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Krishnamoorthy V, Foglizzo M, Dilley RL, Wu A, Datta A, Dutta P, Campbell LJ, Degtjarik O, Musgrove LJ, Calabrese AN, Zeqiraj E, Greenberg RA. The SPATA5-SPATA5L1 ATPase complex directs replisome proteostasis to ensure genome integrity. Cell 2024; 187:2250-2268.e31. [PMID: 38554706 PMCID: PMC11055677 DOI: 10.1016/j.cell.2024.03.002] [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: 02/02/2023] [Revised: 12/27/2023] [Accepted: 03/02/2024] [Indexed: 04/02/2024]
Abstract
Ubiquitin-dependent unfolding of the CMG helicase by VCP/p97 is required to terminate DNA replication. Other replisome components are not processed in the same fashion, suggesting that additional mechanisms underlie replication protein turnover. Here, we identify replisome factor interactions with a protein complex composed of AAA+ ATPases SPATA5-SPATA5L1 together with heterodimeric partners C1orf109-CINP (55LCC). An integrative structural biology approach revealed a molecular architecture of SPATA5-SPATA5L1 N-terminal domains interacting with C1orf109-CINP to form a funnel-like structure above a cylindrically shaped ATPase motor. Deficiency in the 55LCC complex elicited ubiquitin-independent proteotoxicity, replication stress, and severe chromosome instability. 55LCC showed ATPase activity that was specifically enhanced by replication fork DNA and was coupled to cysteine protease-dependent cleavage of replisome substrates in response to replication fork damage. These findings define 55LCC-mediated proteostasis as critical for replication fork progression and genome stability and provide a rationale for pathogenic variants seen in associated human neurodevelopmental disorders.
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Affiliation(s)
- Vidhya Krishnamoorthy
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Martina Foglizzo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Robert L Dilley
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA.
| | - Angela Wu
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Arindam Datta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Parul Dutta
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA
| | - Lisa J Campbell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Oksana Degtjarik
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laura J Musgrove
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Elton Zeqiraj
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Roger A Greenberg
- Department of Cancer Biology, Penn Center for Genome Integrity, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6160, USA.
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2
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Yates M, Marois I, St-Hilaire E, Ronato DA, Djerir B, Brochu C, Morin T, Hammond-Martel I, Gezzar-Dandashi S, Casimir L, Drobetsky E, Cappadocia L, Masson JY, Wurtele H, Maréchal A. SMARCAL1 ubiquitylation controls its association with RPA-coated ssDNA and promotes replication fork stability. PLoS Biol 2024; 22:e3002552. [PMID: 38502677 PMCID: PMC10950228 DOI: 10.1371/journal.pbio.3002552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Impediments in replication fork progression cause genomic instability, mutagenesis, and severe pathologies. At stalled forks, RPA-coated single-stranded DNA (ssDNA) activates the ATR kinase and directs fork remodeling, 2 key early events of the replication stress response. RFWD3, a recently described Fanconi anemia (FA) ubiquitin ligase, associates with RPA and promotes its ubiquitylation, facilitating late steps of homologous recombination (HR). Intriguingly, RFWD3 also regulates fork progression, restart and stability via poorly understood mechanisms. Here, we used proteomics to identify putative RFWD3 substrates during replication stress in human cells. We show that RFWD3 interacts with and ubiquitylates the SMARCAL1 DNA translocase directly in vitro and following DNA damage in vivo. SMARCAL1 ubiquitylation does not trigger its subsequent proteasomal degradation but instead disengages it from RPA thereby regulating its function at replication forks. Proper regulation of SMARCAL1 by RFWD3 at stalled forks protects them from excessive MUS81-mediated cleavage in response to UV irradiation, thereby limiting DNA replication stress. Collectively, our results identify RFWD3-mediated SMARCAL1 ubiquitylation as a novel mechanism that modulates fork remodeling to avoid genome instability triggered by aberrant fork processing.
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Affiliation(s)
- Maïlyn Yates
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Isabelle Marois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Edlie St-Hilaire
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Billel Djerir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Chloé Brochu
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Théo Morin
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | | | | | - Lisa Casimir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Elliot Drobetsky
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Laurent Cappadocia
- Faculty of Sciences, Department of Chemistry, Université du Québec à Montréal, Montréal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Hugo Wurtele
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
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3
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Ni C, Yu L, Vona B, Park D, Wei Y, Schmitz DA, Wei Y, Ding Y, Sakurai M, Ballard E, Liu Y, Kumar A, Xing C, Kim HG, Ekmekci C, Karimiani EG, Imannezhad S, Eghbal F, Badv RS, Schwaibold EMC, Dehghani M, Mehrjardi MYV, Metanat Z, Eslamiyeh H, Khouj E, Alhajj SMN, Chedrawi A, Alves CAPF, Houlden H, Kruer M, Alkuraya FS, Cenik C, Maroofian R, Wu J, Buszczak M. An inappropriate decline in ribosome levels drives a diverse set of neurodevelopmental disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574708. [PMID: 38260472 PMCID: PMC10802443 DOI: 10.1101/2024.01.09.574708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Many neurodevelopmental defects are linked to perturbations in genes involved in housekeeping functions, such as those encoding ribosome biogenesis factors. However, how reductions in ribosome biogenesis can result in tissue and developmental specific defects remains a mystery. Here we describe new allelic variants in the ribosome biogenesis factor AIRIM primarily associated with neurodevelopmental disorders. Using human cerebral organoids in combination with proteomic analysis, single-cell transcriptome analysis across multiple developmental stages, and single organoid translatome analysis, we identify a previously unappreciated mechanism linking changes in ribosome levels and the timing of cell fate specification during early brain development. We find ribosome levels decrease during neuroepithelial differentiation, making differentiating cells particularly vulnerable to perturbations in ribosome biogenesis during this time. Reduced ribosome availability more profoundly impacts the translation of specific transcripts, disrupting both survival and cell fate commitment of transitioning neuroepithelia. Enhancing mTOR activity by both genetic and pharmacologic approaches ameliorates the growth and developmental defects associated with intellectual disability linked variants, identifying potential treatment options for specific brain ribosomopathies. This work reveals the cellular and molecular origins of protein synthesis defect-related disorders of human brain development. Highlights AIRIM variants reduce ribosome levels specifically in neural progenitor cells. Inappropriately low ribosome levels cause a transient delay in radial glia fate commitment.Reduced ribosome levels impair translation of a selected subset of mRNAs.Genetic and pharmacologic activation of mTORC1 suppresses AIRIM-linked phenotypes.
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Yoo SS, Lee S, Choi JE, Hong MJ, Do SK, Lee JH, Lee WK, Park JE, Lee YH, Choi SH, Seo H, Lee J, Lee SY, Cha SI, Kim CH, Kang HG, Park JY. Promoter-Specific Variants in NeuroD1 and H3K4me3 Coincident Regions and Clinical Outcomes of Small Cell Lung Cancer. J Korean Med Sci 2023; 38:e381. [PMID: 37987107 PMCID: PMC10659920 DOI: 10.3346/jkms.2023.38.e381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/11/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Neurogenic differentiation 1 (NeuroD1) is a representative small cell lung cancer (SCLC) transcription regulator involved in the carcinogenesis and behavior of SCLC. Histone modifications play an important role in transcription, and H3 lysine 4 trimethylation (H3K4me3) is primarily associated with promoter regions. METHODS We investigated the association between single nucleotide polymorphisms (SNPs) in NeuroD1 and H3K4me3 coincident regions, selected using ChIP sequencing (ChIP-seq), and the clinical outcomes of 261 patients with SCLC. RESULTS Among 230 SNPs, two were significantly associated with both the chemotherapy response and overall survival (OS) of patients with SCLC. RNF145 rs2043268A>G was associated with worse chemotherapy response and OS (under a recessive model, adjusted odds ratio [aOR], 0.50, 95% confidence interval [CI], 0.26-0.94, P = 0.031, and adjusted hazard ratio [aHR], 1.88, 95% CI, 1.38-2.57, P < 0.001). CINP rs762105A>G was also associated with worse chemotherapy response and OS (under a dominant model, aOR, 0.47, 95% CI, 0.23-0.99, P = 0.046, and aHR, 2.03, 95% CI, 1.47-2.82, P < 0.001). ChIP-quantitative polymerase chain reaction and luciferase assay confirmed that the two SNPs were located in the active promoter regions and influenced the promoter activity of each gene. CONCLUSION To summarize, among SNPs selected using ChIP-seq in promoter regions with high peaks in both NeuroD1 and H3K4me3, RNF145 rs2043268A>G and CINP rs762105A>G were associated with clinical outcomes in patients with SCLC and also affected the promoter activity of each gene.
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Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sunwoong Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
| | - Jin Eun Choi
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Mi Jeong Hong
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sook Kyung Do
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Won Kee Lee
- Medical Research Collaboration Center in Kyungpook National University Hospital and School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Eun Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Yong Hoon Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Sun Ha Choi
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyewon Seo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Hyo-Gyoung Kang
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea.
| | - Jae Yong Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, Korea
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, Korea
- BK21 Plus KNU Biomedical Convergence Program, Department of Biomedical Science, Kyungpook National University, Daegu, Korea
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Korea.
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5
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Li J, Guo D, Wang F, Tian M, Wang C, Guo X, Xu B, Wang Y. Functional analysis of AccCDK2-like and AccCINP-like genes in Apis cerana cerana under pesticide and heavy metal stress. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 195:105540. [PMID: 37666611 DOI: 10.1016/j.pestbp.2023.105540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 09/06/2023]
Abstract
Heavy metals and pesticides represent prominent sources of pollution in the natural habitat of Apis cerana cerana, potentially endangering their health through the induction of oxidative stress reactions. This study aimed to address this issue by isolating AccCDK2-like and AccCINP-like proteins from Apis cerana cerana and investigating their functional roles in honey bee resistance against pesticide and heavy metal stresses. Bioinformatics analysis revealed significant homology of these proteins with those found in other species. Functional studies confirmed their participation in interaction with each other, alongside demonstrating distinct patterns of expression and localization. Specifically, AccCDK2-like exhibited higher expression levels in prepupae and muscle tissues, while AccCINP-like showed maximal expression in brown pupae and abdomen. Furthermore, the expression levels of these proteins were found to be modulated in response to pesticide and heavy metal stresses. Notably, overexpression of AccCDK2-like and AccCINP-like led to a noticeable alteration in E. coli's ability to withstand external stresses. Additionally, silencing of the AccCDK2-like and AccCINP-like genes resulted in a significant reduction in antioxidant enzyme activity and the expression levels of genes related to antioxidant function. Consequently, the mortality rate of Apis cerana cerana under pesticide and heavy metal stresses conspicuously increased. Hence, our findings suggest that AccCDK2-like and AccCINP-like proteins potentially play a crucial role in the response of Apis cerana cerana to pesticide and heavy metal stress, likely by modulating the antioxidant pathway.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Dezheng Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Fang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Ming Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Chen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China
| | - Ying Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, People's Republic of China.
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6
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Legrand AJ, Choul-li S, Villeret V, Aumercier M. Poly(ADP-ribose) Polyremase-1 (PARP-1) Inhibition: A Promising Therapeutic Strategy for ETS-Expressing Tumours. Int J Mol Sci 2023; 24:13454. [PMID: 37686260 PMCID: PMC10487777 DOI: 10.3390/ijms241713454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
ETS transcription factors are a highly conserved family of proteins involved in the progression of many cancers, such as breast and prostate carcinomas, Ewing's sarcoma, and leukaemias. This significant involvement can be explained by their roles at all stages of carcinogenesis progression. Generally, their expression in tumours is associated with a poor prognosis and an aggressive phenotype. Until now, no efficient therapeutic strategy had emerged to specifically target ETS-expressing tumours. Nevertheless, there is evidence that pharmacological inhibition of poly(ADP-ribose) polymerase-1 (PARP-1), a key DNA repair enzyme, specifically sensitises ETS-expressing cancer cells to DNA damage and limits tumour progression by leading some of the cancer cells to death. These effects result from a strong interplay between ETS transcription factors and the PARP-1 enzyme. This review summarises the existing knowledge of this molecular interaction and discusses the promising therapeutic applications.
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Affiliation(s)
- Arnaud J. Legrand
- CNRS, EMR9002 Integrative Structural Biology, F-59000 Lille, France; (A.J.L.); (V.V.)
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Risk Factors and Molecular Deter-minants of Aging-Related Diseases, F-59000 Lille, France
| | - Souhaila Choul-li
- Département de Biologie, Faculté des Sciences, Université Chouaib Doukkali, BP-20, El Jadida 24000, Morocco;
| | - Vincent Villeret
- CNRS, EMR9002 Integrative Structural Biology, F-59000 Lille, France; (A.J.L.); (V.V.)
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Risk Factors and Molecular Deter-minants of Aging-Related Diseases, F-59000 Lille, France
| | - Marc Aumercier
- CNRS, EMR9002 Integrative Structural Biology, F-59000 Lille, France; (A.J.L.); (V.V.)
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE-Risk Factors and Molecular Deter-minants of Aging-Related Diseases, F-59000 Lille, France
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7
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Bland P, Saville H, Wai PT, Curnow L, Muirhead G, Nieminuszczy J, Ravindran N, John MB, Hedayat S, Barker HE, Wright J, Yu L, Mavrommati I, Read A, Peck B, Allen M, Gazinska P, Pemberton HN, Gulati A, Nash S, Noor F, Guppy N, Roxanis I, Pratt G, Oldreive C, Stankovic T, Barlow S, Kalirai H, Coupland SE, Broderick R, Alsafadi S, Houy A, Stern MH, Pettit S, Choudhary JS, Haider S, Niedzwiedz W, Lord CJ, Natrajan R. SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response. Nat Genet 2023; 55:1311-1323. [PMID: 37524790 PMCID: PMC10412459 DOI: 10.1038/s41588-023-01460-5] [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: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
SF3B1 hotspot mutations are associated with a poor prognosis in several tumor types and lead to global disruption of canonical splicing. Through synthetic lethal drug screens, we identify that SF3B1 mutant (SF3B1MUT) cells are selectively sensitive to poly (ADP-ribose) polymerase inhibitors (PARPi), independent of hotspot mutation and tumor site. SF3B1MUT cells display a defective response to PARPi-induced replication stress that occurs via downregulation of the cyclin-dependent kinase 2 interacting protein (CINP), leading to increased replication fork origin firing and loss of phosphorylated CHK1 (pCHK1; S317) induction. This results in subsequent failure to resolve DNA replication intermediates and G2/M cell cycle arrest. These defects are rescued through CINP overexpression, or further targeted by a combination of ataxia-telangiectasia mutated and PARP inhibition. In vivo, PARPi produce profound antitumor effects in multiple SF3B1MUT cancer models and eliminate distant metastases. These data provide the rationale for testing the clinical efficacy of PARPi in a biomarker-driven, homologous recombination proficient, patient population.
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Affiliation(s)
- Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Harry Saville
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lucinda Curnow
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Nivedita Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Marie Beatrix John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Somaieh Hedayat
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - James Wright
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Abigail Read
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Translational Cancer Metabolism Team, Centre for Tumour Biology, Barts Cancer Institute, Cancer Research UK Centre of Excellence, Queen Mary University of London, Charterhouse Square, London, UK
| | - Mark Allen
- Biological Services Unit, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen N Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Sarah Nash
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Guy Pratt
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Ceri Oldreive
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Samantha Barlow
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Ronan Broderick
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Samar Alsafadi
- Inserm U830, PSL University, Institut Curie, Paris, France
| | - Alexandre Houy
- Inserm U830, PSL University, Institut Curie, Paris, France
| | | | - Stephen Pettit
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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8
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Murdocca M, Spitalieri P, D'Apice MR, Novelli G, Sangiuolo F. From cue to meaning: The involvement of POLD1 gene in DNA replication, repair and aging. Mech Ageing Dev 2023; 211:111790. [PMID: 36764464 DOI: 10.1016/j.mad.2023.111790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/06/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Aging is an extremely complex biological process. Aging, cancer and inflammation represent a trinity, object of many interesting researches. The accumulation of DNA damage and its consequences progressively interfere with cellular function and increase susceptibility to developing aging condition. DNA Polymerase delta (Pol δ), encoded by POLD1 gene (MIM#174761) on 19q13.3, is well implicated in many steps of the replication program and repair. Thanks to its exonuclease and polymerase activities, the enzyme is involved in the regulation of the cell cycle, DNA synthesis, and DNA damage repair processes. Damaging variants within the exonuclease domain predispose to cancers, while those occurring in the polymerase active site cause the autosomal dominant Progeroid Syndrome called MDPL, Mandibular hypoplasia, Deafness and Progeroid features with concomitant Lipodystrophy Since DNA damage represents the main cause of ageing and age-related pathologies, an overview of critical Pol δ activities will allow to better understand the associations between DNA damage and nearly every aspect of the ageing process, helping the researchers to counteract all the ageing-pathologies at the same time.
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Affiliation(s)
- Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
| | - Paola Spitalieri
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
| | | | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy; University of Nevada, Department of Pharmacology, Reno, USA; Neuromed Institute, IRCCS, Pozzilli, IS, Italy.
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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9
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Ni C, Schmitz DA, Lee J, Pawłowski K, Wu J, Buszczak M. Labeling of heterochronic ribosomes reveals C1ORF109 and SPATA5 control a late step in human ribosome assembly. Cell Rep 2022; 38:110597. [PMID: 35354024 PMCID: PMC9004343 DOI: 10.1016/j.celrep.2022.110597] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/03/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022] Open
Abstract
Although features of ribosome assembly are shared between species, our understanding of the diversity, complexity, dynamics, and regulation of ribosome production in multicellular organisms remains incomplete. To gain insights into ribosome biogenesis in human cells, we perform a genome-wide loss-of-function screen combined with differential labeling of pre-existing and newly assembled ribosomes. These efforts identify two functionally uncharacterized genes, C1orf109 and SPATA5. We provide evidence that these factors, together with CINP and SPATA5L1, control a late step of human pre-60S maturation in the cytoplasm. Loss of either C1orf109 or SPATA5 impairs global protein synthesis. These results link ribosome assembly with neurodevelopmental disorders associated with recessive SPATA5 mutations. Based on these findings, we propose that the expanded repertoire of ribosome biogenesis factors likely enables multicellular organisms to coordinate multiple steps of ribosome production in response to different developmental and environmental stimuli. Ni et al. describe a live-cell labeling technique to track the production and movement of old and new ribosomes. Through a CRISPR screen, they identify C1ORF109 and SPATA5 as two ribosome biogenesis factors. They further reveal that SPATA5 allelic variants associated with neurodevelopmental defects impair ribosome maturation.
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Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Daniel A Schmitz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Jeon Lee
- Lyda Hill-Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9365, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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10
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Borowczak J, Szczerbowski K, Maniewski M, Zdrenka M, Słupski P, Antosik P, Kołodziejska S, Sekielska-Domanowska M, Dubiel M, Bodnar M, Szylberg Ł. The Prognostic Role of CDK9 in Bladder Cancer. Cancers (Basel) 2022; 14:cancers14061492. [PMID: 35326643 PMCID: PMC8945910 DOI: 10.3390/cancers14061492] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/27/2022] Open
Abstract
Introduction: Most patients with urothelial carcinoma are diagnosed with non-invasive tumors, but the prognosis worsens with the progression of the disease. Overexpression of cyclin-dependent kinase 9 has been recently linked to increased cancer proliferation, faster progression, and worse prognosis. However, some cancers seem to contradict this rule. In this work, we explored the prognostic role of CDK9 expression in urothelial carcinoma. Materials and Methods: We performed immunohistochemical analysis on 72 bladder cancer samples. To assess a larger group of patients, the Cancer Genome Atlas (TCGA) database containing 406 cases and transcriptomics information through the Human Pathology Atlas were analyzed. Results: CDK9 is overexpressed in urothelial cancer tissues when compared to normal urothelial tissues (p < 0.05). High CDK9 expression was observed in low-stage, low-grade, and non-muscle-invasive tumors (p < 0.05). The patients with high CDK9 expression had a significantly higher 5-year overall survival rate than those with low CDK9 expression (77.54% vs. 53.6% in the TMA group and 57.75% vs. 35.44% in the TCGA group, respectively) (p < 0.05). The results were consistent in both cohorts. Multivariate Cox regression analysis indicated that low CDK9 status was an independent predictor for poor prognosis in the TCGA cohort (HR 1.60, CL95% 1.1−2.33, p = 0.014). Conclusions: High CDK9 expression predicts a favorable prognosis in urothelial carcinoma and is associated with clinicopathological features characteristic for early-stage disease. The decrease in CDK9 expression can be associated with the build-up of genetic instability and may indicate a key role for CDK9 in the early stages of urothelial carcinoma.
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Affiliation(s)
- Jędrzej Borowczak
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland; (K.S.); (M.M.); (P.A.); (M.B.); (Ł.S.)
- Correspondence: ; Tel.: +48-52-5854200; Fax: +48-52-5854049
| | - Krzysztof Szczerbowski
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland; (K.S.); (M.M.); (P.A.); (M.B.); (Ł.S.)
| | - Mateusz Maniewski
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland; (K.S.); (M.M.); (P.A.); (M.B.); (Ł.S.)
| | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Centre—Prof. Franciszek Łukaszczyk Memorial Hospital, 85-796 Bydgoszcz, Poland;
| | - Piotr Słupski
- Department of Urology, University Hospital No. 2 im. Dr. Jan Biziel in Bydgoszcz, 85-168 Bydgoszcz, Poland;
| | - Paulina Antosik
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland; (K.S.); (M.M.); (P.A.); (M.B.); (Ł.S.)
| | - Sylwia Kołodziejska
- Chair of Pathology, University Hospital No. 2 im. Dr. Jan Biziel in Bydgoszcz, 85-168 Bydgoszcz, Poland;
| | - Marta Sekielska-Domanowska
- Department of Obstetrics, Gynecology and Oncology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (M.S.-D.); (M.D.)
| | - Mariusz Dubiel
- Department of Obstetrics, Gynecology and Oncology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-168 Bydgoszcz, Poland; (M.S.-D.); (M.D.)
| | - Magdalena Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland; (K.S.); (M.M.); (P.A.); (M.B.); (Ł.S.)
- Chair of Pathology, University Hospital No. 2 im. Dr. Jan Biziel in Bydgoszcz, 85-168 Bydgoszcz, Poland;
| | - Łukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, 85-094 Bydgoszcz, Poland; (K.S.); (M.M.); (P.A.); (M.B.); (Ł.S.)
- Department of Tumor Pathology and Pathomorphology, Oncology Centre—Prof. Franciszek Łukaszczyk Memorial Hospital, 85-796 Bydgoszcz, Poland;
- Chair of Pathology, University Hospital No. 2 im. Dr. Jan Biziel in Bydgoszcz, 85-168 Bydgoszcz, Poland;
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11
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Schlam-Babayov S, Bensimon A, Harel M, Geiger T, Aebersold R, Ziv Y, Shiloh Y. Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. EMBO J 2020; 40:e104400. [PMID: 33215756 DOI: 10.15252/embj.2020104400] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 08/13/2020] [Accepted: 10/12/2020] [Indexed: 01/10/2023] Open
Abstract
The DNA damage response (DDR) is a complex signaling network that relies on cascades of protein phosphorylation, which are initiated by three protein kinases of the family of PI3-kinase-related protein kinases (PIKKs): ATM, ATR, and DNA-PK. ATM is missing or inactivated in the genome instability syndrome, ataxia-telangiectasia (A-T). The relative shares of these PIKKs in the response to genotoxic stress and the functional relationships among them are central questions in the genome stability field. We conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells treated with the double-strand break-inducing chemical, neocarzinostatin, and validated the results with the targeted proteomic technique, selected reaction monitoring. We also matched our results with 34 published screens for DDR factors, creating a valuable resource for identifying strong candidates for novel DDR players. We uncovered fine-tuned dynamics between the PIKKs following genotoxic stress, such as DNA-PK-dependent attenuation of ATM. In A-T cells, partial compensation for ATM absence was provided by ATR and DNA-PK, with distinct roles and kinetics. The results highlight intricate relationships between these PIKKs in the DDR.
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Affiliation(s)
- Sapir Schlam-Babayov
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ariel Bensimon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michal Harel
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Yael Ziv
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
| | - Yosef Shiloh
- The David and Inez Myers Laboratory of Cancer Genetics, Department of Human Molecular Genetics and Biochemistry, Tel Aviv University School of Medicine, Tel Aviv, Israel
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12
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Neuropathology-driven Whole-genome Sequencing Study Points to Novel Candidate Genes for Healthy Brain Aging. Alzheimer Dis Assoc Disord 2020; 33:7-14. [PMID: 30681437 DOI: 10.1097/wad.0000000000000294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE Understanding the healthy brain aging process is key to uncover the mechanisms that lead to pathologic age-related neurodegeneration, including progression to Alzheimer disease (AD). We aimed to address the issue of pathologic heterogeneity that often underlies a clinical AD diagnosis. METHODS We performed a deep whole-genome sequencing study aiming to identify variants that are associated specifically with healthy brain aging. PATIENTS We examined samples from the community-based longitudinal Vienna Transdanubian Aging study comparing neuropathologically "healthy" aging in individuals above 80 years of age with pure AD patients of the same age. RESULTS Focusing on potentially functional variants, we discovered a single variant (rs10149146) that lies on the autophagy-associated TECPR2 gene and was carried by 53.6% of the "healthy" brain elderly individuals (15/28). An additional nonsynonymous variant on the CINP gene (encoding a cell cycle checkpoint protein) was also found in 46% of healthy controls. Both variants are absent from all AD cases. TECPR2 and CINP appear to be "partner" genes in terms of regulation and their associated transcription factors have been previously implicated in AD and neurodegeneration. CONCLUSIONS Our study underlines the strength of neuropathology-driven definitions in genetic association studies and points to a potentially neuroprotective effect of key molecules of autophagy and cell cycle control.
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13
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Rotelli MD, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Calvi BR. An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. G3 (BETHESDA, MD.) 2019; 9:3087-3100. [PMID: 31387856 PMCID: PMC6778782 DOI: 10.1534/g3.119.400581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 12/23/2022]
Abstract
Cell division and tissue growth must be coordinated with development. Defects in these processes are the basis for a number of diseases, including developmental malformations and cancer. We have conducted an unbiased RNAi screen for genes that are required for growth in the Drosophila wing, using GAL4-inducible short hairpin RNA (shRNA) fly strains made by the Drosophila RNAi Screening Center. shRNA expression down the center of the larval wing disc using dpp-GAL4, and the central region of the adult wing was then scored for tissue growth and wing hair morphology. Out of 4,753 shRNA crosses that survived to adulthood, 18 had impaired wing growth. FlyBase and the new Alliance of Genome Resources knowledgebases were used to determine the known or predicted functions of these genes and the association of their human orthologs with disease. The function of eight of the genes identified has not been previously defined in Drosophila The genes identified included those with known or predicted functions in cell cycle, chromosome segregation, morphogenesis, metabolism, steroid processing, transcription, and translation. All but one of the genes are similar to those in humans, and many are associated with disease. Knockdown of lin-52, a subunit of the Myb-MuvB transcription factor, or βNACtes6, a gene involved in protein folding and trafficking, resulted in a switch from cell proliferation to an endoreplication growth program through which wing tissue grew by an increase in cell size (hypertrophy). It is anticipated that further analysis of the genes that we have identified will reveal new mechanisms that regulate tissue growth during development.
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Affiliation(s)
- Michael D Rotelli
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Anna M Bolling
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Andrew W Killion
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | | | - Michael J Dixon
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405 and
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202
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14
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Xia J, Chiu LY, Nehring RB, Bravo Núñez MA, Mei Q, Perez M, Zhai Y, Fitzgerald DM, Pribis JP, Wang Y, Hu CW, Powell RT, LaBonte SA, Jalali A, Matadamas Guzmán ML, Lentzsch AM, Szafran AT, Joshi MC, Richters M, Gibson JL, Frisch RL, Hastings PJ, Bates D, Queitsch C, Hilsenbeck SG, Coarfa C, Hu JC, Siegele DA, Scott KL, Liang H, Mancini MA, Herman C, Miller KM, Rosenberg SM. Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. Cell 2019; 176:127-143.e24. [PMID: 30633903 PMCID: PMC6344048 DOI: 10.1016/j.cell.2018.12.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 09/05/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022]
Abstract
DNA damage provokes mutations and cancer and results from external carcinogens or endogenous cellular processes. However, the intrinsic instigators of endogenous DNA damage are poorly understood. Here, we identify proteins that promote endogenous DNA damage when overproduced: the DNA "damage-up" proteins (DDPs). We discover a large network of DDPs in Escherichia coli and deconvolute them into six function clusters, demonstrating DDP mechanisms in three: reactive oxygen increase by transmembrane transporters, chromosome loss by replisome binding, and replication stalling by transcription factors. Their 284 human homologs are over-represented among known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis. Half of the tested human homologs promote DNA damage and mutation when overproduced in human cells, with DNA damage-elevating mechanisms like those in E. coli. Our work identifies networks of DDPs that provoke endogenous DNA damage and may reveal DNA damage-associated functions of many human known and newly implicated cancer-promoting proteins.
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Affiliation(s)
- Jun Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li-Ya Chiu
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Ralf B Nehring
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - María Angélica Bravo Núñez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qian Mei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77030, USA
| | - Mercedes Perez
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Yin Zhai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Devon M Fitzgerald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - John P Pribis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumeng Wang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chenyue W Hu
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Reid T Powell
- Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Sandra A LaBonte
- Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX 77843, USA
| | - Ali Jalali
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meztli L Matadamas Guzmán
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alfred M Lentzsch
- Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA
| | - Adam T Szafran
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohan C Joshi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megan Richters
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Janet L Gibson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan L Frisch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susan G Hilsenbeck
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - James C Hu
- Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX 77843, USA
| | - Deborah A Siegele
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Han Liang
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Mancini
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christophe Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Kyle M Miller
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Biosciences, LIVESTRONG Cancer Institute of the Dell Medical School, University of Texas at Austin, Austin, TX 78712, USA.
| | - Susan M Rosenberg
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA; Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX 77030, USA.
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15
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Wu Q, Fu C, Li M, Li J, Li Z, Qi L, Ci X, Ma G, Gao A, Fu X, A J, An N, Liu M, Li Y, King JL, Fu L, Zhang B, Dong JT. CINP is a novel cofactor of KLF5 required for its role in the promotion of cell proliferation, survival and tumor growth. Int J Cancer 2018; 144:582-594. [PMID: 30289973 DOI: 10.1002/ijc.31908] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/21/2018] [Indexed: 02/01/2023]
Abstract
Krüppel-like factor 5 (KLF5) both suppresses and promotes tumor growth depending on cellular context. The mechanisms underlying tumor promotion could be targetable for therapy. Although a number of transcriptional targets of KLF5 have been identified and implicated in KLF5-mediated tumor growth, how KLF5 regulates these genes remains to be addressed. Here we performed coimmunoprecipitation (co-IP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) in the TSU-Pr1 bladder cancer cell line, in which KLF5 is shown to promote tumor growth, to identify KLF5-interacting nuclear proteins that are necessary for KLF5's tumor promoting function. LC-MS/MS revealed 122 potential KLF5 binding proteins in the nuclear proteins precipitated by the KLF5 antibody, and the top nine candidates included AHNAK, TFAM, HSDL2, HNRNPC, CINP, IST1, FBL, PABPC1 and SNRNP40. SRB assays of these nine proteins indicated that silencing CINP had the most potent inhibitory effect on cell growth in KLF5-expressing cells but did not affect parental TSU-Pr1 cells. Further analyses not only confirmed the physical interaction between KLF5 and CINP, also demonstrated that knockdown of CINP attenuated the effects of KLF5 on cell cycle progression, apoptosis and tumorigenesis. Silencing CINP also attenuated the effect of KLF5 on the expression of a number of genes and signaling pathways, including cell cycle regulator Cyclin D1 and apoptosis-related Caspase 7. These results suggest that CINP is a cofactor of KLF5 that is crucial for the promotion of tumor growth, and that the KLF5-CINP interaction could be a novel therapeutic target for inhibiting KLF5-promoted tumor growth.
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Affiliation(s)
- Qiao Wu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Changying Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Menglin Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Juan Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhigui Li
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT
| | - Leilei Qi
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xinpei Ci
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ang Gao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xing Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Jun A
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Na An
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingcheng Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yixiang Li
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Jamie L King
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Baotong Zhang
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
| | - Jin-Tang Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China.,Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA
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16
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Gavish-Izakson M, Velpula BB, Elkon R, Prados-Carvajal R, Barnabas GD, Ugalde AP, Agami R, Geiger T, Huertas P, Ziv Y, Shiloh Y. Nuclear poly(A)-binding protein 1 is an ATM target and essential for DNA double-strand break repair. Nucleic Acids Res 2018; 46:730-747. [PMID: 29253183 PMCID: PMC5778506 DOI: 10.1093/nar/gkx1240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 12/13/2022] Open
Abstract
The DNA damage response (DDR) is an extensive signaling network that is robustly mobilized by DNA double-strand breaks (DSBs). The primary transducer of the DSB response is the protein kinase, ataxia-telangiectasia, mutated (ATM). Here, we establish nuclear poly(A)-binding protein 1 (PABPN1) as a novel target of ATM and a crucial player in the DSB response. PABPN1 usually functions in regulation of RNA processing and stability. We establish that PABPN1 is recruited to the DDR as a critical regulator of DSB repair. A portion of PABPN1 relocalizes to DSB sites and is phosphorylated on Ser95 in an ATM-dependent manner. PABPN1 depletion sensitizes cells to DSB-inducing agents and prolongs the DSB-induced G2/M cell-cycle arrest, and DSB repair is hampered by PABPN1 depletion or elimination of its phosphorylation site. PABPN1 is required for optimal DSB repair via both nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR), and specifically is essential for efficient DNA-end resection, an initial, key step in HRR. Using mass spectrometry analysis, we capture DNA damage-induced interactions of phospho-PABPN1, including well-established DDR players as well as other RNA metabolizing proteins. Our results uncover a novel ATM-dependent axis in the rapidly growing interface between RNA metabolism and the DDR.
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Affiliation(s)
- Michal Gavish-Izakson
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Bhagya Bhavana Velpula
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rosario Prados-Carvajal
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alejandro Pineiro Ugalde
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Reuven Agami
- Division of Biological Stress Response, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pablo Huertas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER) and Department of Genetics, University of Sevilla, Sevilla, Spain
| | - Yael Ziv
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yosef Shiloh
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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17
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Vilas CK, Emery LE, Denchi EL, Miller KM. Caught with One's Zinc Fingers in the Genome Integrity Cookie Jar. Trends Genet 2018; 34:313-325. [PMID: 29370947 DOI: 10.1016/j.tig.2017.12.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/04/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022]
Abstract
Zinc finger (ZnF) domains are present in at least 5% of human proteins. First characterized as binding to DNA, ZnFs display extraordinary binding plasticity and can bind to RNA, lipids, proteins, and protein post-translational modifications (PTMs). The diverse binding properties of ZnFs have made their functional characterization challenging. While once confined to large and poorly characterized protein families, proteomic, cellular, and molecular studies have begun to shed light on their involvement as protectors of the genome. We focus here on the emergent roles of ZnF domain-containing proteins in promoting genome integrity, including their involvement in telomere maintenance and DNA repair. These findings have highlighted the need for further characterization of ZnF proteins, which can reveal the functions of this large gene class in normal cell function and human diseases, including those involving genome instability such as aging and cancer.
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Affiliation(s)
- Caroline K Vilas
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Lara E Emery
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Eros Lazzerini Denchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA.
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18
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Clearance of a persistent picornavirus infection is associated with enhanced pro-apoptotic and cellular immune responses. Sci Rep 2017; 7:17800. [PMID: 29259271 PMCID: PMC5736604 DOI: 10.1038/s41598-017-18112-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/04/2017] [Indexed: 12/22/2022] Open
Abstract
Long-term persistent viral infections cause substantial morbidity and associated economic losses in human and veterinary contexts. Yet, the mechanisms associated with establishment of persistent infections are poorly elucidated. We investigated immunomodulatory mechanisms associated with clearance versus persistence of foot-and-mouth disease virus (FMDV) in micro-dissected compartments of the bovine nasopharynx by microarray. The use of laser-capture microdissection allowed elucidation of differential gene regulation within distinct anatomic compartments critical to FMDV infection. Analysis of samples from transitional and persistent phases of infection demonstrated significant differences in transcriptome profiles of animals that cleared infection versus those that became persistently infected carriers. Specifically, it was demonstrated that clearance of FMDV from the nasopharyngeal mucosa was associated with upregulation of targets associated with activation of T cell-mediated immunity. Contrastingly, gene regulation in FMDV carriers suggested inhibition of T cell activation and promotion of Th2 polarization. These findings were corroborated by immunofluorescence microscopy which demonstrated relative abundance of CD8+ T cells in the nasopharyngeal mucosa in association with clearance of FMDV. The findings presented herein emphasize that a critical balance between Th1 and Th2 -mediated immunity is essential for successful clearance of FMDV infection and should be considered for development of next-generation vaccines and antiviral products.
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19
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Cooper DJ, Zunino G, Bixby JL, Lemmon VP. Phenotypic screening with primary neurons to identify drug targets for regeneration and degeneration. Mol Cell Neurosci 2017; 80:161-169. [PMID: 27444126 PMCID: PMC5243932 DOI: 10.1016/j.mcn.2016.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/04/2016] [Accepted: 07/16/2016] [Indexed: 12/13/2022] Open
Abstract
High-throughput, target-based screening techniques have been utilized extensively for drug discovery in the past several decades. However, the need for more predictive in vitro models of in vivo disease states has generated a shift in strategy towards phenotype-based screens. Phenotype based screens are particularly valuable in studying complex conditions such as CNS injury and degenerative disease, as many factors can contribute to a specific cellular response. In this review, we will discuss different screening frameworks and their relative utility in examining mechanisms of neurodegeneration and axon regrowth, particularly in cell-based in vitro disease models.
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Affiliation(s)
- Daniel J. Cooper
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
| | - Giulia Zunino
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
| | - John L. Bixby
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
- Center for Computational Science, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
| | - Vance P. Lemmon
- The Miami Project to Cure Paralysis, Department of Neurological Surgery, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
- Center for Computational Science, University of Miami, 1400 NW 12th Ave, Miami, FL 33136, USA
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20
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Roles of human POLD1 and POLD3 in genome stability. Sci Rep 2016; 6:38873. [PMID: 27974823 PMCID: PMC5156928 DOI: 10.1038/srep38873] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022] Open
Abstract
DNA replication is essential for cellular proliferation. If improperly controlled it can constitute a major source of genome instability, frequently associated with cancer and aging. POLD1 is the catalytic subunit and POLD3 is an accessory subunit of the replicative Pol δ polymerase, which also functions in DNA repair, as well as the translesion synthesis polymerase Pol ζ, whose catalytic subunit is REV3L. In cells depleted of POLD1 or POLD3 we found a differential but general increase in genome instability as manifested by DNA breaks, S-phase progression impairment and chromosome abnormalities. Importantly, we showed that both proteins are needed to maintain the proper amount of active replication origins and that POLD3-depletion causes anaphase bridges accumulation. In addition, POLD3-associated DNA damage showed to be dependent on RNA-DNA hybrids pointing toward an additional and specific role of this subunit in genome stability. Interestingly, a similar increase in RNA-DNA hybrids-dependent genome instability was observed in REV3L-depleted cells. Our findings demonstrate a key role of POLD1 and POLD3 in genome stability and S-phase progression revealing RNA-DNA hybrids-dependent effects for POLD3 that might be partly due to its Pol ζ interaction.
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21
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Olazabal-Herrero A, García-Santisteban I, Rodríguez JA. Mutations in the ‘Fingers’ subdomain of the deubiquitinase USP1 modulate its function and activity. FEBS J 2016; 283:929-46. [DOI: 10.1111/febs.13648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/16/2015] [Accepted: 01/08/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Anne Olazabal-Herrero
- Department of Genetics, Physical Anthropology and Animal Physiology; University of the Basque Country (UPV/EHU); Leioa Spain
| | - Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology; University of the Basque Country (UPV/EHU); Leioa Spain
| | - Jose Antonio Rodríguez
- Department of Genetics, Physical Anthropology and Animal Physiology; University of the Basque Country (UPV/EHU); Leioa Spain
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22
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Li Z, Pearlman AH, Hsieh P. DNA mismatch repair and the DNA damage response. DNA Repair (Amst) 2016; 38:94-101. [PMID: 26704428 PMCID: PMC4740233 DOI: 10.1016/j.dnarep.2015.11.019] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 09/17/2015] [Accepted: 11/30/2015] [Indexed: 12/12/2022]
Abstract
This review discusses the role of DNA mismatch repair (MMR) in the DNA damage response (DDR) that triggers cell cycle arrest and, in some cases, apoptosis. Although the focus is on findings from mammalian cells, much has been learned from studies in other organisms including bacteria and yeast [1,2]. MMR promotes a DDR mediated by a key signaling kinase, ATM and Rad3-related (ATR), in response to various types of DNA damage including some encountered in widely used chemotherapy regimes. An introduction to the DDR mediated by ATR reveals its immense complexity and highlights the many biological and mechanistic questions that remain. Recent findings and future directions are highlighted.
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Affiliation(s)
- Zhongdao Li
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Alexander H Pearlman
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA
| | - Peggy Hsieh
- Genetics & Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 5 Rm. 324, 5 Memorial Dr. MSC 0538, Bethesda, MD 20892-0538, USA.
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23
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Kavanaugh G, Ye F, Mohni KN, Luzwick JW, Glick G, Cortez D. A whole genome RNAi screen identifies replication stress response genes. DNA Repair (Amst) 2015; 35:55-62. [PMID: 26454783 DOI: 10.1016/j.dnarep.2015.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/30/2015] [Accepted: 09/08/2015] [Indexed: 01/16/2023]
Abstract
Proper DNA replication is critical to maintain genome stability. When the DNA replication machinery encounters obstacles to replication, replication forks stall and the replication stress response is activated. This response includes activation of cell cycle checkpoints, stabilization of the replication fork, and DNA damage repair and tolerance mechanisms. Defects in the replication stress response can result in alterations to the DNA sequence causing changes in protein function and expression, ultimately leading to disease states such as cancer. To identify additional genes that control the replication stress response, we performed a three-parameter, high content, whole genome siRNA screen measuring DNA replication before and after a challenge with replication stress as well as a marker of checkpoint kinase signalling. We identified over 200 replication stress response genes and subsequently analyzed how they influence cellular viability in response to replication stress. These data will serve as a useful resource for understanding the replication stress response.
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Affiliation(s)
- Gina Kavanaugh
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Fei Ye
- Department of Statistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kareem N Mohni
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jessica W Luzwick
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gloria Glick
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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24
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Growth factor dependent regulation of centrosome function and genomic instability by HuR. Biomolecules 2015; 5:263-81. [PMID: 25803745 PMCID: PMC4384122 DOI: 10.3390/biom5010263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/06/2015] [Accepted: 03/11/2015] [Indexed: 01/10/2023] Open
Abstract
The mRNA binding protein HuR is over expressed in cancer cells and contributes to disease progression through post-transcriptional regulation of mRNA. The regulation of HuR and how this relates to glioma is the focus of this report. SRC and c-Abl kinases regulate HuR sub-cellular trafficking and influence accumulation in the pericentriolar matrix (PCM) via a growth factor dependent signaling mechanism. Growth factor stimulation of glioma cell lines results in the associate of HuR with the PCM and amplification of centrosome number. This process is regulated by tyrosine phosphorylation of HuR and is abolished by mutating tyrosine residues. HuR is overexpressed in tumor samples from patients with glioblastoma and associated with a reduced survival. These findings suggest HuR plays a significant role in centrosome amplification and genomic instability, which contributes to a worse disease outcome.
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25
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Abstract
Homologous recombination provides high-fidelity DNA repair throughout all domains of life. Live cell fluorescence microscopy offers the opportunity to image individual recombination events in real time providing insight into the in vivo biochemistry of the involved proteins and DNA molecules as well as the cellular organization of the process of homologous recombination. Herein we review the cell biological aspects of mitotic homologous recombination with a focus on Saccharomyces cerevisiae and mammalian cells, but will also draw on findings from other experimental systems. Key topics of this review include the stoichiometry and dynamics of recombination complexes in vivo, the choreography of assembly and disassembly of recombination proteins at sites of DNA damage, the mobilization of damaged DNA during homology search, and the functional compartmentalization of the nucleus with respect to capacity of homologous recombination.
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Affiliation(s)
- Michael Lisby
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Rodney Rothstein
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032
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27
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Luzwick JW, Nam EA, Zhao R, Cortez D. Mutation of serine 1333 in the ATR HEAT repeats creates a hyperactive kinase. PLoS One 2014; 9:e99397. [PMID: 24901225 PMCID: PMC4047089 DOI: 10.1371/journal.pone.0099397] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/14/2014] [Indexed: 11/18/2022] Open
Abstract
Subcellular localization, protein interactions, and post-translational modifications regulate the DNA damage response kinases ATR, ATM, and DNA-PK. During an analysis of putative ATR phosphorylation sites, we found that a single mutation at S1333 creates a hyperactive kinase. In vitro and in cells, mutation of S1333 to alanine (S1333A-ATR) causes elevated levels of kinase activity with and without the addition of the protein activator TOPBP1. S1333 mutations to glycine, arginine, or lysine also create a hyperactive kinase, while mutation to aspartic acid decreases ATR activity. S1333A-ATR maintains the G2 checkpoint and promotes completion of DNA replication after transient exposure to replication stress but the less active kinase, S1333D-ATR, has modest defects in both of these functions. While we find no evidence that S1333 is phosphorylated in cultured cells, our data indicate that small changes in the HEAT repeats can have large effects on kinase activity. These mutants may serve as useful tools for future studies of the ATR pathway.
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Affiliation(s)
- Jessica W. Luzwick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Edward A. Nam
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Runxiang Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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28
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Sirbu BM, McDonald WH, Dungrawala H, Badu-Nkansah A, Kavanaugh GM, Chen Y, Tabb DL, Cortez D. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry. J Biol Chem 2013; 288:31458-67. [PMID: 24047897 DOI: 10.1074/jbc.m113.511337] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Both DNA and chromatin need to be duplicated during each cell division cycle. Replication happens in the context of defects in the DNA template and other forms of replication stress that present challenges to both genetic and epigenetic inheritance. The replication machinery is highly regulated by replication stress responses to accomplish this goal. To identify important replication and stress response proteins, we combined isolation of proteins on nascent DNA (iPOND) with quantitative mass spectrometry. We identified 290 proteins enriched on newly replicated DNA at active, stalled, and collapsed replication forks. Approximately 16% of these proteins are known replication or DNA damage response proteins. Genetic analysis indicates that several of the newly identified proteins are needed to facilitate DNA replication, especially under stressed conditions. Our data provide a useful resource for investigators studying DNA replication and the replication stress response and validate the use of iPOND combined with mass spectrometry as a discovery tool.
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29
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Sirbu BM, Cortez D. DNA damage response: three levels of DNA repair regulation. Cold Spring Harb Perspect Biol 2013; 5:a012724. [PMID: 23813586 DOI: 10.1101/cshperspect.a012724] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome integrity is challenged by DNA damage from both endogenous and environmental sources. This damage must be repaired to allow both RNA and DNA polymerases to accurately read and duplicate the information in the genome. Multiple repair enzymes scan the DNA for problems, remove the offending damage, and restore the DNA duplex. These repair mechanisms are regulated by DNA damage response kinases including DNA-PKcs, ATM, and ATR that are activated at DNA lesions. These kinases improve the efficiency of DNA repair by phosphorylating repair proteins to modify their activities, by initiating a complex series of changes in the local chromatin structure near the damage site, and by altering the overall cellular environment to make it more conducive to repair. In this review, we focus on these three levels of regulation to illustrate how the DNA damage kinases promote efficient repair to maintain genome integrity and prevent disease.
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Affiliation(s)
- Bianca M Sirbu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37027, USA
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30
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Legrand AJ, Choul-Li S, Spriet C, Idziorek T, Vicogne D, Drobecq H, Dantzer F, Villeret V, Aumercier M. The level of Ets-1 protein is regulated by poly(ADP-ribose) polymerase-1 (PARP-1) in cancer cells to prevent DNA damage. PLoS One 2013; 8:e55883. [PMID: 23405229 PMCID: PMC3566071 DOI: 10.1371/journal.pone.0055883] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 01/03/2013] [Indexed: 12/24/2022] Open
Abstract
Ets-1 is a transcription factor that regulates many genes involved in cancer progression and in tumour invasion. It is a poor prognostic marker for breast, lung, colorectal and ovary carcinomas. Here, we identified poly(ADP-ribose) polymerase-1 (PARP-1) as a novel interaction partner of Ets-1. We show that Ets-1 activates, by direct interaction, the catalytic activity of PARP-1 and is then poly(ADP-ribosyl)ated in a DNA-independent manner. The catalytic inhibition of PARP-1 enhanced Ets-1 transcriptional activity and caused its massive accumulation in cell nuclei. Ets-1 expression was correlated with an increase in DNA damage when PARP-1 was inhibited, leading to cancer cell death. Moreover, PARP-1 inhibitors caused only Ets-1-expressing cells to accumulate DNA damage. These results provide new insight into Ets-1 regulation in cancer cells and its link with DNA repair proteins. Furthermore, our findings suggest that PARP-1 inhibitors would be useful in a new therapeutic strategy that specifically targets Ets-1-expressing tumours.
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Affiliation(s)
- Arnaud J Legrand
- CNRS USR 3078, Institut de Recherche Interdisciplinaire, Campus CNRS de la Haute Borne, Université Lille Nord de France, IFR 147, BP 70478, Villeneuve d'Ascq, France
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Mohni KN, Dee AR, Smith S, Schumacher AJ, Weller SK. Efficient herpes simplex virus 1 replication requires cellular ATR pathway proteins. J Virol 2013; 87:531-42. [PMID: 23097436 PMCID: PMC3536419 DOI: 10.1128/jvi.02504-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/15/2012] [Indexed: 02/02/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) is a double-stranded DNA virus that replicates in the nucleus of the host cell and is known to interact with several components of the cellular DNA-damage-signaling machinery. We have previously reported that the DNA damage response kinase, ATR, is specifically inactivated in HSV-1-infected cells. On the other hand, we have also shown that ATR and its scaffolding protein, ATRIP, are recruited to viral replication compartments, where they play beneficial roles during HSV-1 replication. In order to better understand this apparent discrepancy, we tested the hypothesis that some of the components of the ATR pathway may exert an antiviral effect on infection. In fact, we learned that all 10 of the canonical ATR pathway proteins are stable in HSV-infected cells and are recruited to viral replication compartments; furthermore, short hairpin RNA (shRNA) knockdown shows that several, including ATRIP, RPA70, TopBP1, Claspin, and CINP, are required for efficient HSV-1 replication. We also determined that activation of the ATR kinase prior to infection did not affect virus yield but did result in reduced levels of recombination between coinfecting viruses. Together, these data suggest that ATR pathway proteins are not antiviral per se but that activation of ATR signaling may have negative consequences during viral replication, such as inhibiting recombination.
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Affiliation(s)
- Kareem N Mohni
- Department of Molecular, Microbial and Structural Biology and the Molecular Biology and Biochemistry Graduate Program, University of Connecticut Health Center, Farmington, Connecticut, USA
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32
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Molekulare Mechanismen des Seckel-Syndroms. MED GENET-BERLIN 2012. [DOI: 10.1007/s11825-012-0359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Zusammenfassung
Das Seckel-Syndrom ist eine autosomal-rezessiv vererbte Erkrankung, die durch einen proportionalen, bereits bei Geburt vorhandenen Kleinwuchs, eine ausgeprägte Mikrozephalie sowie charakteristische kraniofaziale Dysmorphien gekennzeichnet ist. Patienten mit Seckel-Syndrom zeigen zusätzlich eine geistige Behinderung, und bei einigen Patienten kommt es zum frühzeitigen Auftreten altersabhängiger Erkrankungen. Genetisch betrachtet stellt das Seckel-Syndrom eine heterogene Erkrankung dar, für die in den letzten Jahren mehrere kausale Gene identifiziert werden konnten. Diese spielen auf zellulärer Ebene sowohl bei Vorgängen der Zellteilung als auch bei der Aktivierung von Schutzmechanismen nach DNA-Schädigungen eine wichtige Rolle.
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Chaki M, Airik R, Ghosh AK, Giles RH, Chen R, Slaats GG, Wang H, Hurd TW, Zhou W, Cluckey A, Gee HY, Ramaswami G, Hong CJ, Hamilton BA, Cervenka I, Ganji RS, Bryja V, Arts HH, van Reeuwijk J, Oud MM, Letteboer SJF, Roepman R, Husson H, Ibraghimov-Beskrovnaya O, Yasunaga T, Walz G, Eley L, Sayer JA, Schermer B, Liebau MC, Benzing T, Le Corre S, Drummond I, Janssen S, Allen SJ, Natarajan S, O'Toole JF, Attanasio M, Saunier S, Antignac C, Koenekoop RK, Ren H, Lopez I, Nayir A, Stoetzel C, Dollfus H, Massoudi R, Gleeson JG, Andreoli SP, Doherty DG, Lindstrad A, Golzio C, Katsanis N, Pape L, Abboud EB, Al-Rajhi AA, Lewis RA, Omran H, Lee EYHP, Wang S, Sekiguchi JM, Saunders R, Johnson CA, Garner E, Vanselow K, Andersen JS, Shlomai J, Nurnberg G, Nurnberg P, Levy S, Smogorzewska A, Otto EA, Hildebrandt F. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell 2012; 150:533-48. [PMID: 22863007 DOI: 10.1016/j.cell.2012.06.028] [Citation(s) in RCA: 288] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Revised: 02/01/2012] [Accepted: 06/25/2012] [Indexed: 01/03/2023]
Abstract
Nephronophthisis-related ciliopathies (NPHP-RC) are degenerative recessive diseases that affect kidney, retina, and brain. Genetic defects in NPHP gene products that localize to cilia and centrosomes defined them as "ciliopathies." However, disease mechanisms remain poorly understood. Here, we identify by whole-exome resequencing, mutations of MRE11, ZNF423, and CEP164 as causing NPHP-RC. All three genes function within the DNA damage response (DDR) pathway. We demonstrate that, upon induced DNA damage, the NPHP-RC proteins ZNF423, CEP164, and NPHP10 colocalize to nuclear foci positive for TIP60, known to activate ATM at sites of DNA damage. We show that knockdown of CEP164 or ZNF423 causes sensitivity to DNA damaging agents and that cep164 knockdown in zebrafish results in dysregulated DDR and an NPHP-RC phenotype. Our findings link degenerative diseases of the kidney and retina, disorders of increasing prevalence, to mechanisms of DDR.
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Affiliation(s)
- Moumita Chaki
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
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34
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Forment JV, Kaidi A, Jackson SP. Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer 2012; 12:663-70. [PMID: 22972457 DOI: 10.1038/nrc3352] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Genomic alterations that lead to oncogene activation and tumour suppressor loss are important driving forces for cancer development. Although these changes can accumulate progressively during cancer evolution, recent studies have revealed that many cancer cells harbour chromosomes bearing tens to hundreds of clustered genome rearrangements. In this Review, we describe how this striking phenomenon, termed chromothripsis, is likely to arise through chromosome breakage and inaccurate reassembly. We also discuss the potential diagnostic, prognostic and therapeutic implications of chromothripsis in cancer.
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Affiliation(s)
- Josep V Forment
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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35
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Thomas F, Delmar P, Vergez S, Rochaix P, Hennebelle I, McLoughlin P, Benlyazid A, Sarini J, Delord JP. Gene expression profiling on pre- and post-erlotinib tumors from patients with head and neck squamous cell carcinoma. Head Neck 2012; 35:809-18. [PMID: 22791662 DOI: 10.1002/hed.23036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2012] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The purpose of our work was to identify genomic predictive markers of erlotinib response in patients with head and neck squamous cell carcinoma (HNSCC). METHODS Tumor tissue biopsies were collected before and after treatment for 39 patients. We analyzed genomic expression of the tumors using microarrays to (1) identify genes differentially expressed in baseline samples in patients who were responders vs nonresponders, (2) characterize erlotinib's effect on gene expression, and (3) identify the pharmacodynamic marker of erlotinib. RESULTS Gene expression profiles found no statistically significant differentially expressed genes between responders and nonresponders. An exploratory analysis by combining statistical criteria allowed us to identify genes differentially expressed in nonresponders compared to responders and genes whose expression was modified during erlotinib treatment. Finally, the search of pharmacodynamic markers identified cyclin-dependent kinase 2-interacting protein (CINP) as a potential marker of erlotinib efficacy because its expression decreased only in patients who were responders to the treatment. CONCLUSION This study provides candidate genes potentially involved in erlotinib response in HNSCC.
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Affiliation(s)
- Fabienne Thomas
- EA4553 and Université de Toulouse, 20-24 Rue du Pont St Pierre, 31052 Toulouse, France.
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36
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Svensson JP, Fry RC, Wang E, Somoza LA, Samson LD. Identification of novel human damage response proteins targeted through yeast orthology. PLoS One 2012; 7:e37368. [PMID: 22615993 PMCID: PMC3353887 DOI: 10.1371/journal.pone.0037368] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 04/21/2012] [Indexed: 01/09/2023] Open
Abstract
Studies in Saccharomyces cerevisiae show that many proteins influence cellular survival upon exposure to DNA damaging agents. We hypothesized that human orthologs of these S. cerevisiae proteins would also be required for cellular survival after treatment with DNA damaging agents. For this purpose, human homologs of S. cerevisiae proteins were identified and mapped onto the human protein-protein interaction network. The resulting human network was highly modular and a series of selection rules were implemented to identify 45 candidates for human toxicity-modulating proteins. The corresponding transcripts were targeted by RNA interference in human cells. The cell lines with depleted target expression were challenged with three DNA damaging agents: the alkylating agents MMS and 4-NQO, and the oxidizing agent t-BuOOH. A comparison of the survival revealed that the majority (74%) of proteins conferred either sensitivity or resistance. The identified human toxicity-modulating proteins represent a variety of biological functions: autophagy, chromatin modifications, RNA and protein metabolism, and telomere maintenance. Further studies revealed that MMS-induced autophagy increase the survival of cells treated with DNA damaging agents. In summary, we show that damage recovery proteins in humans can be identified through homology to S. cerevisiae and that many of the same pathways are represented among the toxicity modulators.
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Affiliation(s)
- J. Peter Svensson
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rebecca C. Fry
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Computation and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emma Wang
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Luis A. Somoza
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Leona D. Samson
- Biological Engineering Department, Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Computation and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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37
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Ekins S, Shigeta R, Bunin BA. Bottlenecks caused by software gaps in miRNA and RNAi research. Pharm Res 2012; 29:1717-21. [PMID: 22362409 DOI: 10.1007/s11095-012-0712-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
Abstract
Understanding the regulation of gene expression is critical to many areas of biology while control via RNAs has found considerable interest as a tool for scientific discovery and potential therapeutic applications. For example whole genome RNA interference (RNAi) screens and whole proteome scans provide views of how the entire transcriptome or proteome responds to biological, chemical or environmental perturbations of a gene's activity. Small RNA (sRNA) or MicroRNA (miRNA) are known to regulate pathways and bind mRNA, while the function of miRNAs discovered in experimental studies is often unknown. In both cases, RNAi and miRNA require labor intensive studies to tease out their functions within gene networks. Available software to analyze relationships is currently an ad hoc and often a manual process that can take up to several hours to analyze a single candidate RNAi or miRNA. With experiments frequently highlighting tens to hundreds of candidates this represents a considerable bottleneck. We suggest there is a gap in miRNA and RNAi research caused by inadequate current software that could be improved. For example a new software application could be created that provides interactive, comprehensive target analysis that leverages past datasets to lead to statistically stronger analyses.
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Affiliation(s)
- Sean Ekins
- Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, USA.
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38
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Bétous R, Mason AC, Rambo RP, Bansbach CE, Badu-Nkansah A, Sirbu BM, Eichman BF, Cortez D. SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication. Genes Dev 2012; 26:151-62. [PMID: 22279047 PMCID: PMC3273839 DOI: 10.1101/gad.178459.111] [Citation(s) in RCA: 227] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Accepted: 12/12/2011] [Indexed: 01/14/2023]
Abstract
SMARCAL1 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A-like1) maintains genome integrity during DNA replication. Here we investigated its mechanism of action. We found that SMARCAL1 travels with elongating replication forks, and its absence leads to MUS81-dependent double-strand break formation. Binding to specific nucleic acid substrates activates SMARCAL1 activity in a reaction that requires its HARP2 (Hep-A-related protein 2) domain. Homology modeling indicates that the HARP domain is similar in structure to the DNA-binding domain of the PUR proteins. Limited proteolysis, small-angle X-ray scattering, and functional assays indicate that the core enzymatic unit consists of the HARP2 and ATPase domains that fold into a stable structure. Surprisingly, SMARCAL1 is capable of binding three-way and four-way Holliday junctions and model replication forks that lack a designed ssDNA region. Furthermore, SMARCAL1 remodels these DNA substrates by promoting branch migration and fork regression. SMARCAL1 mutations that cause Schimke immunoosseous dysplasia or that inactivate the HARP2 domain abrogate these activities. These results suggest that SMARCAL1 continuously surveys replication forks for damage. If damage is present, it remodels the fork to promote repair and restart. Failures in the process lead to activation of an alternative repair mechanism that depends on MUS81-catalyzed cleavage of the damaged fork.
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Affiliation(s)
- Rémy Bétous
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Aaron C. Mason
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37240, USA
| | - Robert P. Rambo
- Life Sciences Division, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Carol E. Bansbach
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Akosua Badu-Nkansah
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Bianca M. Sirbu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Brandt F. Eichman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37240, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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39
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Recolin B, Van der Laan S, Maiorano D. Role of replication protein A as sensor in activation of the S-phase checkpoint in Xenopus egg extracts. Nucleic Acids Res 2011; 40:3431-42. [PMID: 22187152 PMCID: PMC3333866 DOI: 10.1093/nar/gkr1241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Uncoupling between DNA polymerases and helicase activities at replication forks, induced by diverse DNA lesions or replication inhibitors, generate long stretches of primed single-stranded DNA that is implicated in activation of the S-phase checkpoint. It is currently unclear whether nucleation of the essential replication factor RPA onto this substrate stimulates the ATR-dependent checkpoint response independently of its role in DNA synthesis. Using Xenopus egg extracts to investigate the role of RPA recruitment at uncoupled forks in checkpoint activation we have surprisingly found that in conditions in which DNA synthesis occurs, RPA accumulation at forks stalled by either replication stress or UV irradiation is dispensable for Chk1 phosphorylation. In contrast, when both replication fork uncoupling and RPA hyperloading are suppressed, Chk1 phosphorylation is inhibited. Moreover, we show that extracts containing reduced levels of RPA accumulate ssDNA and induce spontaneous, caffeine-sensitive, Chk1 phosphorylation in S-phase. These results strongly suggest that disturbance of enzymatic activities of replication forks, rather than RPA hyperloading at stalled forks, is a critical determinant of ATR activation.
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Affiliation(s)
- Bénédicte Recolin
- Genome Surveillance and Stability Laboratory, CNRS-UPR1142, Institute of Human Genetics, 141 rue de la Cardonille, Montpellier 34396 Cedex 5, France
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40
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Bansbach CE, Cortez D. Defining genome maintenance pathways using functional genomic approaches. Crit Rev Biochem Mol Biol 2011; 46:327-41. [PMID: 21787120 DOI: 10.3109/10409238.2011.588938] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genome maintenance activities including DNA repair, cell division cycle control, and checkpoint signaling pathways preserve genome integrity and prevent disease. Defects in these pathways cause birth defects, neurodegeneration, premature aging, and cancer. Recent technical advances in functional genomic approaches such as expression profiling, proteomics, and RNA interference (RNAi) technologies have rapidly expanded our knowledge of the proteins that work in these pathways. In this review, we examine the use of these high-throughput methodologies in higher eukaryotic organisms for the interrogation of genome maintenance activities.
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Affiliation(s)
- Carol E Bansbach
- Department of Biochemistry, Vanderbilt University School of Medicine, Light Hall, Nashville, TN 37232, USA
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41
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Freije JMP, Fraile JM, López-Otín C. Protease addiction and synthetic lethality in cancer. Front Oncol 2011; 1:25. [PMID: 22655236 PMCID: PMC3356009 DOI: 10.3389/fonc.2011.00025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 08/17/2011] [Indexed: 01/03/2023] Open
Abstract
The “oncogene addiction” concept refers to the dependence of cancer cells on the function of the oncogenes responsible for their transformed phenotype, while the term “non-oncogene addiction” has been introduced to define the exacerbated necessity of the normal function of non-mutated genes. In this Perspective, we focus on the importance of proteolytic enzymes to maintain the viability of cancer cells and hypothesize that most, if not all, tumors present “addiction” to a number of proteolytic activities, which in turn may represent valuable targets of anti-cancer therapies, even without being mutated or over-expressed by the malignant cells.
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Affiliation(s)
- José M P Freije
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo Oviedo, Spain
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42
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Blasius M, Forment JV, Thakkar N, Wagner SA, Choudhary C, Jackson SP. A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1. Genome Biol 2011; 12:R78. [PMID: 21851590 PMCID: PMC3245618 DOI: 10.1186/gb-2011-12-8-r78] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/03/2011] [Accepted: 08/18/2011] [Indexed: 12/12/2022] Open
Abstract
Background The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto been identified. Results Here, we combine a chemical genetics approach with high-resolution mass spectrometry to identify novel Chk1 substrates and their phosphorylation sites. The list of targets produced reveals the potential impact of Chk1 function not only on processes where Chk1 was already known to be involved, but also on other key cellular events such as transcription, RNA splicing and cell fate determination. In addition, we validate and explore the phosphorylation of transcriptional co-repressor KAP1 Ser473 as a novel DNA-damage-induced Chk1 site. Conclusions By providing a substantial set of potential Chk1 substrates, we present opportunities for studying unanticipated functions for Chk1 in controlling a wide range of cellular processes. We also refine the Chk1 consensus sequence, facilitating the future prediction of Chk1 target sites. In addition, our identification of KAP1 Ser473 phosphorylation as a robust readout for Chk1 activity could be used to explore the in vivo effects of Chk1 inhibitors that are being developed for clinical evaluation.
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Affiliation(s)
- Melanie Blasius
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK
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43
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Abstract
Preservation of genome integrity via the DNA-damage response is critical to prevent disease. ATR (ataxia telangiectasia mutated- and Rad3-related) is essential for life and functions as a master regulator of the DNA-damage response, especially during DNA replication. ATR controls and co-ordinates DNA replication origin firing, replication fork stability, cell cycle checkpoints and DNA repair. Since its identification 15 years ago, a model of ATR activation and signalling has emerged that involves localization to sites of DNA damage and activation through protein-protein interactions. Recent research has added an increasingly detailed understanding of the canonical ATR pathway, and an appreciation that the canonical model does not fully capture the complexity of ATR regulation. In the present article, we review the ATR signalling process, focusing on mechanistic findings garnered from the identification of new ATR-interacting proteins and substrates. We discuss how to incorporate these new insights into a model of ATR regulation and point out the significant gaps in our understanding of this essential genome-maintenance pathway.
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44
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Wang Y, Wang Y, Xu Y, Tong W, Pan T, Li J, Sun S, Shao J, Ding H, Toyoda T, Yuan Z. Hepatitis C virus NS5B protein delays s phase progression in human hepatocyte-derived cells by relocalizing cyclin-dependent kinase 2-interacting protein (CINP). J Biol Chem 2011; 286:26603-15. [PMID: 21628470 DOI: 10.1074/jbc.m111.225672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell cycle dysregulation is a critical event in virus infection-associated tumorigenesis. Previous studies have suggested that hepatitis C virus NS5B modulates cell cycle progression in addition to participating in RNA synthesis as an RNA-dependent RNA polymerase. However, the molecular mechanisms have thus far remained unclear. In this study, a HepG2 Tet-On NS5B stable cell line was generated to confirm the effect of NS5B on the cell cycle. To better understand the role of NS5B in cell cycle regulation, yeast two-hybrid assays were performed using a human liver cDNA library. The cyclin-dependent kinase 2-interacting protein (CINP) was identified. The interaction between NS5B and CINP was further demonstrated by in vivo and in vitro assays, and their association was found to be indispensable for S phase delay and cell proliferation suppression. Further experiments indicated that NS5B relocalized CINP from the nucleus to the cytoplasm. Directly knocking down CINP by specific siRNA resulted in a significant alteration in the DNA damage response and expression of cell cycle checkpoint proteins, including an increase in p21 and a decrease in phosphorylated Retinoblastoma and Chk1. Similar results were observed in cells expressing NS5B, and the effects were partially reversed upon ectopic overexpression of CINP. These studies suggest that the DNA damage response might be exploited by NS5B to hinder cell cycle progression. Taken together, our data demonstrate that NS5B delays cells in S phase through interaction with CINP and relocalization of the protein from the nucleus to the cytoplasm. Such effects might contribute to hepatitis C virus persistence and pathogenesis.
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Affiliation(s)
- Yaohui Wang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Shanghai 200032, China
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45
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Brenner JC, Ateeq B, Li Y, Yocum AK, Cao Q, Asangani IA, Patel S, Wang X, Liang H, Yu J, Palanisamy N, Siddiqui J, Yan W, Cao X, Mehra R, Sabolch A, Basrur V, Lonigro RJ, Yang J, Tomlins SA, Maher CA, Elenitoba-Johnson KS, Hussain M, Navone NM, Pienta KJ, Varambally S, Feng FY, Chinnaiyan AM. Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell 2011; 19:664-78. [PMID: 21575865 PMCID: PMC3113473 DOI: 10.1016/j.ccr.2011.04.010] [Citation(s) in RCA: 346] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 03/02/2011] [Accepted: 04/19/2011] [Indexed: 01/09/2023]
Abstract
Recurrent fusions of ETS genes are considered driving mutations in a diverse array of cancers, including Ewing's sarcoma, acute myeloid leukemia, and prostate cancer. We investigate the mechanisms by which ETS fusions mediate their effects, and find that the product of the predominant ETS gene fusion, TMPRSS2:ERG, interacts in a DNA-independent manner with the enzyme poly (ADP-ribose) polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs). ETS gene-mediated transcription and cell invasion require PARP1 and DNA-PKcs expression and activity. Importantly, pharmacological inhibition of PARP1 inhibits ETS-positive, but not ETS-negative, prostate cancer xenograft growth. Finally, overexpression of the TMPRSS2:ERG fusion induces DNA damage, which is potentiated by PARP1 inhibition in a manner similar to that of BRCA1/2 deficiency.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Catalytic Domain
- Cell Line, Tumor
- Cell Movement
- Chick Embryo
- Chromatin Immunoprecipitation
- DNA Damage
- DNA-Activated Protein Kinase/metabolism
- Enzyme Inhibitors/pharmacology
- Gene Expression Regulation, Neoplastic
- Gene Fusion
- Genes, Reporter
- HEK293 Cells
- Humans
- Male
- Mass Spectrometry
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Mice, SCID
- Models, Molecular
- Neoplasm Invasiveness
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Phthalazines/pharmacology
- Piperazines/pharmacology
- Poly (ADP-Ribose) Polymerase-1
- Poly(ADP-ribose) Polymerase Inhibitors
- Poly(ADP-ribose) Polymerases/genetics
- Poly(ADP-ribose) Polymerases/metabolism
- Prostatic Neoplasms/drug therapy
- Prostatic Neoplasms/enzymology
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/pathology
- Protein Conformation
- RNA Interference
- Recombinant Fusion Proteins/metabolism
- Time Factors
- Transcriptional Activation
- Transfection
- Tumor Burden
- Xenograft Model Antitumor Assays
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Affiliation(s)
- J. Chad Brenner
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Bushra Ateeq
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Yong Li
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Anastasia K. Yocum
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Qi Cao
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Irfan A. Asangani
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Sonam Patel
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Hallie Liang
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Jindan Yu
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Nallasivam Palanisamy
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Wei Yan
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Aaron Sabolch
- Department of Radiation Oncology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Robert J. Lonigro
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Jun Yang
- Department of Genitourinary Medical Oncology, and David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Christopher A. Maher
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Kojo S.J. Elenitoba-Johnson
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Maha Hussain
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Nora M. Navone
- Department of Genitourinary Medical Oncology, and David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Kenneth J. Pienta
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Sooryanarayana Varambally
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Felix Y. Feng
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Radiation Oncology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Corresponding author. Tel.: + 734 615-4062, (A.Chinnaiyan), URL: http://www.pathology.med.umich.edu/dynamo/chinnaiyan/index.jsp
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Bensimon A, Aebersold R, Shiloh Y. Beyond ATM: the protein kinase landscape of the DNA damage response. FEBS Lett 2011; 585:1625-39. [PMID: 21570395 DOI: 10.1016/j.febslet.2011.05.013] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 05/04/2011] [Accepted: 05/04/2011] [Indexed: 01/18/2023]
Abstract
The DNA of all organisms is constantly subjected to damaging agents, both exogenous and endogenous. One extremely harmful lesion is the double-strand break (DSB), which activates a massive signaling network - the DNA damage response (DDR). The chief activator of the DSB response is the ATM protein kinase, which phosphorylates numerous key players in its various branches. Recent phosphoproteomic screens have extended the scope of damage-induced phosphorylations beyond the direct ATM substrates. We review the evidence for the involvement of numerous other protein kinases in the DDR, obtained from documentation of specific pathways as well as high-throughput screens. The emerging picture of the protein phosphorylation landscape in the DDR broadens the current view on the role of this protein modification in the maintenance of genomic stability. Extensive cross-talk between many of these protein kinases forms an interlaced signaling network that spans numerous cellular processes. Versatile protein kinases in this network affect pathways that are different from those they have been identified with to date. The DDR appears to be one of the most extensive signaling responses to cellular stimuli.
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Affiliation(s)
- Ariel Bensimon
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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47
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Affiliation(s)
- S Ladha
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, 980 West 28th Avenue, Vancouver, British Columbia, Canada V5Z 4H4.
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48
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CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet 2010; 43:23-6. [PMID: 21131973 DOI: 10.1038/ng.725] [Citation(s) in RCA: 174] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 11/12/2010] [Indexed: 12/19/2022]
Abstract
Functional impairment of DNA damage response pathways leads to increased genomic instability. Here we describe the centrosomal protein CEP152 as a new regulator of genomic integrity and cellular response to DNA damage. Using homozygosity mapping and exome sequencing, we identified CEP152 mutations in Seckel syndrome and showed that impaired CEP152 function leads to accumulation of genomic defects resulting from replicative stress through enhanced activation of ATM signaling and increased H2AX phosphorylation.
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49
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Yu DS, Zhao R, Hsu EL, Cayer J, Ye F, Guo Y, Shyr Y, Cortez D. Cyclin-dependent kinase 9-cyclin K functions in the replication stress response. EMBO Rep 2010; 11:876-82. [PMID: 20930849 DOI: 10.1038/embor.2010.153] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 08/13/2010] [Accepted: 08/31/2010] [Indexed: 11/09/2022] Open
Abstract
Cyclin-dependent kinase 9 (CDK9) is a well-characterized subunit of the positive transcription elongation factor b complex in which it regulates transcription elongation in cooperation with cyclin T. However, CDK9 also forms a complex with cyclin K, the function of which is less clear. Using a synthetic lethal RNA interference screen in human cells, we identified CDK9 as a component of the replication stress response. Loss of CDK9 activity causes an increase in spontaneous levels of DNA damage signalling in replicating cells and a decreased ability to recover from a transient replication arrest. This activity is restricted to CDK9-cyclin K complexes and is independent of CDK9-cyclin T complex. CDK9 accumulates on chromatin in response to replication stress and limits the amount of single-stranded DNA in cells under stress. Furthermore, we show that CDK9 and cyclin K interact with ataxia telangiectasia and Rad3-related protein and other checkpoint signalling proteins. These results reveal an unexpectedly direct role for CDK9-cyclin K in checkpoint pathways that maintain genome integrity in response to replication stress.
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Affiliation(s)
- David S Yu
- Department of Radiation Oncology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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50
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Wiltshire TD, Lovejoy CA, Wang T, Xia F, O'Connor MJ, Cortez D. Sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition identifies ubiquitin-specific peptidase 11 (USP11) as a regulator of DNA double-strand break repair. J Biol Chem 2010; 285:14565-71. [PMID: 20233726 DOI: 10.1074/jbc.m110.104745] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
DNA damage repair and checkpoint responses prevent genome instability and provide a barrier to the development of cancer. Inherited mutations in DNA damage response (DDR) genes such as those that encode the homologous recombination (HR) proteins BRCA1 and BRCA2 cause cancer predisposition syndromes. PARP inhibitors are an exciting new class of targeted therapy for treating patients with HR repair-defective tumors. In this study, we use an RNAi screen to identify genes that when silenced cause synthetic lethality with the PARP inhibitor AZD2281. This screen identified the deubiquitylating enzyme USP11 as a participant in HR repair of DNA double-strand breaks. Silencing USP11 with siRNA leads to spontaneous DDR activation in otherwise undamaged cells and hypersensitivity to PARP inhibition, ionizing radiation, and other genotoxic stress agents. Moreover, we demonstrate that HR repair is defective in USP11-silenced cells. Finally, the recruitment of a subset of double-strand break repair proteins including RAD51 and 53BP1 to repair foci is misregulated in the absence of USP11 catalytic activity. Thus, our synthetic lethal approach identified USP11 as a component of the HR double-strand break repair pathway.
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Affiliation(s)
- Timothy D Wiltshire
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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