1
|
Kindelay SM, Maggert KA. Insights into ribosomal DNA dominance and magnification through characterization of isogenic deletion alleles. Genetics 2024; 227:iyae063. [PMID: 38797870 DOI: 10.1093/genetics/iyae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/02/2024] [Indexed: 05/29/2024] Open
Abstract
The major loci for the large primary ribosomal RNA (rRNA) genes (35S rRNAs) exist as hundreds to thousands of tandem repeats in all organisms and dozens to hundreds in Drosophila. The highly repetitive nature of the ribosomal DNA (rDNA) makes it intrinsically unstable, and many conditions arise from the reduction in or magnification of copy number, but the conditions under which it does so remain unknown. By targeted DNA damage to the rDNA of the Y chromosome, we created and investigated a series of rDNA alleles. We found that complete loss of rDNA leads to lethality after the completion of embryogenesis, blocking larval molting and metamorphosis. We find that the resident retrotransposons-R1 and R2-are regulated by active rDNA such that reduction in copy number derepresses these elements. Their expression is highest during the early first instar, when loss of rDNA is lethal. Regulation of R1 and R2 may be related to their structural arrangement within the rDNA, as we find they are clustered in the flanks of the nucleolus organizing region (NOR; the cytological appearance of the rDNA). We assessed the complex nucleolar dominance relationship between X- and Y-linked rDNA using a histone H3.3-GFP reporter construct and incorporation at the NOR and found that dominance is controlled by rDNA copy number as at high multiplicity the Y-linked array is dominant, but at low multiplicity the X-linked array becomes derepressed. Finally, we found that multiple conditions that disrupt nucleolar dominance lead to increased rDNA magnification, suggesting that the phenomena of dominance and magnification are related, and a single mechanism may underlie and unify these two longstanding observations in Drosophila.
Collapse
Affiliation(s)
- Selina M Kindelay
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
| | - Keith A Maggert
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85721, USA
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| |
Collapse
|
2
|
Zhang Q, Yang L, Xiao H, Dang Z, Kuang X, Xiong Y, Zhu J, Huang Z, Li M. Pan-cancer analysis of chromothripsis-related gene expression patterns indicates an association with tumor immune and therapeutic agent responses. Front Oncol 2023; 13:1074955. [PMID: 36761982 PMCID: PMC9902954 DOI: 10.3389/fonc.2023.1074955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Chromothripsis is a catastrophic event involving numerous chromosomal rearrangements in confined genomic regions of one or a few chromosomes, causing complex effects on cells via the extensive structural variation. The development of whole-genome sequencing (WGS) has promoted great progress in exploring the mechanism and effect of chromothripsis. However, the gene expression characteristics of tumors undergone chromothripsis have not been well characterized. In this study, we found that the transcriptional profile of five tumor types experiencing chromothripsis is associated with an immune evasion phenotype. A gene set variation analysis (GSVA) was used to develop a CHP score, which is based on differentially expressed gene sets in the TCGA database, revealing that chromothripsis status in multiple cancers is consistent with an abnormal tumor immune microenvironment and immune cell cytotoxicity. Evaluation using four immunotherapy datasets uncovered the ability of the CHP score to predict immunotherapy response in diverse tumor types. In addition, the CHP score was found to be related to resistance against a variety of anti-tumor drugs, including anti-angiogenesis inhibitors and platinum genotoxins, while EGFR pathway inhibitors were found to possibly be sensitizers for high CHP score tumors. Univariate COX regression analysis indicated that the CHP score can be prognostic for several types of tumors. Our study has defined gene expression characteristics of tumors with chromothripsis, supporting the controversial link between chromothripsis and tumor immunity. We also describe the potential value of the CHP score in predicting the efficacy of immunotherapy and other treatments, elevating chromothripsis as a tool in clinical practice.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Zhou Huang
- *Correspondence: Zhou Huang, ; Mengxia Li,
| | - Mengxia Li
- *Correspondence: Zhou Huang, ; Mengxia Li,
| |
Collapse
|
3
|
Ruchert JM, Brady MM, McMahan S, Lacey KJ, Latta LC, Sekelsky J, Stoffregen EP. Blm helicase facilitates rapid replication of repetitive DNA sequences in early Drosophila development. Genetics 2022; 220:iyab169. [PMID: 34849849 PMCID: PMC8733427 DOI: 10.1093/genetics/iyab169] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/18/2021] [Indexed: 11/12/2022] Open
Abstract
The absence of functional BLM DNA helicase, a member of the RecQ family of helicases, is responsible for the rare human disorder Bloom Syndrome, which results in developmental abnormalities, DNA repair defects, genomic instability, and a predisposition to cancer. In Drosophila melanogaster, the orthologous Blm protein is essential during early development when the embryo is under the control of maternal gene products. We show that lack of functional maternal Blm during the syncytial cell cycles of Drosophila embryonic development results in severe nuclear defects and lethality. Amongst the small fraction of embryos from Blm mutant mothers that survive to adulthood, a prominent sex-bias favors the class that inherits less repetitive DNA content, which serves as an endogenous source of replication stress. This selection against repetitive DNA content reflects a role for Blm in facilitating replication through repetitive sequences during the rapid S-phases of syncytial cell cycles. During these syncytial cycles, Blm is not required for complex DNA double-strand break repair; however, the progeny sex-bias resulting from the absence of maternal Blm is exacerbated by repetitive DNA sequences and by the slowing of replication fork progression, suggesting that the essential role for Blm during this stage is to manage replication fork stress brought about by impediments to fork progression. Additionally, our data suggest that Blm is only required to manage this replication stress during embryonic development, and likely only during the early, rapid syncytial cell cycles, and not at later developmental stages. These results provide novel insights into Blm function throughout development.
Collapse
Affiliation(s)
- Jolee M Ruchert
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Morgan M Brady
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Susan McMahan
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Karly J Lacey
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Leigh C Latta
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
| | - Jeff Sekelsky
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric P Stoffregen
- Physical, Life, Movement & Sport Sciences, Lewis-Clark State College, Lewiston, ID 83501, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- SPIRE Postdoctoral Fellowship Program, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
4
|
DNA ligase IV mutations confer shorter lifespan and increased sensitivity to nutrient stress in Drosophila melanogaster. J Appl Genet 2021; 63:141-144. [PMID: 34817771 PMCID: PMC8755683 DOI: 10.1007/s13353-021-00637-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 12/04/2022]
Abstract
The nonhomologous end-joining pathway is a primary DNA double-strand break repair pathway in eukaryotes. DNA ligase IV (Lig4) catalyzes the final step of DNA end ligation in this pathway. Partial loss of Lig4 in mammals causes Lig4 syndrome, while complete loss is embryonically lethal. DNA ligase 4 (DNAlig4) null Drosophila melanogaster is viable, but sensitive to ionizing radiation during early development. We proposed to explore if DNAlig4 loss induced other long-term sensitivities and defects in D. melanogaster. We demonstrated that DNAlig4 mutant strains had decreased lifespan and lower resistance to nutrient deprivation, indicating Lig4 is required for maintaining health and longevity in D. melanogaster.
Collapse
|
5
|
Nazaryan-Petersen L, Bjerregaard VA, Nielsen FC, Tommerup N, Tümer Z. Chromothripsis and DNA Repair Disorders. J Clin Med 2020; 9:jcm9030613. [PMID: 32106411 PMCID: PMC7141117 DOI: 10.3390/jcm9030613] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/15/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Chromothripsis is a mutational mechanism leading to complex and relatively clustered chromosomal rearrangements, resulting in diverse phenotypic outcomes depending on the involved genomic landscapes. It may occur both in the germ and the somatic cells, resulting in congenital and developmental disorders and cancer, respectively. Asymptomatic individuals may be carriers of chromotriptic rearrangements and experience recurrent reproductive failures when two or more chromosomes are involved. Several mechanisms are postulated to underlie chromothripsis. The most attractive hypothesis involves chromosome pulverization in micronuclei, followed by the incorrect reassembly of fragments through DNA repair to explain the clustered nature of the observed complex rearrangements. Moreover, exogenous or endogenous DNA damage induction and dicentric bridge formation may be involved. Chromosome instability is commonly observed in the cells of patients with DNA repair disorders, such as ataxia telangiectasia, Nijmegen breakage syndrome, and Bloom syndrome. In addition, germline variations of TP53 have been associated with chromothripsis in sonic hedgehog medulloblastoma and acute myeloid leukemia. In the present review, we focus on the underlying mechanisms of chromothripsis and the involvement of defective DNA repair genes, resulting in chromosome instability and chromothripsis-like rearrangements.
Collapse
Affiliation(s)
- Lusine Nazaryan-Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (L.N.-P.); (N.T.)
- Center for Genomic Medicine, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Victoria Alexandra Bjerregaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark;
| | | | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (L.N.-P.); (N.T.)
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark;
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence: ; Tel.: +45-292-048-55
| |
Collapse
|
6
|
Cassidy D, Epiney DG, Salameh C, Zhou LT, Salomon RN, Schirmer AE, McVey M, Bolterstein E. Evidence for premature aging in a Drosophila model of Werner syndrome. Exp Gerontol 2019; 127:110733. [PMID: 31518666 PMCID: PMC6935377 DOI: 10.1016/j.exger.2019.110733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 10/26/2022]
Abstract
Werner syndrome (WS) is an autosomal recessive progeroid disease characterized by patients' early onset of aging, increased risk of cancer and other age-related pathologies. WS is caused by mutations in WRN, a RecQ helicase that has essential roles responding to DNA damage and preventing genomic instability. While human WRN has both an exonuclease and helicase domain, Drosophila WRNexo has high genetic and functional homology to only the exonuclease domain of WRN. Like WRN-deficient human cells, Drosophila WRNexo null mutants (WRNexoΔ) are sensitive to replication stress, demonstrating mechanistic similarities between these two models. Compared to age-matched wild-type controls, WRNexoΔ flies exhibit increased physiological signs of aging, such as shorter lifespans, higher tumor incidence, muscle degeneration, reduced climbing ability, altered behavior, and reduced locomotor activity. Interestingly, these effects are more pronounced in females suggesting sex-specific differences in the role of WRNexo in aging. This and future mechanistic studies will contribute to our knowledge in linking faulty DNA repair mechanisms with the process of aging.
Collapse
Affiliation(s)
- Deirdre Cassidy
- Department of Biology, Northeastern Illinois University, 5500 N. Saint Louis Ave, Chicago, IL 60625, United States of America
| | - Derek G Epiney
- Department of Biology, Northeastern Illinois University, 5500 N. Saint Louis Ave, Chicago, IL 60625, United States of America
| | - Charlotte Salameh
- Department of Biology, Northeastern Illinois University, 5500 N. Saint Louis Ave, Chicago, IL 60625, United States of America
| | - Luhan T Zhou
- Department of Biology, Northeastern Illinois University, 5500 N. Saint Louis Ave, Chicago, IL 60625, United States of America
| | - Robert N Salomon
- Department of Pathology, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA 20111, United States of America
| | - Aaron E Schirmer
- Department of Biology, Northeastern Illinois University, 5500 N. Saint Louis Ave, Chicago, IL 60625, United States of America.
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Ave, Ste. 4741, Medford, MA 20155, United States of America.
| | - Elyse Bolterstein
- Department of Biology, Northeastern Illinois University, 5500 N. Saint Louis Ave, Chicago, IL 60625, United States of America.
| |
Collapse
|
7
|
Fischer KE, Riddle NC. Sex Differences in Aging: Genomic Instability. J Gerontol A Biol Sci Med Sci 2019; 73:166-174. [PMID: 28575157 DOI: 10.1093/gerona/glx105] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/26/2017] [Indexed: 11/13/2022] Open
Abstract
Aging is characterized by decreasing physiological integration, reduced function, loss of resilience, and increased risk of death. Paradoxically, although women live longer, they suffer greater morbidity particularly late in life. These sex differences in human lifespan and healthspan are consistently observed in all countries and during every era for which reliable data exist. While these differences are ubiquitous in humans, evidence of sex differences in longevity and health for other species is more equivocal. Among fruit flies, nematodes, and mice, sex differences in lifespan vary depending on strain and treatment. In this review, we focus on sex differences in age-related alterations in DNA damage and mutation rates, telomere attrition, epigenetics, and nuclear architecture. We find that robust sex differences exist, eg, the higher incidence of DNA damage in men compared to women, but sex differences are not often conserved between species. For most mechanisms reviewed here, there are insufficient data to make a clear determination regarding the impact of sex, largely because sex differences have not been analyzed. Overall, our findings reveal an urgent need for well-designed studies that explicitly examine sex differences in molecular drivers of aging.
Collapse
Affiliation(s)
| | - Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham
| |
Collapse
|
8
|
León-Ortiz AM, Panier S, Sarek G, Vannier JB, Patel H, Campbell PJ, Boulton SJ. A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination. Mol Cell 2018; 69:292-305.e6. [PMID: 29351848 PMCID: PMC5783719 DOI: 10.1016/j.molcel.2017.12.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/02/2017] [Accepted: 12/18/2017] [Indexed: 11/25/2022]
Abstract
Erroneous DNA repair by heterologous recombination (Ht-REC) is a potential threat to genome stability, but evidence supporting its prevalence is lacking. Here we demonstrate that recombination is possible between heterologous sequences and that it is a source of chromosomal alterations in mitotic and meiotic cells. Mechanistically, we find that the RTEL1 and HIM-6/BLM helicases and the BRCA1 homolog BRC-1 counteract Ht-REC in Caenorhabditis elegans, whereas mismatch repair does not. Instead, MSH-2/6 drives Ht-REC events in rtel-1 and brc-1 mutants and excessive crossovers in rtel-1 mutant meioses. Loss of vertebrate Rtel1 also causes a variety of unusually large and complex structural variations, including chromothripsis, breakage-fusion-bridge events, and tandem duplications with distant intra-chromosomal insertions, whose structure are consistent with a role for RTEL1 in preventing Ht-REC during break-induced replication. Our data establish Ht-REC as an unappreciated source of genome instability that underpins a novel class of complex genome rearrangements that likely arise during replication stress.
Collapse
Affiliation(s)
- Ana María León-Ortiz
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephanie Panier
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Grzegorz Sarek
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jean-Baptiste Vannier
- Telomere Replication and Stability Group, MRC London Institute of Medical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| |
Collapse
|
9
|
Annealing of Complementary DNA Sequences During Double-Strand Break Repair in Drosophila Is Mediated by the Ortholog of SMARCAL1. Genetics 2017; 206:467-480. [PMID: 28258182 DOI: 10.1534/genetics.117.200238] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 12/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) pose a serious threat to genomic integrity. If unrepaired, they can lead to chromosome fragmentation and cell death. If repaired incorrectly, they can cause mutations and chromosome rearrangements. DSBs are repaired using end-joining or homology-directed repair strategies, with the predominant form of homology-directed repair being synthesis-dependent strand annealing (SDSA). SDSA is the first defense against genomic rearrangements and information loss during DSB repair, making it a vital component of cell health and an attractive target for chemotherapeutic development. SDSA has also been proposed to be the primary mechanism for integration of large insertions during genome editing with CRISPR/Cas9. Despite the central role for SDSA in genome stability, little is known about the defining step: annealing. We hypothesized that annealing during SDSA is performed by the annealing helicase SMARCAL1, which can anneal RPA-coated single DNA strands during replication-associated DNA damage repair. We used unique genetic tools in Drosophila melanogaster to test whether the fly ortholog of SMARCAL1, Marcal1, mediates annealing during SDSA. Repair that requires annealing is significantly reduced in Marcal1 null mutants in both synthesis-dependent and synthesis-independent (single-strand annealing) assays. Elimination of the ATP-binding activity of Marcal1 also reduced annealing-dependent repair, suggesting that the annealing activity requires translocation along DNA. Unlike the null mutant, however, the ATP-binding defect mutant showed reduced end joining, shedding light on the interaction between SDSA and end-joining pathways.
Collapse
|
10
|
Abstract
The accumulation of somatic mutations in adult stem cells contributes to the decline of tissue functions and cancer initiation. In this issue of Cell Stem Cell, Siudeja et al. (2015) investigate the rate and mechanism of naturally occurring mutations in Drosophila midgut intestinal stem cells during aging and find high-frequency mutations arising from multiple mechanisms.
Collapse
Affiliation(s)
- Qi Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Y Tony Ip
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
11
|
Siudeja K, Nassari S, Gervais L, Skorski P, Lameiras S, Stolfa D, Zande M, Bernard V, Frio TR, Bardin AJ. Frequent Somatic Mutation in Adult Intestinal Stem Cells Drives Neoplasia and Genetic Mosaicism during Aging. Cell Stem Cell 2015; 17:663-674. [PMID: 26607382 PMCID: PMC5138153 DOI: 10.1016/j.stem.2015.09.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 07/31/2015] [Accepted: 09/18/2015] [Indexed: 12/21/2022]
Abstract
Adult stem cells may acquire mutations that modify cellular behavior, leading to functional declines in homeostasis or providing a competitive advantage resulting in premalignancy. However, the frequency, phenotypic impact, and mechanisms underlying spontaneous mutagenesis during aging are unclear. Here, we report two mechanisms of genome instability in adult Drosophila intestinal stem cells (ISCs) that cause phenotypic alterations in the aging intestine. First, we found frequent loss of heterozygosity arising from mitotic homologous recombination in ISCs that results in genetic mosaicism. Second, somatic deletion of DNA sequences and large structural rearrangements, resembling those described in cancers and congenital diseases, frequently result in gene inactivation. Such modifications induced somatic inactivation of the X-linked tumor suppressor Notch in ISCs, leading to spontaneous neoplasias in wild-type males. Together, our findings reveal frequent genomic modification in adult stem cells and show that somatic genetic mosaicism has important functional consequences on aging tissues. The aging Drosophila intestine is genetically mosaic Somatic recombination, genomic deletions, and rearrangements occur in aging ISCs Somatic inactivation of the tumor-suppressor Notch causes male-specific neoplasia
Collapse
Affiliation(s)
- Katarzyna Siudeja
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France
| | - Sonya Nassari
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France
| | - Louis Gervais
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France
| | - Patricia Skorski
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France
| | - Sonia Lameiras
- Next-Generation Sequencing Platform, Institut Curie, Hôpital Curie, 8 rue Louis-Thuillier, 75248 Paris Cedex 05, France
| | - Donato Stolfa
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France
| | - Maria Zande
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France
| | - Virginie Bernard
- Next-Generation Sequencing Platform, Institut Curie, Hôpital Curie, 8 rue Louis-Thuillier, 75248 Paris Cedex 05, France
| | - Thomas Rio Frio
- Next-Generation Sequencing Platform, Institut Curie, Hôpital Curie, 8 rue Louis-Thuillier, 75248 Paris Cedex 05, France
| | - Allison J Bardin
- Institut Curie, 26 rue d'Ulm, F-75248 Paris, France; CNRS UMR3215, F-75248 Paris, France; INSERM U934, F-75248 Paris, France.
| |
Collapse
|
12
|
Grupp K, Roettger L, Kluth M, Hube-Magg C, Simon R, Lebok P, Minner S, Tsourlakis MC, Koop C, Graefen M, Adam M, Haese A, Wittmer C, Sauter G, Wilczak W, Huland H, Schlomm T, Steurer S, Krech T. Expression of DNA ligase IV is linked to poor prognosis and characterizes a subset of prostate cancers harboring TMPRSS2:ERG fusion and PTEN deletion. Oncol Rep 2015; 34:1211-20. [PMID: 26134445 DOI: 10.3892/or.2015.4080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/18/2015] [Indexed: 11/05/2022] Open
Abstract
DNA ligases are essential for the maintenance of genome integrity as they are indispensable for DNA replication, recombination and repair. The present study was undertaken to gain insights into the prevalence and clinical significance of ligase IV (LIG4) expression in prostate cancer. A total of 11,152 prostate cancer specimens were analyzed by immunohistochemistry for LIG4 expression. Results were compared to follow-up data, ERG status and deletions at PTEN, 3p13, 5q21 and 6q15. LIG4 expression was predominantly localized in the nucleus of the cells with increased intensities in malignant as compared to benign prostate epithelium. In prostate cancer, LIG4 expression was found in 91% of interpretable tumors, including 12% cancers with weak, 23% with moderate and 56% with strong LIG4 positivity. Strong LIG4 expression was tightly linked to advanced Gleason score (P<0.0001) and positive nodal involvement (P=0.03). There was a remarkable accumulation of strong LIG4 expression in tumors harboring TMPRSS2:ERG fusion and PTEN deletions (P<0.0001 each). High LIG4 expression was also tightly related to early biochemical recurrence when all tumors (P<0.0001) or the subsets of ERG-negative (P=0.0004) or ERG-positive prostate cancers (P=0.006) were analyzed. Multivariate analysis including parameters that are available before surgery demonstrated independent association with biochemical recurrence for advanced Gleason grade on biopsy, high preoperative PSA level, high clinical stage (P<0.0001 each) and for LIG4 immunostaining (P=0.03). Our study identifies LIG4 as a predictor of an increased risk for early PSA recurrence in prostate cancer. Moreover, the strong association with TMPRSS2:ERG fusion and PTEN deletions suggest important interactions between these pathways in prostate cancers.
Collapse
Affiliation(s)
- Katharina Grupp
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Laura Roettger
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Patrick Lebok
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | | | - Christina Koop
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Markus Graefen
- Martini‑Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Meike Adam
- Martini‑Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Alexander Haese
- Martini‑Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Corinna Wittmer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Hartwig Huland
- Martini‑Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Thorsten Schlomm
- Martini‑Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| | - Till Krech
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, D-20246 Hamburg, Germany
| |
Collapse
|
13
|
Böttcher R, Hollmann M, Merk K, Nitschko V, Obermaier C, Philippou-Massier J, Wieland I, Gaul U, Förstemann K. Efficient chromosomal gene modification with CRISPR/cas9 and PCR-based homologous recombination donors in cultured Drosophila cells. Nucleic Acids Res 2014; 42:e89. [PMID: 24748663 PMCID: PMC4066747 DOI: 10.1093/nar/gku289] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/26/2014] [Accepted: 03/26/2014] [Indexed: 12/26/2022] Open
Abstract
The ability to edit the genome is essential for many state-of-the-art experimental paradigms. Since DNA breaks stimulate repair, they can be exploited to target site-specific integration. The clustered, regularly interspaced, short palindromic repeats (CRISPR)/cas9 system from Streptococcus pyogenes has been harnessed into an efficient and programmable nuclease for eukaryotic cells. We thus combined DNA cleavage by cas9, the generation of homologous recombination donors by polymerase chain reaction (PCR) and transient depletion of the non-homologous end joining factor lig4. Using cultured Drosophila melanogaster S2-cells and the phosphoglycerate kinase gene as a model, we reached targeted integration frequencies of up to 50% in drug-selected cell populations. Homology arms as short as 29 nt appended to the PCR primer resulted in detectable integration, slightly longer extensions are beneficial. We confirmed established rules for S. pyogenes cas9 sgRNA design and demonstrate that the complementarity region allows length variation and 5'-extensions. This enables generation of U6-promoter fusion templates by overlap-extension PCR with a standardized protocol. We present a series of PCR template vectors for C-terminal protein tagging and clonal Drosophila S2 cell lines with stable expression of a myc-tagged cas9 protein. The system can be used for epitope tagging or reporter gene knock-ins in an experimental setup that can in principle be fully automated.
Collapse
Affiliation(s)
- Romy Böttcher
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Manuel Hollmann
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Karin Merk
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Volker Nitschko
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Christina Obermaier
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Julia Philippou-Massier
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Isabella Wieland
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Ulrike Gaul
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| | - Klaus Förstemann
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, D-81377 München, Germany
| |
Collapse
|
14
|
Milán M, Clemente-Ruiz M, Dekanty A, Muzzopappa M. Aneuploidy and tumorigenesis in Drosophila. Semin Cell Dev Biol 2014; 28:110-5. [DOI: 10.1016/j.semcdb.2014.03.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/03/2014] [Accepted: 03/10/2014] [Indexed: 12/15/2022]
|
15
|
Dekanty A, Barrio L, Milán M. Contributions of DNA repair, cell cycle checkpoints and cell death to suppressing the DNA damage-induced tumorigenic behavior of Drosophila epithelial cells. Oncogene 2014; 34:978-85. [DOI: 10.1038/onc.2014.42] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 02/04/2014] [Accepted: 02/07/2014] [Indexed: 12/21/2022]
|
16
|
Grabarz A, Guirouilh-Barbat J, Barascu A, Pennarun G, Genet D, Rass E, Germann SM, Bertrand P, Hickson ID, Lopez BS. A role for BLM in double-strand break repair pathway choice: prevention of CtIP/Mre11-mediated alternative nonhomologous end-joining. Cell Rep 2013; 5:21-8. [PMID: 24095737 DOI: 10.1016/j.celrep.2013.08.034] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/25/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022] Open
Abstract
The choice of the appropriate double-strand break (DSB) repair pathway is essential for the maintenance of genomic stability. Here, we show that the Bloom syndrome gene product, BLM, counteracts CtIP/MRE11-dependent long-range deletions (>200 bp) generated by alternative end-joining (A-EJ). BLM represses A-EJ in an epistatic manner with 53BP1 and RIF1 and is required for ionizing-radiation-induced 53BP1 focus assembly. Conversely, in the absence of 53BP1 or RIF1, BLM promotes formation of A-EJ long deletions, consistent with a role for BLM in DSB end resection. These data highlight a dual role for BLM that influences the DSB repair pathway choice: (1) protection against CtIP/MRE11 long-range deletions associated with A-EJ and (2) promotion of DNA resection. These antagonist roles can be regulated, according to cell-cycle stage, by interacting partners such as 53BP1 and TopIII, to avoid unscheduled resection that might jeopardize genome integrity.
Collapse
Affiliation(s)
- Anastazja Grabarz
- CNRS UMR217, CEA, DSV, Institut de Radiobiologie Cellulaire et Moléculaire, 18 Route du Panorama, Fontenay aux Roses F-92265, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
|
18
|
Greer C, Lee M, Westerhof M, Milholland B, Spokony R, Vijg J, Secombe J. Myc-dependent genome instability and lifespan in Drosophila. PLoS One 2013; 8:e74641. [PMID: 24040302 PMCID: PMC3765364 DOI: 10.1371/journal.pone.0074641] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/05/2013] [Indexed: 01/21/2023] Open
Abstract
The Myc family of transcription factors are key regulators of cell growth and proliferation that are dysregulated in a large number of human cancers. When overexpressed, Myc family proteins also cause genomic instability, a hallmark of both transformed and aging cells. Using an in vivo lacZ mutation reporter, we show that overexpression of Myc in Drosophila increases the frequency of large genome rearrangements associated with erroneous repair of DNA double-strand breaks (DSBs). In addition, we find that overexpression of Myc shortens adult lifespan and, conversely, that Myc haploinsufficiency reduces mutation load and extends lifespan. Our data provide the first evidence that Myc may act as a pro-aging factor, possibly through its ability to greatly increase genome instability.
Collapse
Affiliation(s)
- Christina Greer
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Maaike Westerhof
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Rebecca Spokony
- Department of Human Genetics, The University of Chicago, Knapp Center for Biomedical Discovery, Chicago, Illinois, United States of America
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
| |
Collapse
|
19
|
Yamanishi A, Yusa K, Horie K, Tokunaga M, Kusano K, Kokubu C, Takeda J. Enhancement of microhomology-mediated genomic rearrangements by transient loss of mouse Bloom syndrome helicase. Genome Res 2013; 23:1462-73. [PMID: 23908384 PMCID: PMC3759722 DOI: 10.1101/gr.152744.112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bloom syndrome, an autosomal recessive disorder of the BLM gene, confers predisposition to a broad spectrum of early-onset cancers in multiple tissue types. Loss of genomic integrity is a primary hallmark of such human malignancies, but many studies using disease-affected specimens are limited in that they are retrospective and devoid of an appropriate experimental control. To overcome this, we devised an experimental system to recapitulate the early molecular events in genetically engineered mouse embryonic stem cells, in which cells undergoing loss of heterozygosity (LOH) can be enriched after inducible down-regulation of Blm expression, with or without site-directed DNA double-strand break (DSB) induction. Transient loss of BLM increased the rate of LOH, whose breakpoints were distributed along the chromosome. Combined with site-directed DSB induction, loss of BLM synergistically increased the rate of LOH and concentrated the breakpoints around the targeted chromosomal region. We characterized the LOH events using specifically tailored genomic tools, such as high-resolution array comparative genomic hybridization and high-density single nucleotide polymorphism genotyping, revealing that the combination of BLM suppression and DSB induction enhanced genomic rearrangements, including deletions and insertions, whose breakpoints were clustered in genomic inverted repeats and associated with junctional microhomologies. Our experimental approach successfully uncovered the detailed molecular mechanisms of as-yet-uncharacterized loss of heterozygosities and reveals the significant contribution of microhomology-mediated genomic rearrangements, which could be widely applicable to the early steps of cancer formation in general.
Collapse
Affiliation(s)
- Ayako Yamanishi
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | | | |
Collapse
|
20
|
Zhou LP, Luan H, Dong XH, Jin GJ, Man DL, Shang H. Lack of association between LIG4 gene polymorphisms and the risk of breast cancer: a HuGE review and meta-analysis. Asian Pac J Cancer Prev 2013; 13:3417-22. [PMID: 22994770 DOI: 10.7314/apjcp.2012.13.7.3417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Non-homologous end joining (NHEJ) is one of the pathways of repair of DNA double-strand breaks. A number of genes involved in NHEJ have been implicated as breast cancer susceptibility genes such as LIG4. However, some studies have generated conflicting results. The aim of this Human Genome Epidemiology (HuGE) review and meta-analysis was to investigate association between LIG4 gene polymorphisms in the NHEJ pathway and breast cancer risk. METHODS Studies focusing on the relationship between LIG4 gene polymorphisms and susceptibility to breast cancer were selected from the Pubmed, Cochrane library, Embase, Web of Science, Springerlink, CNKI and CBM databases. Data were extracted by two independent reviewers and the meta-analysis was performed with Review Manager Version 5.1.6 and STATA Version 12.0 software, calculating odds ratios (ORs) with 95% confidence intervals (95%CIs). RESULTS According to the inclusion criteria, we final included seven studies with a total of 10,321 breast cancer cases and 10,160 healthy controls in the meta-analysis. The results showed no association between LIG4 gene polymorphisms (rs1805386 T>C, rs1805389 C>T, rs1805388 C>T and rs2232641 A>G) and breast cancer risk, suggesting that the mutant situation of these SNPs neither increased nor decreased the risk for breast cancer. In the subgroup analysis by Hardy-Weinberg equilibrium (HWE) and ethnicity, we also found no associations between the variants of LIG4 gene and breast cancer risk among HWE, non-HWE, Caucasians, Asians and Africans. CONCLUSION This meta-analysis suggests that there is a lack of any association between LIG4 gene polymorphisms and the risk of breast cancer.
Collapse
Affiliation(s)
- Li-Ping Zhou
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, China
| | | | | | | | | | | |
Collapse
|
21
|
Gonzalez C. Drosophila melanogaster: a model and a tool to investigate malignancy and identify new therapeutics. Nat Rev Cancer 2013; 13:172-83. [PMID: 23388617 DOI: 10.1038/nrc3461] [Citation(s) in RCA: 206] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
For decades, lower-model organisms such as Drosophila melanogaster have often provided the first glimpse into the mechanism of action of human cancer-related proteins, thus making a substantial contribution to elucidating the molecular basis of the disease. More recently, D. melanogaster strains that are engineered to recapitulate key aspects of specific types of human cancer have been paving the way for the future role of this 'workhorse' of biomedical research, helping to further investigate the process of malignancy, and serving as platforms for therapeutic drug discovery.
Collapse
Affiliation(s)
- Cayetano Gonzalez
- IRB-Barcelona, c/Baldiri Reixac 10-12, Barcelona, Spain. gonzalez@ irbbarcelona.org
| |
Collapse
|