transcription sites. Here, we show that PSIP1 interacts with R-loops and other proteins involved in R-loop homeostasis, including PARP1. Genome-wide mapping of PSIP1, R-loops and γ-H2AX in PSIP1-depleted human and mouse cell lines revealed an accumulation of R-loops and DNA damage at gene promoters in the absence of PSIP1. R-loop accumulation causes local transcriptional arrest and transcription-replication conflict, leading to DNA damage. PSIP1 depletion increases 53BP1 foci and reduces RAD51 foci, suggesting altered DNA repair choice. Furthermore, PSIP1 depletion increases the sensitivity of cancer cells to PARP1 inhibitors and DNA-damaging agents that induce R-loop-induced DNA damage. These findings provide insights into the mechanism through which PSIP1 maintains genome integrity at the site of transcription.
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Affiliation(s)
- Sundarraj Jayakumar
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
- Bhabha Atomic Research Centre, Mumbai, India
| | - Manthan Patel
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Fanny Boulet
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hadicha Aziz
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Greg N Brooke
- School of Life Sciences, University of Essex, Colchester, UK
| | - Hemanth Tummala
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Madapura M Pradeepa
- Blizard Institute; Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK.
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9
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Theil AF, Häckes D, Lans H. TFIIH central activity in nucleotide excision repair to prevent disease. DNA Repair (Amst) 2023; 132:103568. [PMID: 37977600 DOI: 10.1016/j.dnarep.2023.103568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/22/2023] [Accepted: 09/03/2023] [Indexed: 11/19/2023]
Abstract
The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD Rotterdam, the Netherlands.
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10
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Prosz A, Duan H, Tisza V, Sahgal P, Topka S, Klus GT, Börcsök J, Sztupinszki Z, Hanlon T, Diossy M, Vizkeleti L, Stormoen DR, Csabai I, Pappot H, Vijai J, Offit K, Ried T, Sethi N, Mouw KW, Spisak S, Pathania S, Szallasi Z. Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma. Sci Rep 2023; 13:20567. [PMID: 37996508 PMCID: PMC10667362 DOI: 10.1038/s41598-023-47946-4] [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: 08/08/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023] Open
Abstract
Due to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration. We used functional assays that detect UV-induced 6-4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer. Functional assays showed NER deficiency in ccRCC cells. Some cell lines showed irofulven sensitivity at a concentration that is well tolerated by patients. Prostaglandin reductase 1 (PTGR1), which activates irofulven, was also associated with this sensitivity. Next generation sequencing data of the cell lines showed NER deficiency-associated mutational signatures. A significant subset of ccRCC patients had the same signature and high PTGR1 expression. ccRCC cell line-based analysis showed that NER deficiency is likely present in this cancer type. Approximately 10% of ccRCC patients in the TCGA cohort showed mutational signatures consistent with ERCC2 inactivation associated NER deficiency and also substantial levels of PTGR1 expression. These patients may be responsive to irofulven, a previously abandoned anticancer agent that has minimal activity in NER-proficient cells.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Institute, Copenhagen, Denmark
| | - Haohui Duan
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA, USA
- Department of Biology, University of Massachusetts, Boston, MA, USA
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Pranshu Sahgal
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT), Harvard University, Cambridge, MA, USA
| | - Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gregory T Klus
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Judit Börcsök
- Danish Cancer Institute, Copenhagen, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Miklos Diossy
- Danish Cancer Institute, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
| | - Laura Vizkeleti
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Dag Rune Stormoen
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, NY, USA
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT), Harvard University, Cambridge, MA, USA
| | - Kent W Mouw
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Radiation Oncology, Brigham & Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sandor Spisak
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA, USA.
- Department of Biology, University of Massachusetts, Boston, MA, USA.
| | - Zoltan Szallasi
- Danish Cancer Institute, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA.
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary.
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11
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Restifo D, McDermott JR, Cvetkovic D, Santos TD, Ogier C, Surumbayeva A, Handorf EA, Schimke C, Ma C, Cai KQ, Olszanski AJ, Kathad U, Bhatia K, Sharma P, Kulkarni A, Astsaturov I. Conditional Dependency of LP-184 on Prostaglandin Reductase 1 is Synthetic Lethal in Pancreatic Cancers with DNA Damage Repair Deficiencies. Mol Cancer Ther 2023; 22:1182-1190. [PMID: 37552607 PMCID: PMC10592171 DOI: 10.1158/1535-7163.mct-22-0818] [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: 12/27/2022] [Revised: 03/22/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The greater efficacy of DNA-damaging drugs for pancreatic adenocarcinoma (PDAC) relies on targeting cancer-specific vulnerabilities while sparing normal organs and tissues due to their inherent toxicities. We tested LP-184, a novel acylfulvene analog, for its activity in preclinical models of PDAC carrying mutations in the DNA damage repair (DDR) pathways. Cytotoxicity of LP-184 is solely dependent on prostaglandin reductase 1 (PTGR1), so that PTGR1 expression robustly correlates with LP-184 cytotoxicity in vitro and in vivo. Low-passage patient-derived PDAC xenografts with DDR deficiencies treated ex vivo are more sensitive to LP-184 compared with DDR-proficient tumors. Additional in vivo testing of PDAC xenografts for their sensitivity to LP-184 demonstrates marked tumor growth inhibition in models harboring pathogenic mutations in ATR, BRCA1, and BRCA2. Depletion of PTGR1, however, completely abrogates the antitumor effect of LP-184. Testing combinatorial strategies for LP-184 aimed at deregulation of nucleotide excision repair proteins ERCC3 and ERCC4 established synergy. Our results provide valuable biomarkers for clinical testing of LP-184 in a large subset of genetically defined characterized refractory carcinomas. High PTGR1 expression and deleterious DDR mutations are present in approximately one third of PDAC making these patients ideal candidates for clinical trials of LP-184.
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Affiliation(s)
- Diana Restifo
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | - Dusica Cvetkovic
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Troy Dos Santos
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Charline Ogier
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Aizhan Surumbayeva
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | - Charlie Ma
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Kathy Q. Cai
- Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Anthony J. Olszanski
- Department of Hematology and Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | | | | | | | | | - Igor Astsaturov
- The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Hematology and Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
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12
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Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst 2023; 14:447-463.e8. [PMID: 37220749 PMCID: PMC10330685 DOI: 10.1016/j.cels.2023.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into complexes, including constitutive interactions and those responding to genomic insult. Here, we use multi-conditional network analysis to systematically map DDR assemblies at multiple scales. Affinity purifications of 21 DDR proteins, with/without genotoxin exposure, are combined with multi-omics data to reveal a hierarchical organization of 605 proteins into 109 assemblies. The map captures canonical repair mechanisms and proposes new DDR-associated proteins extending to stress, transport, and chromatin functions. We find that protein assemblies closely align with genetic dependencies in processing specific genotoxins and that proteins in multiple assemblies typically act in multiple genotoxin responses. Follow-up by DDR functional readouts newly implicates 12 assembly members in double-strand-break repair. The DNA damage response assemblies map is available for interactive visualization and query (ccmi.org/ddram/).
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Affiliation(s)
- Anton Kratz
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Minkyu Kim
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA; University of Texas Health Science Center San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX 78229, USA
| | - Marcus R Kelly
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Fan Zheng
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Christopher A Koczor
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Jianfeng Li
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Keiichiro Ono
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Yue Qin
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Christopher Churas
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jing Chen
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Rudolf T Pillich
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jisoo Park
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Rachel Collier
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Kate Licon
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Dexter Pratt
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Robert W Sobol
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA; Brown University, Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Providence, RI 02903, USA.
| | - Nevan J Krogan
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
| | - Trey Ideker
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
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13
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van den Heuvel D, Kim M, Wondergem AP, van der Meer PJ, Witkamp M, Lambregtse F, Kim HS, Kan F, Apelt K, Kragten A, González-Prieto R, Vertegaal ACO, Yeo JE, Kim BG, van Doorn R, Schärer OD, Luijsterburg MS. A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair. Proc Natl Acad Sci U S A 2023; 120:e2208860120. [PMID: 36893274 PMCID: PMC10089173 DOI: 10.1073/pnas.2208860120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023] Open
Abstract
XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum (XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPA-H244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (~50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Annelotte P. Wondergem
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Paula J. van der Meer
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Myrèse Witkamp
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Ferdy Lambregtse
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Folkert Kan
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine, University of Sevilla, 41092Seville, Spain
- Department of Cell Biology, University of Seville, 41012Seville, Spain
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2333 ZALeiden, The Netherlands
| | - Orlando D. Schärer
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Martijn S. Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
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14
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Prosz A, Duan H, Tisza V, Sahgal P, Topka S, Klus GT, Börcsök J, Sztupinszki Z, Hanlon T, Diossy M, Vizkeleti L, Stormoen DR, Csabai I, Pappot H, Vijai J, Offit K, Ried T, Sethi N, Mouw KW, Spisak S, Pathania S, Szallasi Z. Nucleotide excision repair deficiency is a targetable therapeutic vulnerability in clear cell renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527498. [PMID: 36798363 PMCID: PMC9934582 DOI: 10.1101/2023.02.07.527498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Purpose Due to a demonstrated lack of DNA repair deficiencies, clear cell renal cell carcinoma (ccRCC) has not benefitted from targeted synthetic lethality-based therapies. We investigated whether nucleotide excision repair (NER) deficiency is present in an identifiable subset of ccRCC cases that would render those tumors sensitive to therapy targeting this specific DNA repair pathway aberration. Experimental Design We used functional assays that detect UV-induced 6-4 pyrimidine-pyrimidone photoproducts to quantify NER deficiency in ccRCC cell lines. We also measured sensitivity to irofulven, an experimental cancer therapeutic agent that specifically targets cells with inactivated transcription-coupled nucleotide excision repair (TC-NER). In order to detect NER deficiency in clinical biopsies, we assessed whole exome sequencing data for the presence of an NER deficiency associated mutational signature previously identified in ERCC2 mutant bladder cancer. Results Functional assays showed NER deficiency in ccRCC cells. Irofulven sensitivity increased in some cell lines. Prostaglandin reductase 1 (PTGR1), which activates irofulven, was also associated with this sensitivity. Next generation sequencing data of the cell lines showed NER deficiency-associated mutational signatures. A significant subset of ccRCC patients had the same signature and high PTGR1 expression. Conclusions ccRCC cell line based analysis showed that NER deficiency is likely present in this cancer type. Approximately 10% of ccRCC patients in the TCGA cohort showed mutational signatures consistent with ERCC2 inactivation associated NER deficiency and also substantial levels of PTGR1 expression. These patients may be responsive to irofulven, a previously abandoned anticancer agent that has minimal activity in NER-proficient cells.
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Affiliation(s)
- Aurel Prosz
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Haohui Duan
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA
- Department of Biology, University of Massachusetts, Boston, MA
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Pranshu Sahgal
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gregory T Klus
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Zsofia Sztupinszki
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
| | - Timothy Hanlon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Miklos Diossy
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
| | - Laura Vizkeleti
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
| | - Dag Rune Stormoen
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University Hospital of Copenhagen, Denmark
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York,New York
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York,New York
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Nilay Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, USA
| | - Kent W. Mouw
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Radiation Oncology, Brigham & Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Sandor Spisak
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA
- Department of Biology, University of Massachusetts, Boston, MA
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
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15
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Casimir L, Zimmer S, Racine-Brassard F, Jacques PÉ, Maréchal A. The mutational impact of Illudin S on human cells. DNA Repair (Amst) 2023; 122:103433. [PMID: 36566616 DOI: 10.1016/j.dnarep.2022.103433] [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: 08/09/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Illudin S (ILS) is a fungal sesquiterpene secondary metabolite with potent genotoxic and cytotoxic properties. Early genetic studies and more recent genome-wide CRISPR screens showed that Illudin-induced lesions are preferentially repaired by transcription-coupled nucleotide excision repair (TC-NER) with some contribution from post-replication repair pathways. In line with these results, Irofulven, a semi-synthetic ILS analog was recently shown to be particularly effective on cell lines and patient-derived xenografts with impaired NER (e.g. ERCC2/3 mutations), raising hope that ILS-derived molecules may soon enter the clinic. Despite the therapeutic potential of ILS and its analogs, we still lack a global understanding of their mutagenic potential. Here, we characterize the mutational signatures associated with chronic exposure to ILS in human cells. ILS treatment rapidly stalls DNA replication and transcription, leading to the activation of the replication stress response and the accumulation of DNA damage. Novel single and double base substitution signatures as well as a characteristic indel signature indicate that ILS treatment preferentially alkylates purine residues and induces oxidative stress, confirming prior in vitro data. Many mutation contexts exhibit a strong transcriptional strand bias, highlighting the contribution of TC-NER to the repair of ILS lesions. Finally, collateral mutations are also observed in response to ILS, suggesting a contribution of translesion synthesis pathways to ILS tolerance. Accordingly, ILS treatment led to the rapid recruitment of the Y-family DNA polymerase kappa onto chromatin, supporting its preferential use for ILS lesion bypass. Altogether, our work provides the first global assessment of the genomic impact of ILS, demonstrating the contribution of multiple DNA repair pathways to ILS resistance and mutagenicity.
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Affiliation(s)
- Lisa Casimir
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Samuel Zimmer
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Félix Racine-Brassard
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
| | - Alexandre Maréchal
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, Canada J1K 2R1; Institut de Recherche sur le Cancer de l'Université de Sherbrooke (IRCUS), Sherbrooke, QC, Canada J1E 4K8; Centre de recherche du Centre hospitalier universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada J1H 5N3.
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16
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Kanao R, Kawai H, Taniguchi T, Takata M, Masutani C. RFWD3 and translesion DNA polymerases contribute to PCNA modification-dependent DNA damage tolerance. Life Sci Alliance 2022; 5:e202201584. [PMID: 35905994 PMCID: PMC9348633 DOI: 10.26508/lsa.202201584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022] Open
Abstract
DNA damage tolerance pathways are regulated by proliferating cell nuclear antigen (PCNA) modifications at lysine 164. Translesion DNA synthesis by DNA polymerase η (Polη) is well studied, but less is known about Polη-independent mechanisms. Illudin S and its derivatives induce alkyl DNA adducts, which are repaired by transcription-coupled nucleotide excision repair (TC-NER). We demonstrate that in addition to TC-NER, PCNA modification at K164 plays an essential role in cellular resistance to these compounds by overcoming replication blockages, with no requirement for Polη. Polκ and RING finger and WD repeat domain 3 (RFWD3) contribute to tolerance, and are both dependent on PCNA modifications. Although RFWD3 is a FANC protein, we demonstrate that it plays a role in DNA damage tolerance independent of the FANC pathway. Finally, we demonstrate that RFWD3-mediated cellular survival after UV irradiation is dependent on PCNA modifications but is independent of Polη. Thus, RFWD3 contributes to PCNA modification-dependent DNA damage tolerance in addition to translesion DNA polymerases.
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Affiliation(s)
- Rie Kanao
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Molecular Pharmaco-Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidehiko Kawai
- Department of Nucleic Acids Biochemistry, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Toshiyasu Taniguchi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Chikahide Masutani
- Department of Genome Dynamics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
- Department of Molecular Pharmaco-Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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17
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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.
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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.
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18
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Zhang X, Yin M, Hu J. Nucleotide excision repair: a versatile and smart toolkit. Acta Biochim Biophys Sin (Shanghai) 2022; 54:807-819. [PMID: 35975604 PMCID: PMC9828404 DOI: 10.3724/abbs.2022054] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.
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Affiliation(s)
| | | | - Jinchuan Hu
- Correspondence address. Tel: +86-21-54237702; E-mail:
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19
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Vougioukalaki M, Demmers J, Vermeij WP, Baar M, Bruens S, Magaraki A, Kuijk E, Jager M, Merzouk S, Brandt RM, Kouwenberg J, van Boxtel R, Cuppen E, Pothof J, Hoeijmakers JHJ. Different responses to DNA damage determine ageing differences between organs. Aging Cell 2022; 21:e13562. [PMID: 35246937 PMCID: PMC9009128 DOI: 10.1111/acel.13562] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/17/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Organs age differently, causing wide heterogeneity in multimorbidity, but underlying mechanisms are largely elusive. To investigate the basis of organ-specific ageing, we utilized progeroid repair-deficient Ercc1Δ /- mouse mutants and systematically compared at the tissue, stem cell and organoid level two organs representing ageing extremes. Ercc1Δ /- intestine shows hardly any accelerated ageing. Nevertheless, we found apoptosis and reduced numbers of intestinal stem cells (ISCs), but cell loss appears compensated by over-proliferation. ISCs retain their organoid-forming capacity, but organoids perform poorly in culture, compared with WT. Conversely, liver ages dramatically, even causing early death in Ercc1-KO mice. Apoptosis, p21, polyploidization and proliferation of various (stem) cells were prominently elevated in Ercc1Δ /- liver and stem cell populations were either largely unaffected (Sox9+), or expanding (Lgr5+), but were functionally exhausted in organoid formation and development in vitro. Paradoxically, while intestine displays less ageing, repair in WT ISCs appears inferior to liver as shown by enhanced sensitivity to various DNA-damaging agents, and lower lesion removal. Our findings reveal organ-specific anti-ageing strategies. Intestine, with short lifespan limiting time for damage accumulation and repair, favours apoptosis of damaged cells relying on ISC plasticity. Liver with low renewal rates depends more on repair pathways specifically protecting the transcribed compartment of the genome to promote sustained functionality and cell preservation. As shown before, the hematopoietic system with intermediate self-renewal mainly invokes replication-linked mechanisms, apoptosis and senescence. Hence, organs employ different genome maintenance strategies, explaining heterogeneity in organ ageing and the segmental nature of DNA-repair-deficient progerias.
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Affiliation(s)
- Maria Vougioukalaki
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Joris Demmers
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology Oncode Institute Utrecht The Netherlands
| | - Marjolein Baar
- Center for Molecular Medicine University Medical Center Utrecht Utrecht The Netherlands
| | - Serena Bruens
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Aristea Magaraki
- Department of Developmental Biology Oncode Institute Rotterdam The Netherlands
| | - Ewart Kuijk
- Division Biomedical Genetics Center for Molecular Medicine and Cancer Genomics Netherlands University Medical Center Utrecht Utrecht University Utrecht The Netherlands
| | - Myrthe Jager
- Department of Genetics Center for Molecular Medicine University Medical Center Utrecht Utrecht University Utrecht The Netherlands
| | - Sarra Merzouk
- Department of Developmental Biology Oncode Institute Rotterdam The Netherlands
| | - Renata M.C. Brandt
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Janneke Kouwenberg
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology Oncode Institute Utrecht The Netherlands
| | - Edwin Cuppen
- Division Biomedical Genetics Center for Molecular Medicine and Cancer Genomics Netherlands University Medical Center Utrecht Utrecht University Utrecht The Netherlands
- Hartwig Medical Foundation Amsterdam Netherlands
| | - Joris Pothof
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
| | - Jan H. J. Hoeijmakers
- Department Molecular Genetics Erasmus University Medical Center Rotterdam Rotterdam The Netherlands
- Princess Máxima Center for Pediatric Oncology Oncode Institute Utrecht The Netherlands
- Institute for Genome Stability in Ageing and Disease Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University Hospital of Cologne Cologne Germany
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20
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Lee S, Yu JS, Lee SR, Kim KH. Non-peptide secondary metabolites from poisonous mushrooms: overview of chemistry, bioactivity, and biosynthesis. Nat Prod Rep 2022; 39:512-559. [PMID: 34608478 DOI: 10.1039/d1np00049g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Covering: up to June 2021A wide variety of mushrooms have traditionally been recognized as edible fungi with high nutritional value and low calories, and abundantly produce structurally diverse and bioactive secondary metabolites. However, accidental ingestion of poisonous mushrooms can result in serious illnesses and even death. Chemically, mushroom poisoning is associated with secondary metabolites produced in poisonous mushrooms, causing specific toxicity. However, many poisonous mushrooms have not been fully investigated for their secondary metabolites, and the secondary metabolites of poisonous mushrooms have not been systematically summarized for details such as chemical composition and biosynthetic mechanisms. The isolation and identification of secondary metabolites from poisonous mushrooms have great research value since these compounds could be lethal toxins that contribute to the toxicity of mushrooms or could provide lead compounds with remarkable biological activities that can promote advances in other related disciplines, such as biochemistry and pharmacology. In this review, we summarize the structures and biological activities of secondary metabolites identified from poisonous mushrooms and provide an overview of the current information on these metabolites, focusing on their chemistry, bioactivity, and biosynthesis.
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Affiliation(s)
- Seulah Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea. .,Division of Life Sciences, Korea Polar Research Institute, KIOST, Incheon 21990, Republic of Korea
| | - Jae Sik Yu
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Seoung Rak Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea. .,Department of Chemistry, Princeton University, New Jersey, 08544, USA
| | - Ki Hyun Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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21
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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.
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22
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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.
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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.
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23
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ELOF1 is a transcription-coupled DNA repair factor that directs RNA polymerase II ubiquitylation. Nat Cell Biol 2021; 23:595-607. [PMID: 34108663 PMCID: PMC8890769 DOI: 10.1038/s41556-021-00688-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/26/2021] [Indexed: 02/05/2023]
Abstract
Cells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation of a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed towards K1268 is unknown. Here, we identify ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to K1268, revealing ELOF1 as a specificity factor that binds and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also revealed a CSB-independent pathway in which ELOF1 prevents R-loops in active genes and protects cells against DNA replication stress. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between transcriptional stress responses and DNA replication.
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24
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Geijer ME, Zhou D, Selvam K, Steurer B, Mukherjee C, Evers B, Cugusi S, van Toorn M, van der Woude M, Janssens RC, Kok YP, Gong W, Raams A, Lo CSY, Lebbink JHG, Geverts B, Plummer DA, Bezstarosti K, Theil AF, Mitter R, Houtsmuller AB, Vermeulen W, Demmers JAA, Li S, van Vugt MATM, Lans H, Bernards R, Svejstrup JQ, Ray Chaudhuri A, Wyrick JJ, Marteijn JA. Elongation factor ELOF1 drives transcription-coupled repair and prevents genome instability. Nat Cell Biol 2021; 23:608-619. [PMID: 34108662 PMCID: PMC7611218 DOI: 10.1038/s41556-021-00692-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/29/2021] [Indexed: 02/05/2023]
Abstract
Correct transcription is crucial for life. However, DNA damage severely impedes elongating RNA polymerase II, causing transcription inhibition and transcription-replication conflicts. Cells are equipped with intricate mechanisms to counteract the severe consequence of these transcription-blocking lesions. However, the exact mechanism and factors involved remain largely unknown. Here, using a genome-wide CRISPR-Cas9 screen, we identified the elongation factor ELOF1 as an important factor in the transcription stress response following DNA damage. We show that ELOF1 has an evolutionarily conserved role in transcription-coupled nucleotide excision repair (TC-NER), where it promotes recruitment of the TC-NER factors UVSSA and TFIIH to efficiently repair transcription-blocking lesions and resume transcription. Additionally, ELOF1 modulates transcription to protect cells against transcription-mediated replication stress, thereby preserving genome stability. Thus, ELOF1 protects the transcription machinery from DNA damage via two distinct mechanisms.
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Affiliation(s)
- Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chirantani Mukherjee
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simona Cugusi
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melanie van der Woude
- 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
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Anja Raams
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce H G Lebbink
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bart Geverts
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dalton A Plummer
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Center, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK
| | - Arnab Ray Chaudhuri
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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25
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The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing. Nat Commun 2021; 12:3153. [PMID: 34039990 PMCID: PMC8155215 DOI: 10.1038/s41467-021-23505-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csbm/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders. XPA-binding protein (XAB)-2 is the human homologue of the yeast pre-mRNA splicing factor Syf1. Here the authors use an in vivo biotinylation tagging approach to show XAB2’s role in DNA repair, RNA splicing and transcription during mammalian development.
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26
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Kulkarni A, McDermott JR, Kathad U, Modali R, Richard JP, Sharma P, Bhatia K. The acylfulvene alkylating agent, LP-184, retains nanomolar potency in non-small cell lung cancer carrying otherwise therapy-refractory mutations. Oncotarget 2021; 12:791-806. [PMID: 33889302 PMCID: PMC8057270 DOI: 10.18632/oncotarget.27943] [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: 01/11/2021] [Accepted: 03/29/2021] [Indexed: 11/25/2022] Open
Abstract
More than 40% of non-small cell lung cancer (NSCLC) patients lack actionable targets and require non-targeted chemotherapeutics. Many become refractory to drugs due to underlying resistance-associated mutations. KEAP1 mutant NSCLCs further activate NRF2 and upregulate its client PTGR1. LP-184, a novel alkylating agent belonging to the acylfulvene class is a prodrug dependent upon PTGR1. We hypothesized that NSCLC with KEAP1 mutations would continue to remain sensitive to LP-184. LP-184 demonstrated highly potent anticancer activity both in primary NSCLC cell lines and in those originating from brain metastases of primary lung cancers. LP-184 activity correlated with PTGR1 transcript levels but was independent of mutations in key oncogenes (KRAS and KEAP1) and tumor suppressors (TP53 and STK11). LP-184 was orders of magnitude more potent in vitro than cisplatin and pemetrexed. Correlative analyses of sensitivity with cell line gene expression patterns indicated that alterations in NRF2, MET, EGFR and BRAF consistently modulated LP-184 sensitivity. These correlations were then extended to TCGA analysis of 517 lung adenocarcinoma patients, out of which 35% showed elevated PTGR1, and 40% of those further displayed statistically significant co-occurrence of KEAP1 mutations. The gene correlates of LP-184 sensitivity allow additional personalization of therapeutic options for future treatment of NSCLC.
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Affiliation(s)
| | | | | | - Rama Modali
- REPROCELL USA Inc., Beltsville, MD 20705, USA
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27
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Topka S, Steinsnyder Z, Ravichandran V, Tkachuk K, Kemel Y, Bandlamudi C, Winkel Madsen M, Furberg H, Ouerfelli O, Rudin CM, Iyer G, Lipkin SM, Mukherjee S, Solit DB, Berger MF, Bajorin DF, Rosenberg JE, Taylor BS, de Stanchina E, Vijai J, Offit K. Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer. Clin Cancer Res 2021; 27:1997-2010. [PMID: 33199492 DOI: 10.1158/1078-0432.ccr-20-3322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/19/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities. EXPERIMENTAL DESIGN We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes. Gene-edited isogenic pairs of wild-type and mutant ERCC2 or ERCC3 cell lines were created and used to assess response to several candidate drugs. RESULTS We found that putative damaging germline and somatic alterations in NER genes were present with frequencies up to 10% across multiple cancer types. Both in vitro and in vivo studies showed significantly enhanced sensitivity to the sesquiterpene irofulven in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to a current standard-of-care agent, cisplatin. Hypomorphic ERCC2/3-mutant cells had impaired ability to repair irofulven-induced DNA damage. Transcriptomic profiling of tumor tissues suggested codependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies. CONCLUSIONS These findings provide novel insights into a synthetic lethal relationship between clinically observed NER gene deficiencies and sensitivity to irofulven and its potential synergistic combination with other drugs.See related commentary by Jiang and Greenberg, p. 1833.
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Affiliation(s)
- Sabine Topka
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Steinsnyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vignesh Ravichandran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Helena Furberg
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ouathek Ouerfelli
- Chemical Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Steven M Lipkin
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Niehaus Center for Inherited Cancer Genomics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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28
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Kathad U, Kulkarni A, McDermott JR, Wegner J, Carr P, Biyani N, Modali R, Richard JP, Sharma P, Bhatia K. A machine learning-based gene signature of response to the novel alkylating agent LP-184 distinguishes its potential tumor indications. BMC Bioinformatics 2021; 22:102. [PMID: 33653269 PMCID: PMC7923321 DOI: 10.1186/s12859-021-04040-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/15/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Non-targeted cytotoxics with anticancer activity are often developed through preclinical stages using response criteria observed in cell lines and xenografts. A panel of the NCI-60 cell lines is frequently the first line to define tumor types that are optimally responsive. Open data on the gene expression of the NCI-60 cell lines, provides a unique opportunity to add another dimension to the preclinical development of such drugs by interrogating correlations with gene expression patterns. Machine learning can be used to reduce the complexity of whole genome gene expression patterns to derive manageable signatures of response. Application of machine learning in early phases of preclinical development is likely to allow a better positioning and ultimate clinical success of molecules. LP-184 is a highly potent novel alkylating agent where the preclinical development is being guided by a dedicated machine learning-derived response signature. We show the feasibility and the accuracy of such a signature of response by accurately predicting the response to LP-184 validated using wet lab derived IC50s on a panel of cell lines. RESULTS We applied our proprietary RADR® platform to an NCI-60 discovery dataset encompassing LP-184 IC50s and publicly available gene expression data. We used multiple feature selection layers followed by the XGBoost regression model and reduced the complexity of 20,000 gene expression values to generate a 16-gene signature leading to the identification of a set of predictive candidate biomarkers which form an LP-184 response gene signature. We further validated this signature and predicted response to an additional panel of cell lines. Considering fold change differences and correlation between actual and predicted LP-184 IC50 values as validation performance measures, we obtained 86% accuracy at four-fold cut-off, and a strong (r = 0.70) and significant (p value 1.36e-06) correlation between actual and predicted LP-184 sensitivity. In agreement with the perceived mechanism of action of LP-184, PTGR1 emerged as the top weighted gene. CONCLUSION Integration of a machine learning-derived signature of response with in vitro assessment of LP-184 efficacy facilitated the derivation of manageable yet robust biomarkers which can be used to predict drug sensitivity with high accuracy and clinical value.
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Affiliation(s)
- Umesh Kathad
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA.
| | - Aditya Kulkarni
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | | | - Jordan Wegner
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Peter Carr
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Neha Biyani
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Rama Modali
- REPROCELL USA Inc., 9000 Virginia Manor Rd, Ste 207, Beltsville, MD, 20705, USA
| | | | - Panna Sharma
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
| | - Kishor Bhatia
- Lantern Pharma, Inc., 1920 McKinney Ave, 7th floor, Dallas, TX, 75201, USA
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29
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van den Heuvel D, Spruijt CG, González-Prieto R, Kragten A, Paulsen MT, Zhou D, Wu H, Apelt K, van der Weegen Y, Yang K, Dijk M, Daxinger L, Marteijn JA, Vertegaal ACO, Ljungman M, Vermeulen M, Luijsterburg MS. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. Nat Commun 2021; 12:1342. [PMID: 33637760 PMCID: PMC7910549 DOI: 10.1038/s41467-021-21520-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/28/2021] [Indexed: 02/06/2023] Open
Abstract
Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress. The transcription-coupled repair pathway removes transcription-blocking DNA lesions, but how transcription is restored following DNA repair is not clear. Here the authors reveal that the PAF1 complex, while dispensable for the repair process, restores transcription after DNA damage.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia G Spruijt
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.,Prinses Maxima Center, Utrecht, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kevin Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Madelon Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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30
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Jiang H, Greenberg RA. Morning for Irofulven, What Could be fiNER? Clin Cancer Res 2021; 27:1833-1835. [PMID: 33472911 DOI: 10.1158/1078-0432.ccr-20-4708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 12/31/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022]
Abstract
Cancers with DNA repair dysfunction are vulnerable to DNA-damaging agents that invoke a requirement for the disabled repair mechanism. Genome sequencing, coupled with a detailed understanding of mechanisms of DNA repair, has accelerated the discovery of pathway-selective agents that target DNA repair deficiencies in a tumor tissue agnostic manner.See related articles by Topka et al., p. 1997 and Börcsök et al., p. 2011.
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Affiliation(s)
- Haoyang Jiang
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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31
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Nowakowski P, Markiewicz-Żukowska R, Gromkowska-Kępka K, Naliwajko SK, Moskwa J, Bielecka J, Grabia M, Borawska M, Socha K. Mushrooms as potential therapeutic agents in the treatment of cancer: Evaluation of anti-glioma effects of Coprinus comatus, Cantharellus cibarius, Lycoperdon perlatum and Lactarius deliciosus extracts. Biomed Pharmacother 2020; 133:111090. [PMID: 33378984 DOI: 10.1016/j.biopha.2020.111090] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/15/2020] [Accepted: 11/28/2020] [Indexed: 02/04/2023] Open
Abstract
Cancer incidence rates are on the increase worldwide. The most common brain cancer in adults is glioblastoma. Currently available treatment modalities are limited and natural products such as mushrooms could enhance them. Apart from nutritional value, mushrooms are an excellent source of bioactive compounds and therefore could be used to treat various disorders. The aim of the study was to assess the anti-glioma potential of selected mushrooms on U87MG, LN-18 glioblastoma and SVGp12 normal human astroglial cell lines. The materials were Cantharellus cibarius, Coprinus comatus, Lycoperdon perlatum and Lactarius delicious. Aqueous, 70 % ethanol or 95 % ethanol extracts from mushrooms were used for analysis including assessment of antioxidant activity by DPPH assay, cell viability by MTT assay, DNA biosynthesis by thymidine incorporation assay, activity of metalloproteinase by gelatin zymography and cell cycle assay by flow cytometry. Mushroom extracts influenced the viability and DNA biosynthesis of cancer cells. Activity of ethanol mushroom extracts was stronger than that of aqueous extracts. Anti-glioma mechanism consisted in inhibition of cancer cell proliferation and induction of apoptosis associated with arrest of cells in subG1 or G2/M phase of cell cycle, and inhibition of metalloproteinases activity. Among investigated mushrooms, L. deliciosus and C. comatus showed the greatest anti-glioma potential.
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Affiliation(s)
- Patryk Nowakowski
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1).
| | - Renata Markiewicz-Żukowska
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Krystyna Gromkowska-Kępka
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Sylwia Katarzyna Naliwajko
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Justyna Moskwa
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Joanna Bielecka
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Monika Grabia
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Maria Borawska
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
| | - Katarzyna Socha
- Department of Bromatology, Faculty of Pharmacy with the Division of Laboratory Medicine, Medical University of Bialystok, ul. Mickiewicza 2D, 15-222 Bialystok, Poland(1)
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32
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Börcsök J, Sztupinszki Z, Bekele R, Gao SP, Diossy M, Samant AS, Dillon KM, Tisza V, Spisák S, Rusz O, Csabai I, Pappot H, Frazier ZJ, Konieczkowski DJ, Liu D, Vasani N, Rodrigues JA, Solit DB, Hoffman-Censits JH, Plimack ER, Rosenberg JE, Lazaro JB, Taplin ME, Iyer G, Brunak S, Lozsa R, Van Allen EM, Szüts D, Mouw KW, Szallasi Z. Identification of a Synthetic Lethal Relationship between Nucleotide Excision Repair Deficiency and Irofulven Sensitivity in Urothelial Cancer. Clin Cancer Res 2020; 27:2011-2022. [PMID: 33208343 DOI: 10.1158/1078-0432.ccr-20-3316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/16/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Cisplatin-based chemotherapy is a first-line treatment for muscle-invasive and metastatic urothelial cancer. Approximately 10% of bladder urothelial tumors have a somatic missense mutation in the nucleotide excision repair (NER) gene, ERCC2, which confers increased sensitivity to cisplatin-based chemotherapy. However, a significant subset of patients is ineligible to receive cisplatin-based therapy due to medical contraindications, and no NER-targeted approaches are available for platinum-ineligible or platinum-refractory ERCC2-mutant cases. EXPERIMENTAL DESIGN We used a series of NER-proficient and NER-deficient preclinical tumor models to test sensitivity to irofulven, an abandoned anticancer agent. In addition, we used available clinical and sequencing data from multiple urothelial tumor cohorts to develop and validate a composite mutational signature of ERCC2 deficiency and cisplatin sensitivity. RESULTS We identified a novel synthetic lethal relationship between tumor NER deficiency and sensitivity to irofulven. Irofulven specifically targets cells with inactivation of the transcription-coupled NER (TC-NER) pathway and leads to robust responses in vitro and in vivo, including in models with acquired cisplatin resistance, while having minimal effect on cells with intact NER. We also found that a composite mutational signature of ERCC2 deficiency was strongly associated with cisplatin response in patients and was also associated with cisplatin and irofulven sensitivity in preclinical models. CONCLUSIONS Tumor NER deficiency confers sensitivity to irofulven, a previously abandoned anticancer agent, with minimal activity in NER-proficient cells. A composite mutational signature of NER deficiency may be useful in identifying patients likely to respond to NER-targeting agents, including cisplatin and irofulven.See related commentary by Jiang and Greenberg, p. 1833.
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Affiliation(s)
- Judit Börcsök
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Raie Bekele
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Sizhi P Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Miklos Diossy
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Amruta S Samant
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kasia M Dillon
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Viktoria Tisza
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
| | - Sándor Spisák
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Orsolya Rusz
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
| | - Istvan Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Zoë J Frazier
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David J Konieczkowski
- Department of Radiation Oncology, Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Naresh Vasani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Rodrigues
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Jean H Hoffman-Censits
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth R Plimack
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jonathan E Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gopa Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Rita Lozsa
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Radiation Oncology, Brigham & Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Zoltan Szallasi
- Danish Cancer Society Research Center, Copenhagen, Denmark.
- Computational Health Informatics Program, Boston Children's Hospital, Boston, Massachusetts
- 2nd Department of Pathology, SE NAP, Brain Metastasis Research Group, Semmelweis University, Budapest, Hungary
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Lopes AFC, Bozek K, Herholz M, Trifunovic A, Rieckher M, Schumacher B. A C. elegans model for neurodegeneration in Cockayne syndrome. Nucleic Acids Res 2020; 48:10973-10985. [PMID: 33021672 PMCID: PMC7641758 DOI: 10.1093/nar/gkaa795] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/08/2020] [Accepted: 09/27/2020] [Indexed: 12/22/2022] Open
Abstract
Cockayne syndrome (CS) is a congenital syndrome characterized by growth and mental retardation, and premature ageing. The complexity of CS and mammalian models warrants simpler metazoan models that display CS-like phenotypes that could be studied in the context of a live organism. Here, we provide a characterization of neuronal and mitochondrial aberrations caused by a mutation in the csb-1 gene in Caenorhabditis elegans. We report a progressive neurodegeneration in adult animals that is enhanced upon UV-induced DNA damage. The csb-1 mutants show dysfunctional hyperfused mitochondria that degrade upon DNA damage, resulting in diminished respiratory activity. Our data support the role of endogenous DNA damage as a driving factor of CS-related neuropathology and underline the role of mitochondrial dysfunction in the disease.
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Affiliation(s)
- Amanda F C Lopes
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Katarzyna Bozek
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
| | - Marija Herholz
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
- Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
- Center for Molecular Medicine (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Robert-Koch-Str. 21, 50931 Cologne, Germany
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Lee J, Hilgers F, Loeschke A, Jaeger KE, Feldbrügge M. Ustilago maydis Serves as a Novel Production Host for the Synthesis of Plant and Fungal Sesquiterpenoids. Front Microbiol 2020; 11:1655. [PMID: 32849341 PMCID: PMC7396576 DOI: 10.3389/fmicb.2020.01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022] Open
Abstract
Sesquiterpenoids are important secondary metabolites with various pharma- and nutraceutical properties. In particular, higher basidiomycetes possess a versatile biosynthetic repertoire for these bioactive compounds. To date, only a few microbial production systems for fungal sesquiterpenoids have been established. Here, we introduce Ustilago maydis as a novel production host. This model fungus is a close relative of higher basidiomycetes. It offers the advantage of metabolic compatibility and potential tolerance for substances toxic to other microorganisms. We successfully implemented a heterologous pathway to produce the carotenoid lycopene that served as a straightforward read-out for precursor pathway engineering. Overexpressing genes encoding enzymes of the mevalonate pathway resulted in increased lycopene levels. Verifying the subcellular localization of the relevant enzymes revealed that initial metabolic reactions might take place in peroxisomes: despite the absence of a canonical peroxisomal targeting sequence, acetyl-CoA C-acetyltransferase Aat1 localized to peroxisomes. By expressing the plant (+)-valencene synthase CnVS and the basidiomycete sesquiterpenoid synthase Cop6, we succeeded in producing (+)-valencene and α-cuprenene, respectively. Importantly, the fungal compound yielded about tenfold higher titers in comparison to the plant substance. This proof of principle demonstrates that U. maydis can serve as promising novel chassis for the production of terpenoids.
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Affiliation(s)
- Jungho Lee
- Bioeconomy Science Centre, Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fabienne Hilgers
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschke
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Michael Feldbrügge
- Bioeconomy Science Centre, Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Olivieri M, Cho T, Álvarez-Quilón A, Li K, Schellenberg MJ, Zimmermann M, Hustedt N, Rossi SE, Adam S, Melo H, Heijink AM, Sastre-Moreno G, Moatti N, Szilard RK, McEwan A, Ling AK, Serrano-Benitez A, Ubhi T, Feng S, Pawling J, Delgado-Sainz I, Ferguson MW, Dennis JW, Brown GW, Cortés-Ledesma F, Williams RS, Martin A, Xu D, Durocher D. A Genetic Map of the Response to DNA Damage in Human Cells. Cell 2020; 182:481-496.e21. [PMID: 32649862 PMCID: PMC7384976 DOI: 10.1016/j.cell.2020.05.040] [Citation(s) in RCA: 281] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/13/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022]
Abstract
The response to DNA damage is critical for cellular homeostasis, tumor suppression, immunity, and gametogenesis. In order to provide an unbiased and global view of the DNA damage response in human cells, we undertook 31 CRISPR-Cas9 screens against 27 genotoxic agents in the retinal pigment epithelium-1 (RPE1) cell line. These screens identified 890 genes whose loss causes either sensitivity or resistance to DNA-damaging agents. Mining this dataset, we discovered that ERCC6L2 (which is mutated in a bone-marrow failure syndrome) codes for a canonical non-homologous end-joining pathway factor, that the RNA polymerase II component ELOF1 modulates the response to transcription-blocking agents, and that the cytotoxicity of the G-quadruplex ligand pyridostatin involves trapping topoisomerase II on DNA. This map of the DNA damage response provides a rich resource to study this fundamental cellular system and has implications for the development and use of genotoxic agents in cancer therapy.
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Affiliation(s)
- Michele Olivieri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Tiffany Cho
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Alejandro Álvarez-Quilón
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Kejiao Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871 Beijing, China
| | - Matthew J Schellenberg
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA
| | - Michal Zimmermann
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Nicole Hustedt
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Silvia Emma Rossi
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Salomé Adam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Anne Margriet Heijink
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Guillermo Sastre-Moreno
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Nathalie Moatti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Rachel K Szilard
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Andrea McEwan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Alexanda K Ling
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, ON, M5S 1A8, Canada
| | - Almudena Serrano-Benitez
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla Universidad Pablo de Olavide, 41092 Sevilla, Spain
| | - Tajinder Ubhi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Sumin Feng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Judy Pawling
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada
| | - Irene Delgado-Sainz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla Universidad Pablo de Olavide, 41092 Sevilla, Spain
| | - Michael W Ferguson
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - James W Dennis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Grant W Brown
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON, M5S 3E1, Canada; Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad de Sevilla Universidad Pablo de Olavide, 41092 Sevilla, Spain
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC 27709, USA
| | - Alberto Martin
- Department of Immunology, University of Toronto, Medical Sciences Building, Toronto, ON, M5S 1A8, Canada
| | - Dongyi Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871 Beijing, China
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
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van der Weegen Y, Golan-Berman H, Mevissen TET, Apelt K, González-Prieto R, Goedhart J, Heilbrun EE, Vertegaal ACO, van den Heuvel D, Walter JC, Adar S, Luijsterburg MS. The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II. Nat Commun 2020; 11:2104. [PMID: 32355176 PMCID: PMC7192910 DOI: 10.1038/s41467-020-15903-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 03/27/2020] [Indexed: 12/13/2022] Open
Abstract
The response to DNA damage-stalled RNA polymerase II (RNAPIIo) involves the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. The function of the TCR proteins CSB, CSA and UVSSA and the manner in which the core DNA repair complex, including transcription factor IIH (TFIIH), is recruited are largely unknown. Here, we define the assembly mechanism of the TCR complex in human isogenic knockout cells. We show that TCR is initiated by RNAPIIo-bound CSB, which recruits CSA through a newly identified CSA-interaction motif (CIM). Once recruited, CSA facilitates the association of UVSSA with stalled RNAPIIo. Importantly, we find that UVSSA is the key factor that recruits the TFIIH complex in a manner that is stimulated by CSB and CSA. Together these findings identify a sequential and highly cooperative assembly mechanism of TCR proteins and reveal the mechanism for TFIIH recruitment to DNA damage-stalled RNAPIIo to initiate repair. The response to DNA damage-stalled RNA polymerase II leads to the assembly of the transcription-coupled repair (TCR) complex on actively transcribed strands. Here, the authors reveal the complex assembly mechanism of the TCR complex in human cells.
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Affiliation(s)
- Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Hadar Golan-Berman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Tycho E T Mevissen
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Elisheva E Heilbrun
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Johannes C Walter
- Howard Hughes Medical Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, 91120, Israel
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands.
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Human HMGN1 and HMGN2 are not required for transcription-coupled DNA repair. Sci Rep 2020; 10:4332. [PMID: 32152397 PMCID: PMC7062826 DOI: 10.1038/s41598-020-61243-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/21/2020] [Indexed: 12/30/2022] Open
Abstract
Transcription-coupled repair (TCR) removes DNA lesions from the transcribed strand of active genes. Stalling of RNA polymerase II (RNAPII) at DNA lesions initiates TCR through the recruitment of the CSB and CSA proteins. The full repertoire of proteins required for human TCR – particularly in a chromatin context - remains to be determined. Studies in mice have revealed that the nucleosome-binding protein HMGN1 is required to enhance the repair of UV-induced lesions in transcribed genes. However, whether HMGN1 is required for human TCR remains unaddressed. Here, we show that knockout or knockdown of HMGN1, either alone or in combination with HMGN2, does not render human cells sensitive to UV light or Illudin S-induced transcription-blocking DNA lesions. Moreover, transcription restart after UV irradiation was not impaired in HMGN-deficient cells. In contrast, TCR-deficient cells were highly sensitive to DNA damage and failed to restart transcription. Furthermore, GFP-tagged HMGN1 was not recruited to sites of UV-induced DNA damage under conditions where GFP-CSB readily accumulated. In line with this, HMGN1 did not associate with the TCR complex, nor did TCR proteins require HMGN1 to associate with DNA damage-stalled RNAPII. Together, our findings suggest that HMGN1 and HMGN2 are not required for human TCR.
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Lans H, Hoeijmakers JHJ, Vermeulen W, Marteijn JA. The DNA damage response to transcription stress. Nat Rev Mol Cell Biol 2019; 20:766-784. [DOI: 10.1038/s41580-019-0169-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/30/2022]
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39
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Bianco JN, Schumacher B. MPK-1/ERK pathway regulates DNA damage response during development through DAF-16/FOXO. Nucleic Acids Res 2019; 46:6129-6139. [PMID: 29788264 PMCID: PMC6159517 DOI: 10.1093/nar/gky404] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/01/2018] [Indexed: 01/25/2023] Open
Abstract
Ultraviolet (UV) induces distorting lesions to the DNA that can lead to stalling of the RNA polymerase II (RNAP II) and that are removed by transcription-coupled nucleotide excision repair (TC-NER). In humans, mutations in the TC-NER genes CSA and CSB lead to severe postnatal developmental defects in Cockayne syndrome patients. In Caenorhabditis elegans, mutations in the TC-NER genes csa-1 and csb-1, lead to developmental growth arrest upon UV treatment. We conducted a genetic suppressor screen in the nematode to identify mutations that could suppress the developmental defects in csb-1 mutants. We found that mutations in the ERK1/2 MAP kinase mpk-1 alleviate the developmental retardation in TC-NER mutants, while constitutive activation of the RAS-MAPK pathway exacerbates the DNA damage-induced growth arrest. We show that MPK-1 act via insulin/insulin-like signaling pathway and regulates the FOXO transcription factor DAF-16 to mediate the developmental DNA damage response.
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Affiliation(s)
- Julien N Bianco
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.,Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
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41
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O'Connor PJ, Alonso-Amelot ME, Roberts SA, Povey AC. The role of bracken fern illudanes in bracken fern-induced toxicities. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 782:108276. [PMID: 31843140 DOI: 10.1016/j.mrrev.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 03/29/2019] [Accepted: 05/02/2019] [Indexed: 12/24/2022]
Abstract
Bracken fern is carcinogenic when fed to domestic and laboratory animals inducing bladder and ileal tumours and is currently classified as a possible human carcinogen by IARC. The carcinogenic illudane, ptaquiloside (PTQ) was isolated from bracken fern and is widely assumed to be the major bracken carcinogen. However, several other structurally similar illudanes are found in bracken fern, in some cases at higher levels than PTQ and so may contribute to the overall toxicity and carcinogenicity of bracken fern. In this review, we critically evaluate the role of illudanes in bracken fern induced toxicity and carcinogenicity, the mechanistic basis of these effects including the role of DNA damage, and the potential for human exposure in order to highlight deficiencies in the current literature. Critical gaps remain in our understanding of bracken fern induced carcinogenesis, a better understanding of these processes is essential to establish whether bracken fern is also a human carcinogen.
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Affiliation(s)
- P J O'Connor
- Centre for Occupational and Environmental Health, Centre for Epidemiology, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - M E Alonso-Amelot
- Chemical Ecology Group, Faculty of Sciences, University of Los Andes, Mérida 5101, Venezuela
| | - S A Roberts
- Centre for Biostatistics, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - A C Povey
- Centre for Occupational and Environmental Health, Centre for Epidemiology, Division of Population Health, Health Services Research and Primary Care, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
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42
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Biersack B. Alkylating anticancer agents and their relations to microRNAs. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:1-17. [PMID: 35582140 PMCID: PMC9019174 DOI: 10.20517/cdr.2019.09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 11/12/2022]
Abstract
Alkylating agents represent an important class of anticancer drugs. The occurrence and emergence of tumor resistance to the treatment with alkylating agents denotes a severe problem in the clinics. A detailed understanding of the mechanisms of activity of alkylating drugs is essential in order to overcome drug resistance. In particular, the role of non-coding microRNAs concerning alkylating drug activity and resistance in various cancers is highlighted in this review. Both synthetic and natural alkylating agents, which are approved for cancer therapy, are discussed concerning their interplay with microRNAs.
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Affiliation(s)
- Bernhard Biersack
- Organic Chemistry Laboratory, University of Bayreuth, Bayreuth 95440, Germany
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Klebsiella oxytoca enterotoxins tilimycin and tilivalline have distinct host DNA-damaging and microtubule-stabilizing activities. Proc Natl Acad Sci U S A 2019; 116:3774-3783. [PMID: 30808763 PMCID: PMC6397511 DOI: 10.1073/pnas.1819154116] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Human gut microbes form a complex community with vast biosynthetic potential. Microbial products and metabolites released in the gut impact human health and disease. However, defining causative relationships between specific bacterial products and disease initiation and progression remains an immense challenge. This study advances understanding of the functional capacity of the gut microbiota by determining the presence, concentration, and spatial and temporal variability of two enterotoxic metabolites produced by the gut-resident Klebsiella oxytoca. We present a detailed mode of action for the cytotoxins and recapitulate their functionalities in disease models in vivo. The findings provide distinct molecular mechanisms for the enterotoxicity of the metabolites allowing them to act in tandem to damage the intestinal epithelium and cause colitis. Establishing causal links between bacterial metabolites and human intestinal disease is a significant challenge. This study reveals the molecular basis of antibiotic-associated hemorrhagic colitis (AAHC) caused by intestinal resident Klebsiella oxytoca. Colitogenic strains produce the nonribosomal peptides tilivalline and tilimycin. Here, we verify that these enterotoxins are present in the human intestine during active colitis and determine their concentrations in a murine disease model. Although both toxins share a pyrrolobenzodiazepine structure, they have distinct molecular targets. Tilimycin acts as a genotoxin. Its interaction with DNA activates damage repair mechanisms in cultured cells and causes DNA strand breakage and an increased lesion burden in cecal enterocytes of colonized mice. In contrast, tilivalline binds tubulin and stabilizes microtubules leading to mitotic arrest. To our knowledge, this activity is unique for microbiota-derived metabolites of the human intestine. The capacity of both toxins to induce apoptosis in intestinal epithelial cells—a hallmark feature of AAHC—by independent modes of action, strengthens our proposal that these metabolites act collectively in the pathogenicity of colitis.
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Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2018; 71:43-55. [PMID: 30174298 DOI: 10.1016/j.dnarep.2018.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic transcription-coupled nucleotide excision repair (TC-NER) is a pathway that removes DNA lesions capable of blocking RNA polymerase II (Pol II) transcription from the template strand. This process is initiated by lesion-arrested Pol II and the recruitment of Cockayne Syndrome B protein (CSB). In this review, we will focus on the lesion recognition steps of eukaryotic TC-NER and summarize the recent research progress toward understanding the structural basis of Pol II-mediated lesion recognition and Pol II-CSB interactions. We will discuss the roles of CSB in both TC-NER initiation and transcription elongation. Finally, we propose an updated model of tripartite lesion recognition and verification for TC-NER in which CSB ensures Pol II-mediated recognition of DNA lesions for TC-NER.
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Genome instability is a consequence of transcription deficiency in patients with bone marrow failure harboring biallelic ERCC6L2 variants. Proc Natl Acad Sci U S A 2018; 115:7777-7782. [PMID: 29987015 PMCID: PMC6064997 DOI: 10.1073/pnas.1803275115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bone marrow failure (BMF) is an inherited life-threatening condition characterized by defective hematopoiesis, developmental abnormalities, and predisposition to cancer. BMF caused by ERCC6L2 mutations is considered to be a genome instability syndrome, because DNA repair is compromised in patient cells. In this study, we report BMF cases with biallelic disease-causing variants and provide evidence from patients’ cells that transcription deficiency can explain the genome instability. Specifically, we demonstrate that ERCC6L2 participates in RNA polymerase II-mediated transcription via interaction with DNA-dependent protein kinase (DNA-PK) and resolves DNA–RNA hybrids (R loops). Collectively, our data point to a causal mechanism in BMF in which patients with ERCC6L2 mutations are defective in the repair of transcription-associated DNA damage. Biallelic variants in the ERCC excision repair 6 like 2 gene (ERCC6L2) are known to cause bone marrow failure (BMF) due to defects in DNA repair and mitochondrial function. Here, we report on eight cases of BMF from five families harboring biallelic variants in ERCC6L2, two of whom present with myelodysplasia. We confirm that ERCC6L2 patients’ lymphoblastoid cell lines (LCLs) are hypersensitive to DNA-damaging agents that specifically activate the transcription coupled nucleotide excision repair (TCNER) pathway. Interestingly, patients’ LCLs are also hypersensitive to transcription inhibitors that interfere with RNA polymerase II (RNA Pol II) and display an abnormal delay in transcription recovery. Using affinity-based mass spectrometry we found that ERCC6L2 interacts with DNA-dependent protein kinase (DNA-PK), a regulatory component of the RNA Pol II transcription complex. Chromatin immunoprecipitation PCR studies revealed ERCC6L2 occupancy on gene bodies along with RNA Pol II and DNA-PK. Patients’ LCLs fail to terminate transcript elongation accurately upon DNA damage and display a significant increase in nuclear DNA–RNA hybrids (R loops). Collectively, we conclude that ERCC6L2 is involved in regulating RNA Pol II-mediated transcription via its interaction with DNA-PK to resolve R loops and minimize transcription-associated genome instability. The inherited BMF syndrome caused by biallelic variants in ERCC6L2 can be considered as a primary transcription deficiency rather than a DNA repair defect.
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Pines A, Dijk M, Makowski M, Meulenbroek EM, Vrouwe MG, van der Weegen Y, Baltissen M, French PJ, van Royen ME, Luijsterburg MS, Mullenders LH, Vermeulen M, Vermeulen W, Pannu NS, van Attikum H. TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A. Nat Commun 2018. [PMID: 29531219 PMCID: PMC5847541 DOI: 10.1038/s41467-018-03484-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Transcription-blocking DNA lesions are removed by transcription-coupled nucleotide excision repair (TC-NER) to preserve cell viability. TC-NER is triggered by the stalling of RNA polymerase II at DNA lesions, leading to the recruitment of TC-NER-specific factors such as the CSA–DDB1–CUL4A–RBX1 cullin–RING ubiquitin ligase complex (CRLCSA). Despite its vital role in TC-NER, little is known about the regulation of the CRLCSA complex during TC-NER. Using conventional and cross-linking immunoprecipitations coupled to mass spectrometry, we uncover a stable interaction between CSA and the TRiC chaperonin. TRiC’s binding to CSA ensures its stability and DDB1-dependent assembly into the CRLCSA complex. Consequently, loss of TRiC leads to mislocalization and depletion of CSA, as well as impaired transcription recovery following UV damage, suggesting defects in TC-NER. Furthermore, Cockayne syndrome (CS)-causing mutations in CSA lead to increased TRiC binding and a failure to compose the CRLCSA complex. Thus, we uncover CSA as a TRiC substrate and reveal that TRiC regulates CSA-dependent TC-NER and the development of CS. An integrated network of chaperones and protein degradation machineries called the proteostasis network (PN) is required to maintain protein homeostasis. Here the authors show that one of the components of the PN, the chaperonin TRiC, interacts with the core transcription-coupled nucleotide excision repair protein CSA to ensure its assembly into the CRLCSA complex.
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Affiliation(s)
- Alex Pines
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands.,Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Madelon Dijk
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Matthew Makowski
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Elisabeth M Meulenbroek
- Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mischa G Vrouwe
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Marijke Baltissen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Pim J French
- Department of Neurology, Cancer Treatment Screening Facility (CTSF), Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Cancer Treatment Screening Facility (CTSF), Erasmus Optical Imaging Centre (OIC), Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Leon H Mullenders
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Navraj S Pannu
- Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands.
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Abstract
RNA polymerase II (Pol II) catalyzes the transcription of DNA to RNA in the nucleus. DNA alkylating cancer drugs can stall transcription; however, the basis for Pol II stalling when encountering a DNA template with minor-groove alkylation adducts has remained elusive due to its inherent chemical instability. We characterized the behavior of Pol II in transcription over minor-groove alkylation adducts and uncovered a previously unobserved mode of Pol II stalling wherein clashes between DNA adducts and the mobile trigger loop of RNA Pol II prevent translocation of the enzyme after nucleotide insertion. These results provide a molecular basis for how DNA damage in transcribed portions of the genome initiates DNA repair contributing to drug resistance. Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their capacity to stall RNA polymerase (Pol) II and trigger transcription-coupled nucleotide excision repair. Here we show how different forms of DNA alkylation impair transcription by RNA Pol II in cells and with the isolated enzyme and unravel a mode of RNA Pol II stalling that is due to alkylation of DNA in the minor groove. We incorporated a model for acylfulvene adducts, the stable 3-deaza-3-methoxynaphtylethyl-adenosine analog (3d-Napht-A), and smaller 3-deaza-adenosine analogs, into DNA oligonucleotides to assess RNA Pol II transcription elongation in vitro. RNA Pol II was strongly blocked by a 3d-Napht-A analog but bypassed smaller analogs. Crystal structure analysis revealed that a DNA base containing 3d-Napht-A can occupy the +1 templating position and impair closing of the trigger loop in the Pol II active center and polymerase translocation into the next template position. These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for drug resistance.
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Abstract
The eukaryotic global genomic nucleotide excision repair (GG-NER) pathway is the major mechanism that removes most bulky and some nonbulky lesions from cellular DNA. There is growing evidence that certain DNA lesions are repaired slowly or are entirely resistant to repair in cells, tissues, and in cell extract model assay systems. It is well established that the eukaryotic DNA lesion-sensing proteins do not detect the damaged nucleotide, but recognize the distortions/destabilizations in the native DNA structure caused by the damaged nucleotides. In this article, the nature of the structural features of certain bulky DNA lesions that render them resistant to NER, or cause them to be repaired slowly, is compared to that of those that are good-to-excellent NER substrates. Understanding the structural features that distinguish NER-resistant DNA lesions from good NER substrates may be useful for interpreting the biological significance of biomarkers of exposure of human populations to genotoxic environmental chemicals. NER-resistant lesions can survive to replication and cause mutations that can initiate cancer and other diseases. Furthermore, NER diminishes the efficacy of certain chemotherapeutic drugs, and the design of more potent pharmaceuticals that resist repair can be advanced through a better understanding of the structural properties of DNA lesions that engender repair-resistance.
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Affiliation(s)
- Nicholas E. Geacintov
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
| | - Suse Broyde
- Chemistry and Biology Departments, New York University, New York, New York 10003-5180, United States
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Otto C, Spivak G, Aloisi CMN, Menigatti M, Naegeli H, Hanawalt PC, Tanasova M, Sturla SJ. Modulation of Cytotoxicity by Transcription-Coupled Nucleotide Excision Repair Is Independent of the Requirement for Bioactivation of Acylfulvene. Chem Res Toxicol 2017; 30:769-776. [PMID: 28076683 DOI: 10.1021/acs.chemrestox.6b00240] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioactivation as well as DNA repair affects the susceptibility of cancer cells to the action of DNA-alkylating chemotherapeutic drugs. However, information is limited with regard to the relative contributions of these processes to the biological outcome of metabolically activated DNA alkylating agents. We evaluated the influence of cellular bioactivation capacity and DNA repair on cytotoxicity of the DNA alkylating agent acylfulvene (AF). We compared the cytotoxicity and RNA synthesis inhibition by AF and its synthetic activated analogue iso-M0 in a panel of fibroblast cell lines with deficiencies in transcription-coupled (TC-NER) or global genome nucleotide excision repair (GG-NER). We related these data to the inherent bioactivation capacity of each cell type on the basis of mRNA levels. We demonstrated that specific inactivation of TC-NER by siRNA had the largest positive impact on AF activity in a cancer cell line. These findings establish that transcription-coupled DNA repair reduces cellular sensitivity to AF, independent of the requirement for bioactivation.
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Affiliation(s)
- Claudia Otto
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
| | - Graciela Spivak
- Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Claudia M N Aloisi
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich , 8057 Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse , 8057 Zurich, Switzerland
| | - Philip C Hanawalt
- Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Marina Tanasova
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland.,Department of Chemistry, Michigan Technological University , Houghton, Michigan 49932, United States
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich , 8092 Zurich, Switzerland
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50
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Stornetta A, Zimmermann M, Cimino GD, Henderson PT, Sturla SJ. DNA Adducts from Anticancer Drugs as Candidate Predictive Markers for Precision Medicine. Chem Res Toxicol 2017; 30:388-409. [PMID: 27936622 PMCID: PMC5379252 DOI: 10.1021/acs.chemrestox.6b00380] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 01/23/2023]
Abstract
Biomarker-driven drug selection plays a central role in cancer drug discovery and development, and in diagnostic strategies to improve the use of traditional chemotherapeutic drugs. DNA-modifying anticancer drugs are still used as first line medication, but drawbacks such as resistance and side effects remain an issue. Monitoring the formation and level of DNA modifications induced by anticancer drugs is a potential strategy for stratifying patients and predicting drug efficacy. In this perspective, preclinical and clinical data concerning the relationship between drug-induced DNA adducts and biological response for platinum drugs and combination therapies, nitrogen mustards and half-mustards, hypoxia-activated drugs, reductase-activated drugs, and minor groove binding agents are presented and discussed. Aspects including measurement strategies, identification of adducts, and biological factors that influence the predictive relationship between DNA modification and biological response are addressed. A positive correlation between DNA adduct levels and response was observed for the majority of the studies, demonstrating the high potential of using DNA adducts from anticancer drugs as mechanism-based biomarkers of susceptibility, especially as bioanalysis approaches with higher sensitivity and throughput emerge.
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Affiliation(s)
- Alessia Stornetta
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Maike Zimmermann
- Department
of Internal Medicine, Division of Hematology and Oncology and the
UC Davis Comprehensive Cancer Center, University
of California Davis, 4501 X Street, Sacramento, California 95655, United States
- Accelerated
Medical Diagnostics, Inc., 2121 Second Street, B101, Davis, California 95618, United States
| | - George D. Cimino
- Accelerated
Medical Diagnostics, Inc., 2121 Second Street, B101, Davis, California 95618, United States
| | - Paul T. Henderson
- Department
of Internal Medicine, Division of Hematology and Oncology and the
UC Davis Comprehensive Cancer Center, University
of California Davis, 4501 X Street, Sacramento, California 95655, United States
- Accelerated
Medical Diagnostics, Inc., 2121 Second Street, B101, Davis, California 95618, United States
| | - Shana J. Sturla
- Department
of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
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