551
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Lee JS, Grav LM, Pedersen LE, Lee GM, Kildegaard HF. Accelerated homology-directed targeted integration of transgenes in Chinese hamster ovary cells via CRISPR/Cas9 and fluorescent enrichment. Biotechnol Bioeng 2016; 113:2518-23. [PMID: 27159230 DOI: 10.1002/bit.26002] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 12/29/2022]
Abstract
Targeted gene integration into site-specific loci can be achieved in Chinese hamster ovary (CHO) cells via CRISPR/Cas9 genome editing technology and the homology-directed repair (HDR) pathway. The low efficiency of HDR often requires antibiotic selection, which limits targeted integration of multiple genes at multiple sites. To improve HDR-mediated targeted integration, while avoiding the use of selection markers, chemical treatment for increased HDR, and fluorescent enrichment of genome-edited cells was assessed in CHO cells. Chemical treatment did not improve HDR-mediated targeted integration. In contrast, fluorescent markers in Cas9 and donor constructs enable FACS enrichment, resulting in a threefold increase in the number of cells with HDR-mediated genome editing. Combined with this enrichment method, large transgenes encoding model proteins (including an antibody) were successfully targeted integrated. This approach provides a simple and fast strategy for targeted generation of stable CHO production cell lines in a rational way. Biotechnol. Bioeng. 2016;113: 2518-2523. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark.,Department of Biological Sciences, KAIST, Yuseong-gu, Daejeon, Republic of Korea
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, 2970, Denmark.
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552
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Jenner ZB, Sood AK, Coleman RL. Evaluation of rucaparib and companion diagnostics in the PARP inhibitor landscape for recurrent ovarian cancer therapy. Future Oncol 2016; 12:1439-56. [PMID: 27087632 PMCID: PMC4976841 DOI: 10.2217/fon-2016-0002] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/04/2016] [Indexed: 12/28/2022] Open
Abstract
Rucaparib camsylate (CO-338; 8-fluoro-2-{4-[(methylamino)methyl]phenyl}-1,3,4,5-tetrahydro-6H-azepino[5,4,3-cd]indol-6-one ((1S,4R)-7,7-dimethyl-2-oxobicyclo[2.2.1]hept-1-yl)methanesulfonic acid salt) is a PARP1, 2 and 3 inhibitor. Phase I studies identified a recommended Phase II dose of 600 mg orally twice daily. ARIEL2 Part 1 established a tumor genomic profiling test for homologous recombination loss of heterozygosity quantification using a next-generation sequencing companion diagnostic (CDx). Rucaparib received US FDA Breakthrough Therapy designation for treatment of platinum-sensitive BRCA-mutated advanced ovarian cancer patients who received greater than two lines of platinum-based therapy. Comparable to rucaparib development, other PARP inhibitors, such as olaparib, niraparib, veliparib and talazoparib, are developing CDx tests for targeted therapy. PARP inhibitor clinical trials and CDx assays are discussed in this review, as are potential PARP inhibitor combination therapies and likely resistance mechanisms.
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Affiliation(s)
- Zachary B Jenner
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- McGovern Medical School, formerly The University of Texas Health Science Center at Houston (UTHealth) Medical School, Houston, TX, USA
| | - Anil K Sood
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert L Coleman
- Department of Gynecologic Oncology & Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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553
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Jackson RA, Chen ES. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs. Pharmacol Ther 2016; 162:69-85. [DOI: 10.1016/j.pharmthera.2016.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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554
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DNA double-strand-break repair in higher eukaryotes and its role in genomic instability and cancer: Cell cycle and proliferation-dependent regulation. Semin Cancer Biol 2016; 37-38:51-64. [DOI: 10.1016/j.semcancer.2016.03.003] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 12/18/2022]
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555
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Wisnovsky S, Jean SR, Liyanage S, Schimmer A, Kelley SO. Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes. Nat Chem Biol 2016; 12:567-73. [DOI: 10.1038/nchembio.2102] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/24/2016] [Indexed: 01/16/2023]
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556
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Stop pulling my strings - what telomeres taught us about the DNA damage response. Nat Rev Mol Cell Biol 2016; 17:364-78. [PMID: 27165790 DOI: 10.1038/nrm.2016.43] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mammalian cells have evolved specialized mechanisms to sense and repair double-strand breaks (DSBs) to maintain genomic stability. However, in certain cases, the activity of these pathways can lead to aberrant DNA repair, genomic instability and tumorigenesis. One such case is DNA repair at the natural ends of linear chromosomes, known as telomeres, which can lead to chromosome-end fusions. Here, we review data obtained over the past decade and discuss the mechanisms that protect mammalian chromosome ends from the DNA damage response. We also discuss how telomere research has helped to uncover key steps in DSB repair. Last, we summarize how dysfunctional telomeres and the ensuing genomic instability drive the progression of cancer.
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557
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Ceccaldi R, Sarangi P, D'Andrea AD. The Fanconi anaemia pathway: new players and new functions. Nat Rev Mol Cell Biol 2016; 17:337-49. [PMID: 27145721 DOI: 10.1038/nrm.2016.48] [Citation(s) in RCA: 486] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Fanconi anaemia pathway repairs DNA interstrand crosslinks (ICLs) in the genome. Our understanding of this complex pathway is still evolving, as new components continue to be identified and new biochemical systems are used to elucidate the molecular steps of repair. The Fanconi anaemia pathway uses components of other known DNA repair processes to achieve proper repair of ICLs. Moreover, Fanconi anaemia proteins have functions in genome maintenance beyond their canonical roles of repairing ICLs. Such functions include the stabilization of replication forks and the regulation of cytokinesis. Thus, Fanconi anaemia proteins are emerging as master regulators of genomic integrity that coordinate several repair processes. Here, we summarize our current understanding of the functions of the Fanconi anaemia pathway in ICL repair, together with an overview of its connections with other repair pathways and its emerging roles in genome maintenance.
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Affiliation(s)
- Raphael Ceccaldi
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Prabha Sarangi
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
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558
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Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H, Staaf J, Sieuwerts AM, Brinkman AB, Martin S, Ramakrishna M, Butler A, Kim HY, Borg Å, Sotiriou C, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Stunnenberg HG, van de Vijver MJ, Martens JWM, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Sale J, Rada C, Stratton MR, Birney E, Nik-Zainal S. The topography of mutational processes in breast cancer genomes. Nat Commun 2016; 7:11383. [PMID: 27136393 PMCID: PMC5001788 DOI: 10.1038/ncomms11383] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/18/2016] [Indexed: 12/28/2022] Open
Abstract
Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through the cellular lineage between the fertilized egg and the cancer cell, each composed of specific DNA damage and repair components and leaving its own characteristic mutational signature on the genome. Using somatic mutation catalogues from 560 breast cancer whole-genome sequences, here we show that each of 12 base substitution, 2 insertion/deletion (indel) and 6 rearrangement mutational signatures present in breast tissue, exhibit distinct relationships with genomic features relating to transcription, DNA replication and chromatin organization. This signature-based approach permits visualization of the genomic distribution of mutational processes associated with APOBEC enzymes, mismatch repair deficiency and homologous recombinational repair deficiency, as well as mutational processes of unknown aetiology. Furthermore, it highlights mechanistic insights including a putative replication-dependent mechanism of APOBEC-related mutagenesis.
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Affiliation(s)
- Sandro Morganella
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Cambridgeshire
CB10 1SD, UK
| | - Ludmil B. Alexandrov
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
- Theoretical Biology and Biophysics (T-6), Los Alamos National
Laboratory, Los Alamos
NM 87545, New Mexico, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory,
Los Alamos
NM 87545, New Mexico, USA
| | | | - Xueqing Zou
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | - Helen Davies
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences
Lund, Lund University, Lund
SE-223 81, Sweden
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute and
Cancer Genomics Netherlands, Erasmus University Medical Center,
Rotterdam
3015CN, The Netherlands
| | - Arie B. Brinkman
- Radboud University, Faculty of Science, Department of Molecular
Biology, 6525GA
Nijmegen, The Netherlands
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | | | - Adam Butler
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
| | - Hyung-Yong Kim
- Department of Pathology, College of Medicine, Hanyang
University, Seoul
133-791, South Korea
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences
Lund, Lund University, Lund
SE-223 81, Sweden
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Université
Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121,
B-1000
Brussels, Belgium
| | - P. Andrew Futreal
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Cambridgeshire
CB10 1SD, UK
- Department of Genomic Medicine, UT MD Anderson Cancer
Center, Houston, Texas
77230, USA
| | | | - Paul N. Span
- Department of Radiation Oncology, and department of Laboratory
Medicine, Radboud university medical center, Nijmegen
6525GA, The Netherlands
| | - Steven Van Laere
- Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus,
Wilrijk, Belgium and Center for Oncological Research, University of Antwerp,
Antwerp
B-2610, Belgium
| | - Sunil R. Lakhani
- Centre for Clinical Research and School of Medicine, University of
Queensland, Brisbane, Queensland
4059, Australia
- Pathology Queensland, The Royal Brisbane and Women's
Hospital, Brisbane, Queensland
4029, Australia
| | - Jorunn E. Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of
Iceland, 101
Reykjavik, Iceland
| | - Alastair M. Thompson
- Department of Breast Surgical Oncology, University of Texas MD
Anderson Cancer Center, 1400 Pressler
Street,Houston, Texas
77030, USA
- Department of Surgical Oncology, University of Dundee,
Dundee
DD1 9SY, UK
| | - Hendrik G. Stunnenberg
- Radboud University, Faculty of Science, Department of Molecular
Biology, 6525GA
Nijmegen, The Netherlands
| | - Marc J. van de Vijver
- Department of Pathology, Academic Medical Center,
Meibergdreef 9, 1105 AZ
Amsterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute and
Cancer Genomics Netherlands, Erasmus University Medical Center,
Rotterdam
3015CN, The Netherlands
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo
University Hospital, The Norwegian Radium Hospital, Oslo
0310, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for
Clinical Medicine, University of Oslo, Oslo
0310, Norway
| | - Andrea L. Richardson
- Department of Pathology, Brigham and Women's Hospital,
Boston, Massachusetts
02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, Massachusetts
02215, USA
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang
University, Seoul
133-791, South Korea
| | - Gilles Thomas
- Synergie Lyon Cancer, Centre Léon Bérard,
28 rue Laënnec, Lyon
Cedex 08, France
| | - Julian Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge
CB2 0QH, UK
| | - Cristina Rada
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge
CB2 0QH, UK
| | | | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Trust Genome Campus, Cambridgeshire
CB10 1SD, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Cambridge
CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University
Hospitals NHS Foundation Trust, Cambridge
CB2 9NB, UK
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559
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Liddiard K, Ruis B, Takasugi T, Harvey A, Ashelford KE, Hendrickson EA, Baird DM. Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4. Genome Res 2016; 26:588-600. [PMID: 26941250 PMCID: PMC4864465 DOI: 10.1101/gr.200840.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/02/2016] [Indexed: 01/26/2023]
Abstract
Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combination of high-throughput sequence analysis together with experimentally induced telomeric double-stranded DNA breaks. We show that a single chromosomal dysfunctional telomere can fuse with diverse nontelomeric genomic loci, even in the presence of an otherwise stable genome, and that fusion predominates in coding regions. Fusion frequency was markedly increased in the absence of TP53 checkpoint control and significantly modulated by the cellular capacity for classical, versus alternative, nonhomologous end joining (NHEJ). We observed a striking reduction in inter-chromosomal fusion events in cells lacking DNA ligase 4, in contrast to a remarkably consistent profile of intra-chromosomal fusion in the context of multiple genetic knockouts, including DNA ligase 3 and 4 double-knockouts. We reveal distinct mutational signatures associated with classical NHEJ-mediated inter-chromosomal, as opposed to alternative NHEJ-mediated intra-chromosomal, telomere fusions and evidence for an unanticipated sufficiency of DNA ligase 1 for these intra-chromosomal events. Our findings have implications for mechanisms driving cancer genome evolution.
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Affiliation(s)
- Kate Liddiard
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Taylor Takasugi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Adam Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Kevin E Ashelford
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Duncan M Baird
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
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560
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Thyme SB, Schier AF. Polq-Mediated End Joining Is Essential for Surviving DNA Double-Strand Breaks during Early Zebrafish Development. Cell Rep 2016; 15:707-714. [PMID: 27149851 DOI: 10.1016/j.celrep.2016.03.072] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 02/02/2016] [Accepted: 03/18/2016] [Indexed: 01/12/2023] Open
Abstract
Error-prone repair of DNA double-strand breaks (DSBs) has been postulated to occur through classical non-homologous end joining (NHEJ) in systems ranging from nematode somatic tissues to zebrafish embryos. Contrary to this model, we show that zebrafish embryos mutant for DNA polymerase theta (Polq), a critical component of alternative end joining (alt-EJ), cannot repair DSBs induced by CRISPR/Cas9 or ionizing radiation. In the absence of DSBs, polq mutants are phenotypically normal, but they do not survive mutagenesis and display dramatic differences in the mutation profiles compared with the wild-type. These results show that alt-EJ repair is essential and dominant during the early development of a vertebrate.
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Affiliation(s)
- Summer B Thyme
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, MA 02138, USA.
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561
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Kostyrko K, Mermod N. Assays for DNA double-strand break repair by microhomology-based end-joining repair mechanisms. Nucleic Acids Res 2016; 44:e56. [PMID: 26657630 PMCID: PMC4824085 DOI: 10.1093/nar/gkv1349] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 11/17/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022] Open
Abstract
DNA double stranded breaks (DSBs) are one of the most deleterious types of DNA lesions. The main pathways responsible for repairing these breaks in eukaryotic cells are homologous recombination (HR) and non-homologous end-joining (NHEJ). However, a third group of still poorly characterized DSB repair pathways, collectively termed microhomology-mediated end-joining (MMEJ), relies on short homologies for the end-joining process. Here, we constructed GFP reporter assays to characterize and distinguish MMEJ variant pathways, namely the simple MMEJ and the DNA synthesis-dependent (SD)-MMEJ mechanisms. Transfection of these assay vectors in Chinese hamster ovary (CHO) cells and characterization of the repaired DNA sequences indicated that while simple MMEJ is able to mediate relatively efficient DSB repair if longer microhomologies are present, the majority of DSBs were repaired using the highly error-prone SD-MMEJ pathway. To validate the involvement of DNA synthesis in the repair process, siRNA knock-down of different genes proposed to play a role in MMEJ were performed, revealing that the knock-down of DNA polymerase θ inhibited DNA end resection and repair through simple MMEJ, thus favoring the other repair pathway. Overall, we conclude that this approach provides a convenient assay to study MMEJ-related DNA repair pathways.
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Affiliation(s)
- Kaja Kostyrko
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
| | - Nicolas Mermod
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology UNIL-EPFL, Lausanne, Switzerland
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562
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Czochor JR, Sulkowski P, Glazer PM. miR-155 Overexpression Promotes Genomic Instability by Reducing High-fidelity Polymerase Delta Expression and Activating Error-Prone DSB Repair. Mol Cancer Res 2016; 14:363-73. [PMID: 26850462 PMCID: PMC5021065 DOI: 10.1158/1541-7786.mcr-15-0399] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/28/2016] [Indexed: 12/21/2022]
Abstract
UNLABELLED miR-155 is an oncogenic miRNA that is often overexpressed in cancer and is associated with poor prognosis. miR-155 can target several DNA repair factors, including RAD51, MLH1, and MSH6, and its overexpression results in an increased mutation frequency in vitro, although the mechanism has yet to be fully understood. Here, we demonstrate that overexpression of miR-155 drives an increased mutation frequency both in vitro and in vivo, promoting genomic instability by affecting multiple DNA repair pathways. miR-155 overexpression causes a decrease in homologous recombination, but yields a concurrent increase in the error-prone nonhomologous end-joining pathway. Despite repressing established targets MLH1 and MSH6, the identified mutation pattern upon miR-155 overexpression does not resemble that of a mismatch repair-deficient background. Further investigation revealed that all four subunits of polymerase delta, a high-fidelity DNA replication, and repair polymerase are downregulated at the mRNA level in the context of miR-155 overexpression. FOXO3a, a transcription factor and known target of miR-155, has one or more putative binding site(s) in the promoter of all four polymerase delta subunits. Finally, suppression of FOXO3a by miR-155 or by siRNA knockdown is sufficient to repress the expression of the catalytic subunit of polymerase delta, POLD1, at the protein level, indicating that FOXO3a contributes to the regulation of polymerase delta levels. IMPLICATIONS Taken together, miR-155 overexpression drives an increase in mutation frequency via multifaceted impact on DNA damage response and DNA repair pathways.
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Affiliation(s)
| | | | - Peter M. Glazer
- Department of Genetics, Yale University, New Haven, CT
- Department of Therapeutic Radiology, Yale University, New Haven, CT
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563
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Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 2016. [PMID: 26871470 DOI: 10.18632/oncotarget.7277] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
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Affiliation(s)
- Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sachet A Shukla
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joyce F Liu
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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564
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Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 2016. [PMID: 26871470 DOI: 10.18632/oncotarget.7277]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
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Affiliation(s)
- Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sachet A Shukla
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joyce F Liu
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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565
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Pratz KW, Koh BD, Patel AG, Flatten KS, Poh W, Herman JG, Dilley R, Harrell MI, Smith BD, Karp JE, Swisher EM, McDevitt MA, Kaufmann SH. Poly (ADP-Ribose) Polymerase Inhibitor Hypersensitivity in Aggressive Myeloproliferative Neoplasms. Clin Cancer Res 2016; 22:3894-902. [PMID: 26979391 DOI: 10.1158/1078-0432.ccr-15-2351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/29/2016] [Indexed: 01/31/2023]
Abstract
PURPOSE DNA repair defects have been previously reported in myeloproliferative neoplasms (MPN). Inhibitors of PARP have shown activity in solid tumors with defects in homologous recombination (HR). This study was performed to assess MPN sensitivity to PARP inhibitors ex vivo EXPERIMENTAL DESIGN HR pathway integrity in circulating myeloid cells was evaluated by assessing the formation of RAD51 foci after treatment with ionizing radiation or PARP inhibitors. Sensitivity of MPN erythroid and myeloid progenitors to PARP inhibitors was evaluated using colony formation assays. RESULTS Six of 14 MPN primary samples had reduced formation of RAD51 foci after exposure to ionizing radiation, suggesting impaired HR. This phenotype was not associated with a specific MPN subtype, JAK2 mutation status, or karyotype. MPN samples showed increased sensitivity to the PARP inhibitors veliparib and olaparib compared with normal myeloid progenitors. This hypersensitivity, which was most pronounced in samples deficient in DNA damage-induced RAD51 foci, was observed predominantly in samples from patients with diagnoses of chronic myelogenous leukemia, chronic myelomonocytic leukemia, or unspecified myelodysplastic/MPN overlap syndromes. CONCLUSIONS Like other neoplasms with HR defects, MPNs exhibit PARP inhibitor hypersensitivity compared with normal marrow. These results suggest that further preclinical and possibly clinical study of PARP inhibitors in MPNs is warranted. Clin Cancer Res; 22(15); 3894-902. ©2016 AACR.
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Affiliation(s)
- Keith W Pratz
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland.
| | - Brian D Koh
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Anand G Patel
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | | | - Weijie Poh
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - James G Herman
- Division of Hematology/Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Robert Dilley
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Maria I Harrell
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, Washington
| | - B Douglas Smith
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Judith E Karp
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, Maryland
| | - Elizabeth M Swisher
- Department of Obstetrics & Gynecology, University of Washington School of Medicine, Seattle, Washington
| | - Michael A McDevitt
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Scott H Kaufmann
- Department of Oncology, Mayo Clinic, Rochester, Minnesota. Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
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566
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Jackson RA, Wu JS, Chen ES. C1D family proteins in coordinating RNA processing, chromosome condensation and DNA damage response. Cell Div 2016; 11:2. [PMID: 27030795 PMCID: PMC4812661 DOI: 10.1186/s13008-016-0014-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/22/2016] [Indexed: 12/02/2022] Open
Abstract
Research on the involvement of C1D and its yeast homologues Rrp47 (S. cerevisiae) and Cti1 (S. pombe) in DNA damage repair and RNA processing has remained mutually exclusive, with most studies predominantly concentrating on Rrp47. This review will look to reconcile the functions of these proteins in their involvement with the RNA exosome, in the regulation of chromatin architecture, and in the repair of DNA double-strand breaks, focusing on non-homologous end joining and homologous recombination. We propose that C1D is situated in a central position to maintain genomic stability at highly transcribed gene loci by coordinating these processes through the timely recruitment of relevant regulatory factors. In the event that the damage is beyond repair, C1D induces apoptosis in a p53-dependent manner.
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Affiliation(s)
- Rebecca A Jackson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Jocelyn Shumei Wu
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore ; National University Health System (NUHS), Singapore, 119228 Singapore ; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119228 Singapore
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567
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Complex interactions between the DNA-damage response and mammalian telomeres. Nat Struct Mol Biol 2016; 22:859-66. [PMID: 26581520 DOI: 10.1038/nsmb.3092] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/23/2015] [Indexed: 12/28/2022]
Abstract
Natural chromosome ends resemble double-stranded DNA breaks, but they do not activate a damage response in healthy cells. Telomeres therefore have evolved to solve the 'end-protection problem' by inhibiting multiple DNA damage-response pathways. During the past decade, the view of telomeres has progressed from simple caps that hide chromosome ends to complex machineries that have an active role in organizing the genome. Here we focus on mammalian telomeres and summarize and interpret recent discoveries in detail, focusing on how repair pathways are inhibited, how resection and replication are controlled and how these mechanisms govern cell fate during senescence, crisis and transformation.
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568
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Samadder P, Aithal R, Belan O, Krejci L. Cancer TARGETases: DSB repair as a pharmacological target. Pharmacol Ther 2016; 161:111-131. [PMID: 26899499 DOI: 10.1016/j.pharmthera.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer is a disease attributed to the accumulation of DNA damages due to incapacitation of DNA repair pathways resulting in genomic instability and a mutator phenotype. Among the DNA lesions, double stranded breaks (DSBs) are the most toxic forms of DNA damage which may arise as a result of extrinsic DNA damaging agents or intrinsic replication stress in fast proliferating cancer cells. Accurate repair of DSBs is therefore paramount to the cell survival, and several classes of proteins such as kinases, nucleases, helicases or core recombinational proteins have pre-defined jobs in precise execution of DSB repair pathways. On one hand, the proper functioning of these proteins ensures maintenance of genomic stability in normal cells, and on the other hand results in resistance to various drugs employed in cancer therapy and therefore presents a suitable opportunity for therapeutic targeting. Higher relapse and resistance in cancer patients due to non-specific, cytotoxic therapies is an alarming situation and it is becoming more evident to employ personalized treatment based on the genetic landscape of the cancer cells. For the success of personalized treatment, it is of immense importance to identify more suitable targetable proteins in DSB repair pathways and also to explore new synthetic lethal interactions with these pathways. Here we review the various alternative approaches to target the various protein classes termed as cancer TARGETases in DSB repair pathway to obtain more beneficial and selective therapy.
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Affiliation(s)
- Pounami Samadder
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic
| | - Rakesh Aithal
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Belan
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
| | - Lumir Krejci
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital in Brno, 60200 Brno, Czech Republic; Department of Biology, Masaryk University, 62500 Brno, Czech Republic.
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569
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Abstract
During meiosis, numerous DNA double-strand breaks (DSBs) are formed as part of the normal developmental program. This seemingly destructive behavior is necessary for successful meiosis, since repair of the DSBs through homologous recombination (HR) helps to produce physical links between the homologous chromosomes essential for correct chromosome segregation later in meiosis. However, DSB formation at such a massive scale also introduces opportunities to generate gross chromosomal rearrangements. In this review, we explore ways in which meiotic DSBs can result in such genomic alterations.
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570
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Beagan K, McVey M. Linking DNA polymerase theta structure and function in health and disease. Cell Mol Life Sci 2016; 73:603-15. [PMID: 26514729 PMCID: PMC4715478 DOI: 10.1007/s00018-015-2078-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/10/2015] [Accepted: 10/19/2015] [Indexed: 10/22/2022]
Abstract
DNA polymerase theta (Pol θ) is an error-prone A-family polymerase that is highly conserved among multicellular eukaryotes and plays multiple roles in DNA repair and the regulation of genome integrity. Studies conducted in several model organisms have shown that Pol θ can be utilized during DNA interstrand crosslink repair and during alternative end-joining repair of double-strand breaks. Recent genetic and biochemical studies have begun to elucidate the unique structural features of Pol θ that promote alternative end-joining repair. Importantly, Pol θ-dependent end joining appears to be important for overall genome stability, as it affects chromosome translocation formation in murine and human cell lines. Pol θ has also been suggested to act as a modifier of replication timing in human cells, though the mechanism of action remains unknown. Pol θ is highly upregulated in a number of human cancer types, which could indicate that mutagenic Pol θ-dependent end joining is used during cancer cell proliferation. Here, we review the various roles of Pol θ across species and discuss how these roles may be relevant to cancer therapy.
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Affiliation(s)
- Kelly Beagan
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA, 02155, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA, 02155, USA.
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571
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Rodgers K, McVey M. Error-Prone Repair of DNA Double-Strand Breaks. J Cell Physiol 2016; 231:15-24. [PMID: 26033759 DOI: 10.1002/jcp.25053] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 05/20/2015] [Indexed: 12/14/2022]
Abstract
Preserving the integrity of the DNA double helix is crucial for the maintenance of genomic stability. Therefore, DNA double-strand breaks represent a serious threat to cells. In this review, we describe the two major strategies used to repair double strand breaks: non-homologous end joining and homologous recombination, emphasizing the mutagenic aspects of each. We focus on emerging evidence that homologous recombination, long thought to be an error-free repair process, can in fact be highly mutagenic, particularly in contexts requiring large amounts of DNA synthesis. Recent investigations have begun to illuminate the molecular mechanisms by which error-prone double-strand break repair can create major genomic changes, such as translocations and complex chromosome rearrangements. We highlight these studies and discuss proposed models that may explain some of the more extreme genetic changes observed in human cancers and congenital disorders.
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Affiliation(s)
- Kasey Rodgers
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, Massachusetts
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572
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Sinha S, Villarreal D, Shim EY, Lee SE. Risky business: Microhomology-mediated end joining. Mutat Res 2016; 788:17-24. [PMID: 26790771 DOI: 10.1016/j.mrfmmm.2015.12.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/03/2015] [Accepted: 12/22/2015] [Indexed: 11/16/2022]
Abstract
Prevalence of microhomology (MH) at the breakpoint junctions in somatic and germ-line chromosomal rearrangements and in the programmed immune receptor rearrangements from cells deficient in classical end joining reveals an enigmatic process called MH-mediated end joining (MMEJ). MMEJ repairs DNA double strand breaks (DSBs) by annealing flanking MH and deleting genetic information at the repair junctions from yeast to humans. Being genetically distinct from canonical DNA DSB pathways, MMEJ is involved with the fusions of eroded/uncapped telomeres as well as with the assembly of chromosome fragments in chromothripsis. In this review article, we will discuss an up-to-date model representing the MMEJ process and the mechanism by which cells regulate MMEJ to limit repair-associated mutagenesis. We will also describe the possible therapeutic gains resulting from the inhibition of MMEJ in recombination deficient cancers. Lastly, we will embark on two contentious issues associated with MMEJ such as the significance of MH at the repair junction to be the hallmark of MMEJ and the relationship of MMEJ to other mechanistically related DSB repair pathways.
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Affiliation(s)
- Supriya Sinha
- Department of Molecular Medicine, Institute of Biotechnology, United States
| | - Diana Villarreal
- Children's Hospital of San Antonio, Baylor College of Medicine, San Antonio, TX 78207, United States
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, TX 78229, United States
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, United States; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, TX 78229, United States.
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573
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Federico MB, Vallerga MB, Radl A, Paviolo NS, Bocco JL, Di Giorgio M, Soria G, Gottifredi V. Chromosomal Integrity after UV Irradiation Requires FANCD2-Mediated Repair of Double Strand Breaks. PLoS Genet 2016; 12:e1005792. [PMID: 26765540 PMCID: PMC4712966 DOI: 10.1371/journal.pgen.1005792] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 12/17/2015] [Indexed: 12/29/2022] Open
Abstract
Fanconi Anemia (FA) is a rare autosomal recessive disorder characterized by hypersensitivity to inter-strand crosslinks (ICLs). FANCD2, a central factor of the FA pathway, is essential for the repair of double strand breaks (DSBs) generated during fork collapse at ICLs. While lesions different from ICLs can also trigger fork collapse, the contribution of FANCD2 to the resolution of replication-coupled DSBs generated independently from ICLs is unknown. Intriguingly, FANCD2 is readily activated after UV irradiation, a DNA-damaging agent that generates predominantly intra-strand crosslinks but not ICLs. Hence, UV irradiation is an ideal tool to explore the contribution of FANCD2 to the DNA damage response triggered by DNA lesions other than ICL repair. Here we show that, in contrast to ICL-causing agents, UV radiation compromises cell survival independently from FANCD2. In agreement, FANCD2 depletion does not increase the amount of DSBs generated during the replication of UV-damaged DNA and is dispensable for UV-induced checkpoint activation. Remarkably however, FANCD2 protects UV-dependent, replication-coupled DSBs from aberrant processing by non-homologous end joining, preventing the accumulation of micronuclei and chromatid aberrations including non-homologous chromatid exchanges. Hence, while dispensable for cell survival, FANCD2 selectively safeguards chromosomal stability after UV-triggered replication stress.
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Affiliation(s)
- María Belén Federico
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
| | - María Belén Vallerga
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
| | - Analía Radl
- Laboratorio de Dosimetría Biológica, Autoridad Regulatoria Nuclear, Buenos Aires, Argentina
| | - Natalia Soledad Paviolo
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
| | - José Luis Bocco
- Centro de Investigaciones en Bioquímica Clínica e Inmunología/ CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Marina Di Giorgio
- Laboratorio de Dosimetría Biológica, Autoridad Regulatoria Nuclear, Buenos Aires, Argentina
| | - Gastón Soria
- Centro de Investigaciones en Bioquímica Clínica e Inmunología/ CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Vanesa Gottifredi
- Cell Cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, IIBBA/ CONICET, Buenos Aires, Argentina
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574
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Wolfgruber TK, Nakashima MM, Schneider KL, Sharma A, Xie Z, Albert PS, Xu R, Bilinski P, Dawe RK, Ross-Ibarra J, Birchler JA, Presting GG. High Quality Maize Centromere 10 Sequence Reveals Evidence of Frequent Recombination Events. FRONTIERS IN PLANT SCIENCE 2016; 7:308. [PMID: 27047500 PMCID: PMC4806543 DOI: 10.3389/fpls.2016.00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/27/2016] [Indexed: 05/02/2023]
Abstract
The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR) has presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here, we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 × 10(-6) and 5 × 10(-5) for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb from the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length CR from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB) repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. In many cases examined here, DSB repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to efficiently repair frequent DSBs in centromeres.
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Affiliation(s)
- Thomas K. Wolfgruber
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Megan M. Nakashima
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Kevin L. Schneider
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Anupma Sharma
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Zidian Xie
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Patrice S. Albert
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Ronghui Xu
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
| | - Paul Bilinski
- Department of Plant Sciences, University of California DavisDavis, CA, USA
| | - R. Kelly Dawe
- Department of Plant Biology, University of GeorgiaAthens, GA, USA
| | | | - James A. Birchler
- Division of Biological Sciences, University of MissouriColumbia, MO, USA
| | - Gernot G. Presting
- Department of Molecular Biosciences and Bioengineering, University of Hawaíi at MānoaHonolulu, HI, USA
- *Correspondence: Gernot G. Presting
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575
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Wu Y, Lee SH, Williamson EA, Reinert BL, Cho JH, Xia F, Jaiswal AS, Srinivasan G, Patel B, Brantley A, Zhou D, Shao L, Pathak R, Hauer-Jensen M, Singh S, Kong K, Wu X, Kim HS, Beissbarth T, Gaedcke J, Burma S, Nickoloff JA, Hromas RA. EEPD1 Rescues Stressed Replication Forks and Maintains Genome Stability by Promoting End Resection and Homologous Recombination Repair. PLoS Genet 2015; 11:e1005675. [PMID: 26684013 PMCID: PMC4684289 DOI: 10.1371/journal.pgen.1005675] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022] Open
Abstract
Replication fork stalling and collapse is a major source of genome instability leading to neoplastic transformation or cell death. Such stressed replication forks can be conservatively repaired and restarted using homologous recombination (HR) or non-conservatively repaired using micro-homology mediated end joining (MMEJ). HR repair of stressed forks is initiated by 5’ end resection near the fork junction, which permits 3’ single strand invasion of a homologous template for fork restart. This 5’ end resection also prevents classical non-homologous end-joining (cNHEJ), a competing pathway for DNA double-strand break (DSB) repair. Unopposed NHEJ can cause genome instability during replication stress by abnormally fusing free double strand ends that occur as unstable replication fork repair intermediates. We show here that the previously uncharacterized Exonuclease/Endonuclease/Phosphatase Domain-1 (EEPD1) protein is required for initiating repair and restart of stalled forks. EEPD1 is recruited to stalled forks, enhances 5’ DNA end resection, and promotes restart of stalled forks. Interestingly, EEPD1 directs DSB repair away from cNHEJ, and also away from MMEJ, which requires limited end resection for initiation. EEPD1 is also required for proper ATR and CHK1 phosphorylation, and formation of gamma-H2AX, RAD51 and phospho-RPA32 foci. Consistent with a direct role in stalled replication fork cleavage, EEPD1 is a 5’ overhang nuclease in an obligate complex with the end resection nuclease Exo1 and BLM. EEPD1 depletion causes nuclear and cytogenetic defects, which are made worse by replication stress. Depleting 53BP1, which slows cNHEJ, fully rescues the nuclear and cytogenetic abnormalities seen with EEPD1 depletion. These data demonstrate that genome stability during replication stress is maintained by EEPD1, which initiates HR and inhibits cNHEJ and MMEJ. The cell itself damages its own DNA throughout the cell cycle as a result of oxidative metabolism, and this damage creates barriers for replication fork progression. Thus, DNA replication is not a smooth and continuous process, but rather one of stalls and restarts. Therefore, proper replication fork restart is crucial to maintain the integrity of the cell’s genome, and preventing its own death or immortalization. To restart after stalling, the replication fork subverts a DNA repair pathway termed homologous recombination. Using any other pathway for fork repair will result in an unstable genome. How the homologous recombination repair pathway is initiated at the replication fork is not well defined. In this study we demonstrate the previously uncharacterized EEPD1 protein is a novel gatekeeper for the initiation of this fork repair pathway. EEPD1 promotes 5’ end resection, the initial step of homologous recombination, which also prevents alternative fork repair pathways that lead to unstable chromosomes. Thus, EEPD1 protects the integrity of the cell genome by promoting the safe homologous recombination fork repair pathway.
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Affiliation(s)
- Yuehan Wu
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Suk-Hee Lee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Elizabeth A. Williamson
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Brian L. Reinert
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Ju Hwan Cho
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Fen Xia
- Department of Radiation Oncology, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Aruna Shanker Jaiswal
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Gayathri Srinivasan
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Bhavita Patel
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Alexis Brantley
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Daohong Zhou
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Lijian Shao
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Rupak Pathak
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Martin Hauer-Jensen
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Sudha Singh
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
| | - Kimi Kong
- Department of Craniofacial Regeneration, College of Dental Medicine, Columbia University, New York, New York, United States of America
| | - Xaiohua Wu
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, California, United States of America
| | - Hyun-Suk Kim
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Timothy Beissbarth
- Department of Medical Statistics, and General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Jochen Gaedcke
- Department of Medical Statistics, and General, Visceral, and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Sandeep Burma
- Department of Radiation Oncology, University of Texas Southwestern, Dallas, Texas, United States of America
| | - Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail: (JAN); (RAH)
| | - Robert A. Hromas
- Department of Medicine and the Cancer Center, University of Florida Health, Gainesville, Florida, United States of America
- * E-mail: (JAN); (RAH)
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576
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How cancer cells hijack DNA double-strand break repair pathways to gain genomic instability. Biochem J 2015; 471:1-11. [PMID: 26392571 DOI: 10.1042/bj20150582] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA DSBs (double-strand breaks) are a significant threat to the viability of a normal cell, since they can result in loss of genetic material if mitosis or replication is attempted in their presence. Consequently, evolutionary pressure has resulted in multiple pathways and responses to enable DSBs to be repaired efficiently and faithfully. Cancer cells, which are under pressure to gain genomic instability, have a striking ability to avoid the elegant mechanisms by which normal cells maintain genomic stability. Current models suggest that, in normal cells, DSB repair occurs in a hierarchical manner that promotes rapid and efficient rejoining first, with the utilization of additional steps or pathways of diminished accuracy if rejoining is unsuccessful or delayed. In the present review, we evaluate the fidelity of DSB repair pathways and discuss how cancer cells promote the utilization of less accurate processes. Homologous recombination serves to promote accuracy and stability during replication, providing a battlefield for cancer to gain instability. Non-homologous end-joining, a major DSB repair pathway in mammalian cells, usually operates with high fidelity and only switches to less faithful modes if timely repair fails. The transition step is finely tuned and provides another point of attack during tumour progression. In addition to DSB repair, a DSB signalling response activates processes such as cell cycle checkpoint arrest, which enhance the possibility of accurate DSB repair. We consider the ways by which cancers modify and hijack these processes to gain genomic instability.
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577
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Newman JA, Cooper CDO, Aitkenhead H, Gileadi O. Structure of the Helicase Domain of DNA Polymerase Theta Reveals a Possible Role in the Microhomology-Mediated End-Joining Pathway. Structure 2015; 23:2319-2330. [PMID: 26636256 PMCID: PMC4671958 DOI: 10.1016/j.str.2015.10.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/06/2015] [Accepted: 10/09/2015] [Indexed: 12/21/2022]
Abstract
DNA polymerase theta (Polθ) has been identified as a crucial alternative non-homologous end-joining factor in mammalian cells. Polθ is upregulated in a range of cancer cell types defective in homologous recombination, and knockdown has been shown to inhibit cell survival in a subset of these, making it an attractive target for cancer treatment. We present crystal structures of the helicase domain of human Polθ in the presence and absence of bound nucleotides, and a characterization of its DNA-binding and DNA-stimulated ATPase activities. Comparisons with related helicases from the Hel308 family identify several unique features. Polθ exists as a tetramer both in the crystals and in solution. We propose a model for DNA binding to the Polθ helicase domain in the context of the Polθ tetramer, which suggests a role for the helicase domain in strand annealing of DNA templates for subsequent processing by the polymerase domain.
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Affiliation(s)
- Joseph A Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Christopher D O Cooper
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Hazel Aitkenhead
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.
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578
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Gee HE, Buffa FM, Harris AL, Toohey JM, Carroll SL, Cooper CL, Beith J, McNeil C, Carmalt H, Mak C, Warrier S, Holliday A, Selinger C, Beckers R, Kennedy C, Graham P, Swarbrick A, Millar EKA, O'Toole SA, Molloy T. MicroRNA-Related DNA Repair/Cell-Cycle Genes Independently Associated With Relapse After Radiation Therapy for Early Breast Cancer. Int J Radiat Oncol Biol Phys 2015; 93:1104-14. [PMID: 26581147 DOI: 10.1016/j.ijrobp.2015.08.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/30/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
PURPOSE Local recurrence and distant failure after adjuvant radiation therapy for breast cancer remain significant clinical problems, incompletely predicted by conventional clinicopathologic markers. We had previously identified microRNA-139-5p and microRNA-1274a as key regulators of breast cancer radiation response in vitro. The purpose of this study was to investigate standard clinicopathologic markers of local recurrence in a contemporary series and to establish whether putative target genes of microRNAs involved in DNA repair and cell cycle control could better predict radiation therapy response in vivo. METHODS AND MATERIALS With institutional ethics board approval, local recurrence was measured in a contemporary, prospectively collected series of 458 patients treated with radiation therapy after breast-conserving surgery. Additionally, independent publicly available mRNA/microRNA microarray expression datasets totaling >1000 early-stage breast cancer patients, treated with adjuvant radiation therapy, with >10 years of follow-up, were analyzed. The expression of putative microRNA target biomarkers--TOP2A, POLQ, RAD54L, SKP2, PLK2, and RAG1--were correlated with standard clinicopathologic variables using 2-sided nonparametric tests, and to local/distant relapse and survival using Kaplan-Meier and Cox regression analysis. RESULTS We found a low rate of isolated local recurrence (1.95%) in our modern series, and that few clinicopathologic variables (such as lymphovascular invasion) were significantly predictive. In multiple independent datasets (n>1000), however, high expression of RAD54L, TOP2A, POLQ, and SKP2 significantly correlated with local recurrence, survival, or both in univariate and multivariate analyses (P<.001). Low RAG1 expression significantly correlated with local recurrence (multivariate, P=.008). Additionally, RAD54L, SKP2, and PLK2 may be predictive, being prognostic in radiation therapy-treated patients but not in untreated matched control individuals (n=107; P<.05). CONCLUSIONS Biomarkers of DNA repair and cell cycle control can identify patients at high risk of treatment failure in those receiving radiation therapy for early breast cancer in independent cohorts. These should be further investigated prospectively, especially TOP2A and SKP2, for which targeted therapies are available.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Antineoplastic Agents, Hormonal/therapeutic use
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/radiotherapy
- Case-Control Studies
- DNA Helicases/genetics
- DNA Helicases/metabolism
- DNA Repair
- DNA Topoisomerases, Type II/genetics
- DNA Topoisomerases, Type II/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- DNA-Directed DNA Polymerase/genetics
- DNA-Directed DNA Polymerase/metabolism
- Female
- Gene Expression Profiling/methods
- Genes, cdc
- Genetic Markers
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- MicroRNAs
- Middle Aged
- Multivariate Analysis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/mortality
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Poly-ADP-Ribose Binding Proteins
- Prospective Studies
- Radiation Tolerance/genetics
- Radiotherapy, Adjuvant
- S-Phase Kinase-Associated Proteins/genetics
- S-Phase Kinase-Associated Proteins/metabolism
- DNA Polymerase theta
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Affiliation(s)
- Harriet E Gee
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia; Central Clinical School, Sydney Medical School, University of Sydney, NSW, Australia.
| | - Francesca M Buffa
- Department of Medical Oncology, The University of Oxford, Oxford, UK
| | - Adrian L Harris
- Department of Medical Oncology, The University of Oxford, Oxford, UK
| | - Joanne M Toohey
- The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Susan L Carroll
- The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Caroline L Cooper
- Central Clinical School, Sydney Medical School, University of Sydney, NSW, Australia; Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jane Beith
- The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Catriona McNeil
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Hugh Carmalt
- The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Cindy Mak
- The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Sanjay Warrier
- The Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW, Australia
| | - Anne Holliday
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Christina Selinger
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Rhiannon Beckers
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Catherine Kennedy
- Central Clinical School, Sydney Medical School, University of Sydney, NSW, Australia
| | - Peter Graham
- Department of Radiation Oncology, Cancer Care Centre, St. George Hospital, Kogarah, NSW, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, University of NSW, Kensington, NSW, Australia
| | - Ewan K A Millar
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Department of Anatomical Pathology, South Eastern Area Laboratory Service, St. George Hospital, Kogarah, NSW, Australia; School of Medicine and Health Sciences, University of Western Sydney, Campbelltown, NSW, Australia; Faculty of Medicine, School of Medical Sciences, University of NSW, Kensington, NSW, Australia
| | - Sandra A O'Toole
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Central Clinical School, Sydney Medical School, University of Sydney, NSW, Australia; Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Timothy Molloy
- The Kinghorn Cancer Centre & Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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579
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Abstract
Chromosome rearrangement plays a causal role in tumorigenesis by contributing to the inactivation of tumor suppressor genes, the dysregulated expression or amplification of oncogenes and the generation of novel gene fusions. Chromosome breaks are important intermediates in this process. How, when and where these breaks arise and the specific mechanisms engaged in their repair strongly influence the resulting patterns of chromosome rearrangement. Here, we review recent progress in understanding how certain distinctive features of the cancer genome, including clustered mutagenesis, tandem segmental duplications, complex breakpoints, chromothripsis, chromoplexy and chromoanasynthesis may arise.
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580
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Abdul-Sater Z, Cerabona D, Potchanant ES, Sun Z, Enzor R, He Y, Robertson K, Goebel WS, Nalepa G. FANCA safeguards interphase and mitosis during hematopoiesis in vivo. Exp Hematol 2015; 43:1031-1046.e12. [PMID: 26366677 PMCID: PMC4666759 DOI: 10.1016/j.exphem.2015.08.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 12/20/2022]
Abstract
The Fanconi anemia (FA/BRCA) signaling network controls multiple genome-housekeeping checkpoints, from interphase DNA repair to mitosis. The in vivo role of abnormal cell division in FA remains unknown. Here, we quantified the origins of genomic instability in FA patients and mice in vivo and ex vivo. We found that both mitotic errors and interphase DNA damage significantly contribute to genomic instability during FA-deficient hematopoiesis and in nonhematopoietic human and murine FA primary cells. Super-resolution microscopy coupled with functional assays revealed that FANCA shuttles to the pericentriolar material to regulate spindle assembly at mitotic entry. Loss of FA signaling rendered cells hypersensitive to spindle chemotherapeutics and allowed escape from the chemotherapy-induced spindle assembly checkpoint. In support of these findings, direct comparison of DNA crosslinking and anti-mitotic chemotherapeutics in primary FANCA-/- cells revealed genomic instability originating through divergent cell cycle checkpoint aberrations. Our data indicate that FA/BRCA signaling functions as an in vivo gatekeeper of genomic integrity throughout interphase and mitosis, which may have implications for future targeted therapies in FA and FA-deficient cancers.
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Affiliation(s)
- Zahi Abdul-Sater
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Donna Cerabona
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Elizabeth Sierra Potchanant
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Zejin Sun
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Rikki Enzor
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ying He
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kent Robertson
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - W Scott Goebel
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Grzegorz Nalepa
- Herman B. Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana; Bone Marrow Failure Program, Division of Pediatric Hematology-Oncology, Riley Hospital for Children, Indianapolis, Indiana.
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581
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Frietze KM, Roden RBS, Lee JH, Shi Y, Peabody DS, Chackerian B. Identification of Anti-CA125 Antibody Responses in Ovarian Cancer Patients by a Novel Deep Sequence-Coupled Biopanning Platform. Cancer Immunol Res 2015; 4:157-64. [PMID: 26589767 DOI: 10.1158/2326-6066.cir-15-0165] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/06/2015] [Indexed: 01/22/2023]
Abstract
High-grade epithelial ovarian cancer kills more women than any other gynecologic cancer and is rarely diagnosed at an early stage. We sought to identify tumor-associated antigens (TAA) as candidate diagnostic and/or immunotherapeutic targets by taking advantage of tumor autoantibody responses in individuals with ovarian cancer. Plasma-derived IgG from a pool of five patients with advanced ovarian cancer was subjected to iterative biopanning using a library of bacteriophage MS2 virus-like particles (MS2-VLPs) displaying diverse short random peptides. After two rounds of biopanning, we analyzed the selectant population of MS2-VLPs by Ion Torrent deep sequencing. One of the top 25 most abundant peptides identified (DISGTNTSRA) had sequence similarity to cancer antigen 125 (CA125/MUC16), a well-known ovarian cancer-associated antigen. Mice immunized with MS2-DISGTNTSRA generated antibodies that cross-reacted with purified soluble CA125 from ovarian cancer cells but not membrane-bound CA125, indicating that the DISGTNTSRA peptide was a CA125/MUC16 peptide mimic of soluble CA125. Preoperative ovarian cancer patient plasma (n = 100) was assessed for anti-DISGTNTSRA, anti-CA125, and CA125. Patients with normal CA125 (<35 IU/mL) at the time of diagnosis had significantly more antibodies to DISGTNTSRA and to CA125 than those patients who had high CA125 (>35 IU/mL). A statistically significant survival advantage was observed for patients who had either normal CA125 and/or higher concentrations of antibodies to CA125 at the time of diagnosis. These data show the feasibility of using deep sequence-coupled biopanning to identify TAA autoantibody responses from cancer patient plasma and suggest a possible antibody-mediated mechanism for low CA125 plasma concentrations in some ovarian cancer patients.
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Affiliation(s)
- Kathryn M Frietze
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico
| | - Richard B S Roden
- Department of Pathology, The Johns Hopkins University, Baltimore, Maryland
| | - Ji-Hyun Lee
- Biostatistics Shared Resource, University of New Mexico Cancer Center, Albuquerque, New Mexico
| | - Yang Shi
- Biostatistics Shared Resource, University of New Mexico Cancer Center, Albuquerque, New Mexico
| | - David S Peabody
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, New Mexico.
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582
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Taty-Taty GC, Chailleux C, Quaranta M, So A, Guirouilh-Barbat J, Lopez BS, Bertrand P, Trouche D, Canitrot Y. Control of alternative end joining by the chromatin remodeler p400 ATPase. Nucleic Acids Res 2015; 44:1657-68. [PMID: 26578561 PMCID: PMC4770216 DOI: 10.1093/nar/gkv1202] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022] Open
Abstract
Repair of DNA double-strand breaks occurs in a chromatin context that needs to be modified and remodeled to allow suitable access to the different DNA repair machineries. Of particular importance for the maintenance of genetic stability is the tight control of error-prone pathways, such as the alternative End Joining pathway. Here, we show that the chromatin remodeler p400 ATPase is a brake to the use of alternative End Joining. Using specific intracellular reporter susbstrates we observed that p400 depletion increases the frequency of alternative End Joining events, and generates large deletions following repair of double-strand breaks. This increase of alternative End Joining events is largely dependent on CtIP-mediated resection, indicating that it is probably related to the role of p400 in late steps of homologous recombination. Moreover, p400 depletion leads to the recruitment of poly(ADP) ribose polymerase (PARP) and DNA ligase 3 at DNA double-strand breaks, driving to selective killing by PARP inhibitors. All together these results show that p400 acts as a brake to prevent alternative End Joining-dependent genetic instability and underline its potential value as a clinical marker.
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Affiliation(s)
- Gemael-Cedrick Taty-Taty
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Catherine Chailleux
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Muriel Quaranta
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Ayeong So
- Université Paris Sud, CNRS UMR8200, IGR, Villejuif, France
| | | | | | - Pascale Bertrand
- CEA DSV, UMR 967 CEA-INSERM-Université Paris Diderot-Université Paris Sud, Fontenay aux roses, France
| | - Didier Trouche
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
| | - Yvan Canitrot
- Université de Toulouse, UPS, LBCMCP, F-31062 Toulouse, France CNRS UMR5088, LBCMCP, F-31062 Toulouse, France
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583
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Lemmens B, van Schendel R, Tijsterman M. Mutagenic consequences of a single G-quadruplex demonstrate mitotic inheritance of DNA replication fork barriers. Nat Commun 2015; 6:8909. [PMID: 26563448 PMCID: PMC4654259 DOI: 10.1038/ncomms9909] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/14/2015] [Indexed: 12/29/2022] Open
Abstract
Faithful DNA replication is vital to prevent disease-causing mutations, chromosomal aberrations and malignant transformation. However, accuracy conflicts with pace and flexibility and cells rely on specialized polymerases and helicases to ensure effective and timely replication of genomes that contain DNA lesions or secondary structures. If and how cells can tolerate a permanent barrier to replication is, however, unknown. Here we show that a single unresolved G-quadruplexed DNA structure can persist through multiple mitotic divisions without changing conformation. Failed replication across a G-quadruplex causes single-strand DNA gaps that give rise to DNA double-strand breaks in subsequent cell divisions, which are processed by polymerase theta (POLQ)-mediated alternative end joining. Lineage tracing experiments further reveal that persistent G-quadruplexes cause genetic heterogeneity during organ development. Our data demonstrate that a single lesion can cause multiple unique genomic rearrangements, and that alternative end joining enables cells to proliferate in the presence of mitotically inherited replication blocks.
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Affiliation(s)
- Bennie Lemmens
- Department of Human Genetics, Leiden University Medical Center, Postzone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Postzone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, Postzone S-4-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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584
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Chandramouly G, McDevitt S, Sullivan K, Kent T, Luz A, Glickman JF, Andrake M, Skorski T, Pomerantz RT. Small-Molecule Disruption of RAD52 Rings as a Mechanism for Precision Medicine in BRCA-Deficient Cancers. ACTA ACUST UNITED AC 2015; 22:1491-1504. [PMID: 26548611 DOI: 10.1016/j.chembiol.2015.10.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/08/2015] [Accepted: 10/04/2015] [Indexed: 11/27/2022]
Abstract
Suppression of RAD52 causes synthetic lethality in BRCA-deficient cells. Yet pharmacological inhibition of RAD52, which binds single-strand DNA (ssDNA) and lacks enzymatic activity, has not been demonstrated. Here, we identify the small molecule 6-hydroxy-DL-dopa (6-OH-dopa) as a major allosteric inhibitor of the RAD52 ssDNA binding domain. For example, we find that multiple small molecules bind to and completely transform RAD52 undecamer rings into dimers, which abolishes the ssDNA binding channel observed in crystal structures. 6-OH-Dopa also disrupts RAD52 heptamer and undecamer ring superstructures, and suppresses RAD52 recruitment and recombination activity in cells with negligible effects on other double-strand break repair pathways. Importantly, we show that 6-OH-dopa selectively inhibits the proliferation of BRCA-deficient cancer cells, including those obtained from leukemia patients. Taken together, these data demonstrate small-molecule disruption of RAD52 rings as a promising mechanism for precision medicine in BRCA-deficient cancers.
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Affiliation(s)
- Gurushankar Chandramouly
- Department of Medical Genetics and Molecular Biochemistry, Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Shane McDevitt
- Department of Medical Genetics and Molecular Biochemistry, Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Katherine Sullivan
- Department of Microbiology and Immunology, Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Tatiana Kent
- Department of Medical Genetics and Molecular Biochemistry, Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Antonio Luz
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - J Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Mark Andrake
- Institute for Cancer Research, Fox Chase Cancer Center, Temple Health, Philadelphia, PA 19111, USA
| | - Tomasz Skorski
- Department of Microbiology and Immunology, Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Richard T Pomerantz
- Department of Medical Genetics and Molecular Biochemistry, Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, PA 19140, USA.
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585
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Smith AL, Alirezaie N, Connor A, Chan-Seng-Yue M, Grant R, Selander I, Bascuñana C, Borgida A, Hall A, Whelan T, Holter S, McPherson T, Cleary S, Petersen GM, Omeroglu A, Saloustros E, McPherson J, Stein LD, Foulkes WD, Majewski J, Gallinger S, Zogopoulos G. Candidate DNA repair susceptibility genes identified by exome sequencing in high-risk pancreatic cancer. Cancer Lett 2015; 370:302-12. [PMID: 26546047 DOI: 10.1016/j.canlet.2015.10.030] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/25/2015] [Accepted: 10/26/2015] [Indexed: 02/09/2023]
Abstract
The genetic basis underlying the majority of hereditary pancreatic adenocarcinoma (PC) is unknown. Since DNA repair genes are widely implicated in gastrointestinal malignancies, including PC, we hypothesized that there are novel DNA repair PC susceptibility genes. As germline DNA repair gene mutations may lead to PC subtypes with selective therapeutic responses, we also hypothesized that there is an overall survival (OS) difference in mutation carriers versus non-carriers. We therefore interrogated the germline exomes of 109 high-risk PC cases for rare protein-truncating variants (PTVs) in 513 putative DNA repair genes. We identified PTVs in 41 novel genes among 36 kindred. Additional genetic evidence for causality was obtained for 17 genes, with FAN1, NEK1 and RHNO1 emerging as the strongest candidates. An OS difference was observed for carriers versus non-carriers of PTVs with early stage (≤IIB) disease. This adverse survival trend in carriers with early stage disease was also observed in an independent series of 130 PC cases. We identified candidate DNA repair PC susceptibility genes and suggest that carriers of a germline PTV in a DNA repair gene with early stage disease have worse survival.
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Affiliation(s)
- Alyssa L Smith
- Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montreal, QC, Canada H4A 3J1; Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3
| | - Najmeh Alirezaie
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Montreal, QC, Canada H3A 0G1
| | - Ashton Connor
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; MaRS Centre, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, ON, Canada M5G 0A3
| | - Michelle Chan-Seng-Yue
- MaRS Centre, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, ON, Canada M5G 0A3
| | - Robert Grant
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5
| | - Iris Selander
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5
| | - Claire Bascuñana
- Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montreal, QC, Canada H4A 3J1; Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, 60 Murray Street, Toronto, ON, Canada M5T 3H7
| | - Anita Hall
- Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montreal, QC, Canada H4A 3J1; Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3
| | - Thomas Whelan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5
| | - Spring Holter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, 60 Murray Street, Toronto, ON, Canada M5T 3H7
| | - Treasa McPherson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5
| | - Sean Cleary
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, 60 Murray Street, Toronto, ON, Canada M5T 3H7
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA
| | - Atilla Omeroglu
- Department of Pathology, McGill University Health Centre, 1001 Décarie Boulevard, Montreal, QC, Canada H4A 3J1
| | - Emmanouil Saloustros
- Department of Medical Oncology, Hereditary Cancer Clinic, University Hospital of Heraklion, Voutes, Heraklion 71110, Greece
| | - John McPherson
- MaRS Centre, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, ON, Canada M5G 0A3
| | - Lincoln D Stein
- MaRS Centre, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, ON, Canada M5G 0A3
| | - William D Foulkes
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, QC, Canada H3T 1E2
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Montreal, QC, Canada H3A 0G1
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON, Canada M5G 1X5; MaRS Centre, Ontario Institute for Cancer Research, 661 University Avenue, Toronto, ON, Canada M5G 0A3; Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, 60 Murray Street, Toronto, ON, Canada M5T 3H7.
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, 1001 Décarie Boulevard, Montreal, QC, Canada H4A 3J1; Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue West, Montreal, QC, Canada H3A 1A3; Program in Cancer Genetics, Departments of Oncology and Human Genetics, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, QC, Canada H3T 1E2.
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586
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Kalimutho M, Parsons K, Mittal D, López JA, Srihari S, Khanna KK. Targeted Therapies for Triple-Negative Breast Cancer: Combating a Stubborn Disease. Trends Pharmacol Sci 2015; 36:822-846. [PMID: 26538316 DOI: 10.1016/j.tips.2015.08.009] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 11/17/2022]
Abstract
Triple-negative breast cancers (TNBCs) constitute a heterogeneous subtype of breast cancers that have a poor clinical outcome. Although no approved targeted therapy is available for TNBCs, molecular-profiling efforts have revealed promising molecular targets, with several candidate compounds having now entered clinical trials for TNBC patients. However, initial results remain modest, thereby highlighting challenges potentially involving intra- and intertumoral heterogeneity and acquisition of therapy resistance. We present a comprehensive review on emerging targeted therapies for treating TNBCs, including the promising approach of immunotherapy and the prognostic value of tumor-infiltrating lymphocytes. We discuss the impact of pathway rewiring in the acquisition of drug resistance, and the prospect of employing combination therapy strategies to overcome challenges towards identifying clinically-viable targeted treatment options for TNBC.
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Affiliation(s)
- Murugan Kalimutho
- Signal Transduction Laboratory, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia.
| | - Kate Parsons
- Signal Transduction Laboratory, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia; School of Natural Sciences, Griffith University, Nathan, QLD 411, Australia
| | - Deepak Mittal
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - J Alejandro López
- School of Natural Sciences, Griffith University, Nathan, QLD 411, Australia; Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kum Kum Khanna
- Signal Transduction Laboratory, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia; School of Natural Sciences, Griffith University, Nathan, QLD 411, Australia.
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587
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Dizdar O, Arslan C, Altundag K. Advances in PARP inhibitors for the treatment of breast cancer. Expert Opin Pharmacother 2015; 16:2751-8. [PMID: 26485111 DOI: 10.1517/14656566.2015.1100168] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Poly(ADP-Ribose) polymerases (PARPs) are one of the important components of base excision repair pathway for single strand DNA breaks. Currently accepted hypothesis for the mechanism of action for PARP inhibitors in tumors with homologous recombination deficiency is synthetic lethality, as the simultaneous blockage of both pathways prevents the tumor cells from repairing DNA damage. Other proposed mechanisms include PARP trapping, defective BRCA1 and POLQ recruitment to sites of DNA repair. Breast cancer subgroups with germline BRCA mutations or non-mutational functional defects in BRCA proteins exemplify potential targets for PARP inhibitors. AREAS COVERED Promising results have been achieved with PARP inhibitors in BRCA associated cancers, particularly in ovarian and breast cancer. Olaparib is the only PARP inhibitor approved by FDA in the treatment of patients with germline BRCA mutated advanced ovarian cancer pretreated with ≥3 prior lines of chemotherapy. In this article, we reviewed the current status of PARP inhibitors, completed and ongoing trials, safety and resistance issues in patients with breast cancer. EXPERT OPINION PARP inhibitors show promise in cancers with BRCA mutation and in the treatment of sporadic cancers with defective homologous recombination. Predictors of response, strategies to overcome resistance, combination with other chemotherapies and targeted agents, optimum dose and schedule of administration should be investigated in future trials.
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Affiliation(s)
- Omer Dizdar
- a Department of Preventive Oncology , Hacettepe University Institute of Cancer , Ankara 06100 , Turkey
| | - Cagatay Arslan
- b Department of Medical Oncology , Izmir University Faculty of Medicine , Izmir 35540 , Turkey
| | - Kadri Altundag
- c Department of Medical Oncology , Hacettepe University Institute of Cancer , Ankara 06100 , Turkey
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588
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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589
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Konstantinopoulos PA, Ceccaldi R, Shapiro GI, D'Andrea AD. Homologous Recombination Deficiency: Exploiting the Fundamental Vulnerability of Ovarian Cancer. Cancer Discov 2015; 5:1137-54. [PMID: 26463832 DOI: 10.1158/2159-8290.cd-15-0714] [Citation(s) in RCA: 597] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/11/2015] [Indexed: 12/14/2022]
Abstract
UNLABELLED Approximately 50% of epithelial ovarian cancers (EOC) exhibit defective DNA repair via homologous recombination (HR) due to genetic and epigenetic alterations of HR pathway genes. Defective HR is an important therapeutic target in EOC as exemplified by the efficacy of platinum analogues in this disease, as well as the advent of PARP inhibitors, which exhibit synthetic lethality when applied to HR-deficient cells. Here, we describe the genotypic and phenotypic characteristics of HR-deficient EOCs, discuss current and emerging approaches for targeting these tumors, and present challenges associated with these approaches, focusing on development and overcoming resistance. SIGNIFICANCE Defective DNA repair via HR is a pivotal vulnerability of EOC, particularly of the high-grade serous histologic subtype. Targeting defective HR offers the unique opportunity of exploiting molecular differences between tumor and normal cells, thereby inducing cancer-specific synthetic lethality; the promise and challenges of these approaches in ovarian cancer are discussed in this review.
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Affiliation(s)
- Panagiotis A Konstantinopoulos
- Department of Medical Oncology, Medical Gynecologic Oncology Program, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Raphael Ceccaldi
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Early Drug Development Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Alan D D'Andrea
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts. Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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590
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Microhomology-Mediated End Joining: A Back-up Survival Mechanism or Dedicated Pathway? Trends Biochem Sci 2015; 40:701-714. [PMID: 26439531 DOI: 10.1016/j.tibs.2015.08.006] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/13/2015] [Accepted: 08/18/2015] [Indexed: 12/12/2022]
Abstract
DNA double-strand breaks (DSBs) disrupt the continuity of chromosomes and their repair by error-free mechanisms is essential to preserve genome integrity. Microhomology-mediated end joining (MMEJ) is an error-prone repair mechanism that involves alignment of microhomologous sequences internal to the broken ends before joining, and is associated with deletions and insertions that mark the original break site, as well as chromosome translocations. Whether MMEJ has a physiological role or is simply a back-up repair mechanism is a matter of debate. Here we review recent findings pertaining to the mechanism of MMEJ and discuss its role in normal and cancer cells.
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591
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Ceccaldi R, Rondinelli B, D'Andrea AD. Repair Pathway Choices and Consequences at the Double-Strand Break. Trends Cell Biol 2015; 26:52-64. [PMID: 26437586 DOI: 10.1016/j.tcb.2015.07.009] [Citation(s) in RCA: 985] [Impact Index Per Article: 109.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/16/2015] [Accepted: 07/29/2015] [Indexed: 02/03/2023]
Abstract
DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genomic integrity. Failure to repair a DSB has deleterious consequences, including genomic instability and cell death. Indeed, misrepair of DSBs can lead to inappropriate end-joining events, which commonly underlie oncogenic transformation due to chromosomal translocations. Typically, cells employ two main mechanisms to repair DSBs: homologous recombination (HR) and classical nonhomologous end joining (C-NHEJ). In addition, alternative error-prone DSB repair pathways, namely alternative end joining (alt-EJ) and single-strand annealing (SSA), have been recently shown to operate in many different conditions and to contribute to genome rearrangements and oncogenic transformation. Here, we review the mechanisms regulating DSB repair pathway choice, together with the potential interconnections between HR and the annealing-dependent error-prone DSB repair pathways.
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Affiliation(s)
- Raphael Ceccaldi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Beatrice Rondinelli
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
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592
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Michels J, Adam J, Goubar A, Obrist F, Damotte D, Robin A, Alifano M, Vitale I, Olaussen KA, Girard P, Cremer I, Castedo M, Soria JC, Kroemer G. Negative prognostic value of high levels of intracellular poly(ADP-ribose) in non-small cell lung cancer. Ann Oncol 2015; 26:2470-7. [PMID: 26387143 DOI: 10.1093/annonc/mdv393] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/13/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cisplatin-resistant non-small cell lung cancer (NSCLC) cells are often characterized by alterations in vitamin B-related metabolic processes, including the overexpression and hyperactivation of poly(ADP-ribose) polymerase 1 (PARP1) and the downregulation of pyridoxal kinase (PDXK), correlating with elevated apoptosis resistance. Low PDXK expression is an established negative prognostic factor in NSCLC. PATIENTS AND METHODS We determined by immunohistochemistry the expression of PARP1 and the level of its product, poly(ADP-ribose) (PAR), in two independent cohorts of patients with resected NSCLC. RESULTS Intratumoral high levels (above median) of PAR (but not PARP1 protein levels) had a negative prognostic impact in both the training (92 stage I subjects) and validation (133 stage I and II subjects) cohorts, as determined by univariate and multivariate analyses. The simultaneous assessment of PAR and PDXK protein levels improved risk stratification. CONCLUSION NSCLC patients with high intratumoral PARP1 activity (i.e. elevated PAR levels above median) and low PDXK expression (below median) had a dismal prognosis, while patients with low PARP1 activity and high PDXK expression had a favorable outcome. Altogether, these results underscore the clinical potential and possible therapeutic relevance of these biomarkers.
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Affiliation(s)
- J Michels
- INSERM UMR1138 Group 11, Cordeliers Research Centre, Paris Department of Medical Oncology, Gustave Roussy Comprehensive Cancer Center, Villejuif Paris-Sud University, Villejuif
| | - J Adam
- Paris-Sud University, Villejuif Department of Pathology, Gustave Roussy Comprehensive Cancer Center, Villejuif INSERM U981, Villejuif
| | | | - F Obrist
- INSERM UMR1138 Group 11, Cordeliers Research Centre, Paris Pierre and Marie Curie University, Paris
| | - D Damotte
- INSERM UMR1138 Group 11, Cordeliers Research Centre, Paris Pierre and Marie Curie University, Paris Department of Pathology and Thoracic Surgery, Cochin Hospital, AP-HP, Paris Paris Descartes University, Paris, France
| | | | - M Alifano
- Department of Pathology and Thoracic Surgery, Cochin Hospital, AP-HP, Paris Paris Descartes University, Paris, France
| | - I Vitale
- Regina Elena National Cancer Institute, Rome Department of Biology, University of Rome 'TorVergata', Rome, Italy
| | - K A Olaussen
- Paris-Sud University, Villejuif INSERM U981, Villejuif
| | - P Girard
- Thoracic Department, Mutualiste Montsouris Institute, Paris
| | - I Cremer
- INSERM UMR1138 Group 11, Cordeliers Research Centre, Paris Pierre and Marie Curie University, Paris Paris Descartes University, Paris, France
| | - M Castedo
- INSERM UMR1138 Group 11, Cordeliers Research Centre, Paris Pierre and Marie Curie University, Paris
| | - J-C Soria
- Paris-Sud University, Villejuif INSERM U981, Villejuif Department of Drug Development, Gustave Roussy Comprehensive Cancer Center, Villejuif
| | - G Kroemer
- INSERM UMR1138 Group 11, Cordeliers Research Centre, Paris Pierre and Marie Curie University, Paris Paris Descartes University, Paris, France Metabolomics Platform, Gustave Roussy Comprehensive Cancer Center, Villejuif Department of Biology, Georges Pompidou European Hospital, AP-HP, Paris, France
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593
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hPso4/hPrp19: a critical component of DNA repair and DNA damage checkpoint complexes. Oncogene 2015; 35:2279-86. [PMID: 26364595 DOI: 10.1038/onc.2015.321] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/15/2022]
Abstract
Genome integrity is vital to cellular homeostasis and its forfeiture is linked to deleterious consequences-cancer, immunodeficiency, genetic disorders and premature aging. The human ubiquitin ligase Pso4/Prp19 has emerged as a critical component of multiple DNA damage response (DDR) signaling networks. It not only senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, but also regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Accordingly, by virtue of its regulatory and structural interactions with key proteins critical for genome integrity-DNA double-strand break (DSB) repair, DNA interstrand crosslink repair, repair of stalled replication forks and DNA end joining-it fills a unique niche in restoring genomic integrity after multiple types of DNA damage and thus has a vital role in maintaining chromatin integrity and cellular functions. These properties may underlie its ability to thwart replicative senescence and, not surprisingly, have been linked to the self-renewal and colony-forming ability of murine hematopoietic stem cells. This review highlights recent advances in hPso4 research that provides a fascinating glimpse into the pleiotropic activities of a ubiquitously expressed multifunctional E3 ubiquitin ligase.
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594
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Wiegmans AP, Yap PY, Ward A, Lim YC, Khanna KK. Differences in Expression of Key DNA Damage Repair Genes after Epigenetic-Induced BRCAness Dictate Synthetic Lethality with PARP1 Inhibition. Mol Cancer Ther 2015; 14:2321-31. [PMID: 26294743 DOI: 10.1158/1535-7163.mct-15-0374] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022]
Abstract
The triple-negative breast cancer (TNBC) subtype represents a cancer that is highly aggressive with poor patient outcome. Current preclinical success has been gained through synthetic lethality, targeting genome instability with PARP inhibition in breast cancer cells that harbor silencing of the homologous recombination (HR) pathway. Histone deacetylase inhibitors (HDACi) are a class of drugs that mediate epigenetic changes in expression of HR pathway genes. Here, we compare the activity of the pan-HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), the class I/IIa HDAC inhibitor valproic acid (VPA), and the HDAC1/2-specific inhibitor romidepsin (ROMI) for their capability to regulate DNA damage repair gene expression and in sensitizing TNBC to PARPi. We found that two of the HDACis tested, SAHA and ROMI, but not VPA, indeed inhibit HR repair and that RAD51, BARD1, and FANCD2 represent key proteins whose inhibition is required for HDACi-mediated therapy with PARP inhibition in TNBC. We also observed that restoration of BRCA1 function stabilizes the genome compared with mutant BRCA1 that results in enhanced polyploid population after combination treatment with HDACi and PARPi. Furthermore, we found that overexpression of the key HR protein RAD51 represents a mechanism for this resistance, promoting aberrant repair and the enhanced polyploidy observed. These findings highlight the key components of HR in guiding synthetic lethality with PARP inhibition and support the rationale for utilizing the novel combination of HDACi and PARPi against TNBC in the clinical setting.
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Affiliation(s)
- Adrian P Wiegmans
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia. Tumour Microenvironment Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Pei-Yi Yap
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ambber Ward
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Yi Chieh Lim
- Translational Brain Cancer Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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595
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Jo U, Kim H. Exploiting the Fanconi Anemia Pathway for Targeted Anti-Cancer Therapy. Mol Cells 2015; 38:669-76. [PMID: 26194820 PMCID: PMC4546938 DOI: 10.14348/molcells.2015.0175] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 06/19/2015] [Indexed: 12/24/2022] Open
Abstract
Genome instability, primarily caused by faulty DNA repair mechanisms, drives tumorigenesis. Therapeutic interventions that exploit deregulated DNA repair in cancer have made considerable progress by targeting tumor-specific alterations of DNA repair factors, which either induces synthetic lethality or augments the efficacy of conventional chemotherapy and radiotherapy. The study of Fanconi anemia (FA), a rare inherited blood disorder and cancer predisposition syndrome, has been instrumental in understanding the extent to which DNA repair defects contribute to tumorigenesis. The FA pathway functions to resolve blocked replication forks in response to DNA interstrand cross-links (ICLs), and accumulating knowledge of its activation by the ubiquitin-mediated signaling pathway has provided promising therapeutic opportunities for cancer treatment. Here, we discuss recent advances in our understanding of FA pathway regulation and its potential application for designing tailored therapeutics that take advantage of deregulated DNA ICL repair in cancer.
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Affiliation(s)
- Ukhyun Jo
- Department of Pharmacological Sciences, Stony Brook University, New York 11794,
USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, Stony Brook University, New York 11794,
USA
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596
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Hopkins TA, Shi Y, Rodriguez LE, Solomon LR, Donawho CK, DiGiammarino EL, Panchal SC, Wilsbacher JL, Gao W, Olson AM, Stolarik DF, Osterling DJ, Johnson EF, Maag D. Mechanistic Dissection of PARP1 Trapping and the Impact on In Vivo Tolerability and Efficacy of PARP Inhibitors. Mol Cancer Res 2015. [PMID: 26217019 DOI: 10.1158/1541-7786.mcr-15-0191-t] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Poly(ADP-ribose) polymerases (PARP1, -2, and -3) play important roles in DNA damage repair. As such, a number of PARP inhibitors are undergoing clinical development as anticancer therapies, particularly in tumors with DNA repair deficits and in combination with DNA-damaging agents. Preclinical evidence indicates that PARP inhibitors potentiate the cytotoxicity of DNA alkylating agents. It has been proposed that a major mechanism underlying this activity is the allosteric trapping of PARP1 at DNA single-strand breaks during base excision repair; however, direct evidence of allostery has not been reported. Here the data reveal that veliparib, olaparib, niraparib, and talazoparib (BMN-673) potentiate the cytotoxicity of alkylating agents. Consistent with this, all four drugs possess PARP1 trapping activity. Using biochemical and cellular approaches, we directly probe the trapping mechanism for an allosteric component. These studies indicate that trapping is due to catalytic inhibition and not allostery. The potency of PARP inhibitors with respect to trapping and catalytic inhibition is linearly correlated in biochemical systems but is nonlinear in cells. High-content imaging of γH2Ax levels suggests that this is attributable to differential potentiation of DNA damage in cells. Trapping potency is inversely correlated with tolerability when PARP inhibitors are combined with temozolomide in mouse xenograft studies. As a result, PARP inhibitors with dramatically different trapping potencies elicit comparable in vivo efficacy at maximum tolerated doses. Finally, the impact of trapping on tolerability and efficacy is likely to be context specific. IMPLICATIONS Understanding the context-specific relationships of trapping and catalytic inhibition with both tolerability and efficacy will aid in determining the suitability of a PARP inhibitor for inclusion in a particular clinical regimen.
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Affiliation(s)
| | - Yan Shi
- AbbVie, Inc., North Chicago, Illinois
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597
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Abstract
Although the two B-family human DNA polymerases, pol δ and pol ε, are responsible for the bulk of nuclear genome replication, at least 14 additional polymerases have roles in nuclear DNA repair and replication. In this issue, newly reported crystal structures of two specialized A-family polymerases, pol δ and pol ε, expose these enzymes’ strategies for handling aberrant DNA ends.
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598
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van Schendel R, Roerink SF, Portegijs V, van den Heuvel S, Tijsterman M. Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis. Nat Commun 2015; 6:7394. [PMID: 26077599 PMCID: PMC4490562 DOI: 10.1038/ncomms8394] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/04/2015] [Indexed: 12/22/2022] Open
Abstract
Cells are protected from toxic DNA double-stranded breaks (DSBs) by a number of DNA repair mechanisms, including some that are intrinsically error prone, thus resulting in mutations. To what extent these mechanisms contribute to evolutionary diversification remains unknown. Here, we demonstrate that the A-family polymerase theta (POLQ) is a major driver of inheritable genomic alterations in Caenorhabditis elegans. Unlike somatic cells, which use non-homologous end joining (NHEJ) to repair DNA transposon-induced DSBs, germ cells use polymerase theta-mediated end joining, a conceptually simple repair mechanism requiring only one nucleotide as a template for repair. Also CRISPR/Cas9-induced genomic changes are exclusively generated through polymerase theta-mediated end joining, refuting a previously assumed requirement for NHEJ in their formation. Finally, through whole-genome sequencing of propagated populations, we show that only POLQ-proficient animals accumulate genomic scars that are abundantly present in genomes of wild C. elegans, pointing towards POLQ as a major driver of genome diversification.
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Affiliation(s)
- Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Sophie F. Roerink
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Vincent Portegijs
- Department of Biology, Division of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sander van den Heuvel
- Department of Biology, Division of Developmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marcel Tijsterman
- Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands
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599
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Sistigu A, Manic G, Obrist F, Vitale I. Trial watch - inhibiting PARP enzymes for anticancer therapy. Mol Cell Oncol 2015; 3:e1053594. [PMID: 27308587 DOI: 10.1080/23723556.2015.1053594] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/16/2015] [Accepted: 05/18/2015] [Indexed: 12/25/2022]
Abstract
Poly(ADP-ribose) polymerases (PARPs) are a members of family of enzymes that catalyze poly(ADP-ribosyl)ation (PARylation) and/or mono(ADP-ribosyl)ation (MARylation), two post-translational protein modifications involved in crucial cellular processes including (but not limited to) the DNA damage response (DDR). PARP1, the most abundant family member, is a nuclear protein that is activated upon sensing distinct types of DNA damage and contributes to their resolution by PARylating multiple DDR players. Recent evidence suggests that, along with DDR, activated PARP1 mediates a series of prosurvival and proapoptotic processes aimed at preserving genomic stability. Despite this potential oncosuppressive role, upregulation and/or overactivation of PARP1 or other PARP enzymes has been reported in a variety of human neoplasms. Over the last few decades, several pharmacologic inhibitors of PARP1 and PARP2 have been assessed in preclinical and clinical studies showing potent antineoplastic activity, particularly against homologous recombination (HR)-deficient ovarian and breast cancers. In this Trial Watch, we describe the impact of PARP enzymes and PARylation in cancer, discuss the mechanism of cancer cell killing by PARP1 inactivation, and summarize the results of recent clinical studies aimed at evaluating the safety and therapeutic profile of PARP inhibitors in cancer patients.
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Affiliation(s)
| | - Gwenola Manic
- Regina Elena National Cancer Institute , Rome, Italy
| | - Florine Obrist
- Université Paris-Sud/Paris XI, Le Kremlin-Bicêtre, France; INSERM, UMRS1138, Paris, France; Equipe 11 labelisée par la Ligue Nationale contre le Cancer, Center de Recherche des Cordeliers, Paris, France; Gustave Roussy Cancer Campus, Villejuif, France
| | - Ilio Vitale
- Regina Elena National Cancer Institute, Rome, Italy; Department of Biology, University of Rome "TorVergata", Rome, Italy
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600
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Lee JS, Grav LM, Lewis NE, Faustrup Kildegaard H. CRISPR/Cas9-mediated genome engineering of CHO cell factories: Application and perspectives. Biotechnol J 2015; 10:979-94. [PMID: 26058577 DOI: 10.1002/biot.201500082] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/10/2015] [Accepted: 05/11/2015] [Indexed: 12/13/2022]
Abstract
Chinese hamster ovary (CHO) cells are the most widely used production host for therapeutic proteins. With the recent emergence of CHO genome sequences, CHO cell line engineering has taken on a new aspect through targeted genome editing. The bacterial clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system enables rapid, easy and efficient engineering of mammalian genomes. It has a wide range of applications from modification of individual genes to genome-wide screening or regulation of genes. Facile genome editing using CRISPR/Cas9 empowers researchers in the CHO community to elucidate the mechanistic basis behind high level production of proteins and product quality attributes of interest. In this review, we describe the basis of CRISPR/Cas9-mediated genome editing and its application for development of next generation CHO cell factories while highlighting both future perspectives and challenges. As one of the main drivers for the CHO systems biology era, genome engineering with CRISPR/Cas9 will pave the way for rational design of CHO cell factories.
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Affiliation(s)
- Jae Seong Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lise Marie Grav
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego School of Medicine, CA, USA
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
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