101
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Helman E, Lawrence MS, Stewart C, Sougnez C, Getz G, Meyerson M. Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing. Genome Res 2014; 24:1053-63. [PMID: 24823667 PMCID: PMC4079962 DOI: 10.1101/gr.163659.113] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 04/03/2014] [Indexed: 01/27/2023]
Abstract
Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied TranspoSeq, a computational framework that identifies retrotransposon insertions from sequencing data, to whole genomes from 200 tumor/normal pairs across 11 tumor types as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Project. In addition to novel germline polymorphisms, we find 810 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal, and endometrial carcinomas. Many somatic retrotransposon insertions occur in known cancer genes. We find that high somatic retrotransposition rates in tumors are associated with high rates of genomic rearrangement and somatic mutation. Finally, we developed TranspoSeq-Exome to interrogate an additional 767 tumor samples with hybrid-capture exome data and discovered 35 novel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of the PTEN tumor suppressor gene. The results of this large-scale, comprehensive analysis of retrotransposon movement across tumor types suggest that somatic retrotransposon insertions may represent an important class of structural variation in cancer.
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Affiliation(s)
- Elena Helman
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | | | - Chip Stewart
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | - Carrie Sougnez
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Matthew Meyerson
- Harvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA
- Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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102
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Saponaro M, Kantidakis T, Mitter R, Kelly GP, Heron M, Williams H, Söding J, Stewart A, Svejstrup JQ. RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell 2014; 157:1037-49. [PMID: 24836610 PMCID: PMC4032574 DOI: 10.1016/j.cell.2014.03.048] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 01/21/2014] [Accepted: 03/13/2014] [Indexed: 01/03/2023]
Abstract
RECQL5 is the sole member of the RECQ family of helicases associated with RNA polymerase II (RNAPII). We now show that RECQL5 is a general elongation factor that is important for preserving genome stability during transcription. Depletion or overexpression of RECQL5 results in corresponding shifts in the genome-wide RNAPII density profile. Elongation is particularly affected, with RECQL5 depletion causing a striking increase in the average rate, concurrent with increased stalling, pausing, arrest, and/or backtracking (transcription stress). RECQL5 therefore controls the movement of RNAPII across genes. Loss of RECQL5 also results in the loss or gain of genomic regions, with the breakpoints of lost regions located in genes and common fragile sites. The chromosomal breakpoints overlap with areas of elevated transcription stress, suggesting that RECQL5 suppresses such stress and its detrimental effects, and thereby prevents genome instability in the transcribed region of genes.
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Affiliation(s)
- Marco Saponaro
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, EN6 3LD, UK
| | - Theodoros Kantidakis
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, EN6 3LD, UK
| | - Richard Mitter
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Gavin P Kelly
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Mark Heron
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Hannah Williams
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, EN6 3LD, UK
| | - Johannes Söding
- Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Aengus Stewart
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, EN6 3LD, UK.
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103
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Xiao F, Kim YC, Snyder C, Wen H, Chen PX, Luo J, Becirovic D, Downs B, Cowan KH, Lynch H, Wang SM. Genome instability in blood cells of a BRCA1+ breast cancer family. BMC Cancer 2014; 14:342. [PMID: 24884718 PMCID: PMC4031489 DOI: 10.1186/1471-2407-14-342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/07/2014] [Indexed: 11/28/2022] Open
Abstract
Background BRCA1 plays an essential role in maintaining genome stability. Inherited BRCA1 germline mutation (BRCA1+) is a determined genetic predisposition leading to high risk of breast cancer. While BRCA1+ induces breast cancer by causing genome instability, most of the knowledge is known about somatic genome instability in breast cancer cells but not germline genome instability. Methods Using the exome-sequencing method, we analyzed the genomes of blood cells in a typical BRCA1+ breast cancer family with an exon 13-duplicated founder mutation, including six breast cancer-affected and two breast cancer unaffected members. Results We identified 23 deleterious mutations in the breast cancer-affected family members, which are absent in the unaffected members. Multiple mutations damaged functionally important and breast cancer-related genes, including transcriptional factor BPTF and FOXP1, ubiquitin ligase CUL4B, phosphorylase kinase PHKG2, and nuclear receptor activator SRA1. Analysis of the mutations between the mothers and daughters shows that most mutations were germline mutation inherited from the ancestor(s) while only a few were somatic mutation generated de novo. Conclusion Our study indicates that BRCA1+ can cause genome instability with both germline and somatic mutations in non-breast cells.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Henry Lynch
- Department of Genetics, Cell Biology and Anatomy, Omaha, NE 68198, USA.
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104
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Jang MK, Shen K, McBride AA. Papillomavirus genomes associate with BRD4 to replicate at fragile sites in the host genome. PLoS Pathog 2014; 10:e1004117. [PMID: 24832099 PMCID: PMC4022725 DOI: 10.1371/journal.ppat.1004117] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/28/2014] [Indexed: 12/11/2022] Open
Abstract
It has long been recognized that oncogenic viruses often integrate close to common fragile sites. The papillomavirus E2 protein, in complex with BRD4, tethers the viral genome to host chromatin to ensure persistent replication. Here, we map these targets to a number of large regions of the human genome and name them Persistent E2 and BRD4-Broad Localized Enrichments of Chromatin or PEB-BLOCs. PEB-BLOCs frequently contain deletions, have increased rates of asynchronous DNA replication, and are associated with many known common fragile sites. Cell specific fragile sites were mapped in human C-33 cervical cells by FANCD2 ChIP-chip, confirming the association with PEB-BLOCs. HPV-infected cells amplify viral DNA in nuclear replication foci and we show that these form adjacent to PEB-BLOCs. We propose that HPV replication, which hijacks host DNA damage responses, occurs adjacent to highly susceptible fragile sites, greatly increasing the chances of integration here, as is found in HPV-associated cancers. Papillomavirus cause persistent, but mostly self-limiting, infections of the host epithelium. However, a subset of oncogenic papillomaviruses is the causative agent of certain human cancers. In persistent infection the viral genomes are tethered to host chromosomes to maintain and partition the extrachromosomal viral genomes to daughter cells. However, in cancers viral DNA is often found integrated close to common fragile sites, regions prone to breakage, amplification and deletion. We show that the viral E2 and cellular BRD4 proteins are associated with fragile regions of the human genome and nucleate viral replication foci at these sites. This is a resourceful strategy for a virus that uses the host DNA damage response to amplify viral DNA. However, the outcome may be increased accidental integration of viral DNA, which in the case of the oncogenic viruses can promote carcinogenesis.
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Affiliation(s)
- Moon Kyoo Jang
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kui Shen
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alison A. McBride
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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105
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Arefi M, Robledo C, Peñarrubia MJ, García de Coca A, Cordero M, Hernández-Rivas JM, García JL. Genomic analysis of clonal eosinophils by CGH arrays reveals new genetic regions involved in chronic eosinophilia. Eur J Haematol 2014; 93:422-8. [PMID: 24813417 DOI: 10.1111/ejh.12379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2014] [Indexed: 12/22/2022]
Abstract
To assess the presence of genetic imbalances in patients with myeloproliferative neoplasms (MPNs), 38 patients with chronic eosinophilia were studied by array comparative genomic hybridization (aCGH): seven had chronic myelogenous leukaemia (CML), BCR-ABL1 positive, nine patients had myeloproliferative neoplasia Ph- (MPN-Ph-), three had a myeloid neoplasm associated with a PDGFRA rearrangement, and the remaining two cases were Lymphoproliferative T neoplasms associated with eosinophilia. In addition, 17 patients had a secondary eosinophilia and were used as controls. Eosinophilic enrichment was carried out in all cases. Genomic imbalances were found in 76% of all MPN patients. Losses on 20q were the most frequent genetic abnormality in MPNs (32%), affected the three types of MPN studied. This study also found losses at 11q13.3 in 26% of patients with MPN-Ph- and in 19p13.11 in two of the three patients with an MPN associated with a PDGFRA rearrangement. In addition, 29% of patients with CML had losses on 8q24. In summary, aCGH revealed clonality in eosinophils in most MPNs, suggesting that it could be a useful technique for defining clonality in these diseases. The presence of genetic losses in new regions could provide new insights into the knowledge of these MPN associated with eosinophilia.
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Affiliation(s)
- Maryam Arefi
- Department of Hematology, Hospital Clínico Universitario, Valladolid, Spain
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106
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Campos-Sánchez R, Kapusta A, Feschotte C, Chiaromonte F, Makova KD. Genomic landscape of human, bat, and ex vivo DNA transposon integrations. Mol Biol Evol 2014; 31:1816-32. [PMID: 24809961 DOI: 10.1093/molbev/msu138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The integration and fixation preferences of DNA transposons, one of the major classes of eukaryotic transposable elements, have never been evaluated comprehensively on a genome-wide scale. Here, we present a detailed study of the distribution of DNA transposons in the human and bat genomes. We studied three groups of DNA transposons that integrated at different evolutionary times: 1) ancient (>40 My) and currently inactive human elements, 2) younger (<40 My) bat elements, and 3) ex vivo integrations of piggyBat and Sleeping Beauty elements in HeLa cells. Although the distribution of ex vivo elements reflected integration preferences, the distribution of human and (to a lesser extent) bat elements was also affected by selection. We used regression techniques (linear, negative binomial, and logistic regression models with multiple predictors) applied to 20-kb and 1-Mb windows to investigate how the genomic landscape in the vicinity of DNA transposons contributes to their integration and fixation. Our models indicate that genomic landscape explains 16-79% of variability in DNA transposon genome-wide distribution. Importantly, we not only confirmed previously identified predictors (e.g., DNA conformation and recombination hotspots) but also identified several novel predictors (e.g., signatures of double-strand breaks and telomere hexamer). Ex vivo integrations showed a bias toward actively transcribed regions. Older DNA transposons were located in genomic regions scarce in most conserved elements-likely reflecting purifying selection. Our study highlights how DNA transposons are integral to the evolution of bat and human genomes, and has implications for the development of DNA transposon assays for gene therapy and mutagenesis applications.
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Affiliation(s)
- Rebeca Campos-Sánchez
- Genetics Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, PA
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT
| | - Francesca Chiaromonte
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, PADepartment of Statistics, Penn State University, University Park, PA
| | - Kateryna D Makova
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, PADepartment of Biology, Penn State University, University Park, PA
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107
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Proukakis C, Shoaee M, Morris J, Brier T, Kara E, Sheerin UM, Charlesworth G, Tolosa E, Houlden H, Wood NW, Schapira AH. Analysis of Parkinson's disease brain-derived DNA for alpha-synuclein coding somatic mutations. Mov Disord 2014; 29:1060-4. [PMID: 24752924 PMCID: PMC4190821 DOI: 10.1002/mds.25883] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/16/2014] [Accepted: 03/06/2014] [Indexed: 02/01/2023] Open
Abstract
Background Although alpha-synuclein (SNCA) is crucial to the pathogenesis of Parkinson's disease (PD) and dementia with Lewy bodies (DLB), mutations in the gene appear to be rare. We have recently hypothesized that somatic mutations in early development could contribute to PD. Methods Expanding on our recent negative small study, we used high-resolution melting (HRM) analysis to screen SNCA coding exons for somatic point mutations in DNA from 539 PD and DLB cerebellar samples, with two additional regions (frontal cortex, substantia nigra) for 20 PD cases. We used artificial mosaics to determine sensitivity where possible. Results We did not detect any evidence of somatic coding mutations. Three cases were heterozygous for known silent polymorphisms. The protocol we used was sensitive enough to detect 5% to 10% mutant DNA. Conclusion Using DNA predominantly from cerebellum, but also from frontal cortex and substantia nigra (n = 20 each), we have not detected any somatic coding SNCA point mutations. © 2014 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Christos Proukakis
- Department of Clinical Neuroscience, Institute of Neurology, University College London, London, United Kingdom
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108
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The RBBP6/ZBTB38/MCM10 axis regulates DNA replication and common fragile site stability. Cell Rep 2014; 7:575-587. [PMID: 24726359 DOI: 10.1016/j.celrep.2014.03.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 01/17/2014] [Accepted: 03/09/2014] [Indexed: 11/23/2022] Open
Abstract
Faithful DNA replication is essential for the maintenance of genome integrity. Incomplete genome replication leads to DNA breaks and chromosomal rearrangements, which are causal factors in cancer and other human diseases. Despite their importance, the molecular mechanisms that control human genome stability are incompletely understood. Here, we report a pathway that is required for human genome replication and stability. This pathway has three components: an E3 ubiquitin ligase, a transcriptional repressor, and a replication protein. The E3 ubiquitin ligase RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38. This repressor negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Cells lacking RBBP6 experience reduced replication fork progression and increased damage at common fragile sites due to ZBTB38 accumulation and MCM10 downregulation. Our results uncover a pathway that ensures genome-wide DNA replication and chromosomal stability.
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Abstract
Alus are transposable elements belonging to the short interspersed element family. They occupy over 10% of human genome and have been spreading through genomes over the past 65 million years. In the past, they were considered junk DNA with little function that took up genome volumes. Today, Alus and other transposable elements emerge to be key players in cellular function, including genomic activities, gene expression regulations, and evolution. Here we summarize the current understanding of Alu function in genome and gene expression regulation in human cell nuclei.
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Affiliation(s)
- Chen Wang
- Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine; Chicago, IL USA
| | - Sui Huang
- Department of Cell and Molecular Biology; Northwestern University; Feinberg School of Medicine; Chicago, IL USA
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110
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McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH. Mosaic copy number variation in human neurons. Science 2013; 342:632-7. [PMID: 24179226 DOI: 10.1126/science.1243472] [Citation(s) in RCA: 387] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We used single-cell genomic approaches to map DNA copy number variation (CNV) in neurons obtained from human induced pluripotent stem cell (hiPSC) lines and postmortem human brains. We identified aneuploid neurons, as well as numerous subchromosomal CNVs in euploid neurons. Neurotypic hiPSC-derived neurons had larger CNVs than fibroblasts, and several large deletions were found in hiPSC-derived neurons but not in matched neural progenitor cells. Single-cell sequencing of endogenous human frontal cortex neurons revealed that 13 to 41% of neurons have at least one megabase-scale de novo CNV, that deletions are twice as common as duplications, and that a subset of neurons have highly aberrant genomes marked by multiple alterations. Our results show that mosaic CNV is abundant in human neurons.
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Affiliation(s)
- Michael J McConnell
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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111
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Boyer AS, Grgurevic S, Cazaux C, Hoffmann JS. The Human Specialized DNA Polymerases and Non-B DNA: Vital Relationships to Preserve Genome Integrity. J Mol Biol 2013; 425:4767-81. [DOI: 10.1016/j.jmb.2013.09.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/17/2013] [Accepted: 09/19/2013] [Indexed: 12/26/2022]
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Mutation rates, spectra, and genome-wide distribution of spontaneous mutations in mismatch repair deficient yeast. G3-GENES GENOMES GENETICS 2013; 3:1453-65. [PMID: 23821616 PMCID: PMC3755907 DOI: 10.1534/g3.113.006429] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA mismatch repair is a highly conserved DNA repair pathway. In humans, germline mutations in hMSH2 or hMLH1, key components of mismatch repair, have been associated with Lynch syndrome, a leading cause of inherited cancer mortality. Current estimates of the mutation rate and the mutational spectra in mismatch repair defective cells are primarily limited to a small number of individual reporter loci. Here we use the yeast Saccharomyces cerevisiae to generate a genome-wide view of the rates, spectra, and distribution of mutation in the absence of mismatch repair. We performed mutation accumulation assays and next generation sequencing on 19 strains, including 16 msh2 missense variants implicated in Lynch cancer syndrome. The mutation rate for DNA mismatch repair null strains was approximately 1 mutation per genome per generation, 225-fold greater than the wild-type rate. The mutations were distributed randomly throughout the genome, independent of replication timing. The mutation spectra included insertions/deletions at homopolymeric runs (87.7%) and at larger microsatellites (5.9%), as well as transitions (4.5%) and transversions (1.9%). Additionally, repeat regions with proximal repeats are more likely to be mutated. A bias toward deletions at homopolymers and insertions at (AT)n microsatellites suggests a different mechanism for mismatch generation at these sites. Interestingly, 5% of the single base pair substitutions might represent double-slippage events that occurred at the junction of immediately adjacent repeats, resulting in a shift in the repeat boundary. These data suggest a closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells.
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113
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Rajaram M, Zhang J, Wang T, Li J, Kuscu C, Qi H, Kato M, Grubor V, Weil RJ, Helland A, Borrenson-Dale AL, Cho KR, Levine DA, Houghton AN, Wolchok JD, Myeroff L, Markowitz SD, Lowe SW, Zhang M, Krasnitz A, Lucito R, Mu D, Powers RS. Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS One 2013; 8:e66264. [PMID: 23805207 PMCID: PMC3689739 DOI: 10.1371/journal.pone.0066264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 05/03/2013] [Indexed: 01/07/2023] Open
Abstract
One of the key questions about genomic alterations in cancer is whether they are functional in the sense of contributing to the selective advantage of tumor cells. The frequency with which an alteration occurs might reflect its ability to increase cancer cell growth, or alternatively, enhanced instability of a locus may increase the frequency with which it is found to be aberrant in tumors, regardless of oncogenic impact. Here we’ve addressed this on a genome-wide scale for cancer-associated focal deletions, which are known to pinpoint both tumor suppressor genes (tumor suppressors) and unstable loci. Based on DNA copy number analysis of over one-thousand human cancers representing ten different tumor types, we observed five loci with focal deletion frequencies above 5%, including the A2BP1 gene at 16p13.3 and the MACROD2 gene at 20p12.1. However, neither RNA expression nor functional studies support a tumor suppressor role for either gene. Further analyses suggest instead that these are sites of increased genomic instability and that they resemble common fragile sites (CFS). Genome-wide analysis revealed properties of CFS-like recurrent deletions that distinguish them from deletions affecting tumor suppressor genes, including their isolation at specific loci away from other genomic deletion sites, a considerably smaller deletion size, and dispersal throughout the affected locus rather than assembly at a common site of overlap. Additionally, CFS-like deletions have less impact on gene expression and are enriched in cell lines compared to primary tumors. We show that loci affected by CFS-like deletions are often distinct from known common fragile sites. Indeed, we find that each tumor tissue type has its own spectrum of CFS-like deletions, and that colon cancers have many more CFS-like deletions than other tumor types. We present simple rules that can pinpoint focal deletions that are not CFS-like and more likely to affect functional tumor suppressors.
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Affiliation(s)
- Megha Rajaram
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Jianping Zhang
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Tim Wang
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Jinyu Li
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Cem Kuscu
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Huan Qi
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Mamoru Kato
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Vladimir Grubor
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Robert J. Weil
- Department of Neurosurgery, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Aslaug Helland
- Department of Genetics, The Norwegian Radium Hospital, Oslo, Norway
| | | | - Kathleen R. Cho
- Departments of Internal Medicine and Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Douglas A. Levine
- Departments of Medicine and Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Alan N. Houghton
- Departments of Medicine and Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Jedd D. Wolchok
- Departments of Medicine and Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lois Myeroff
- Department of Medicine and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, United States of America
| | - Sanford D. Markowitz
- Department of Medicine and Ireland Cancer Center, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, United States of America
| | - Scott W. Lowe
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Michael Zhang
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Alex Krasnitz
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Robert Lucito
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - David Mu
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - R. Scott Powers
- Cancer Genome Center, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
- * E-mail:
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114
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Bergoglio V, Boyer AS, Walsh E, Naim V, Legube G, Lee MYWT, Rey L, Rosselli F, Cazaux C, Eckert KA, Hoffmann JS. DNA synthesis by Pol η promotes fragile site stability by preventing under-replicated DNA in mitosis. ACTA ACUST UNITED AC 2013; 201:395-408. [PMID: 23609533 PMCID: PMC3639397 DOI: 10.1083/jcb.201207066] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pol η–dependent DNA synthesis at stalled replication forks during S phase suppresses chronic fragile site instability by preventing checkpoint-blind under-replicated DNA in mitosis. Human DNA polymerase η (Pol η) is best known for its role in responding to UV irradiation–induced genome damage. We have recently observed that Pol η is also required for the stability of common fragile sites (CFSs), whose rearrangements are considered a driving force of oncogenesis. Here, we explored the molecular mechanisms underlying this newly identified role. We demonstrated that Pol η accumulated at CFSs upon partial replication stress and could efficiently replicate non-B DNA sequences within CFSs. Pol η deficiency led to persistence of checkpoint-blind under-replicated CFS regions in mitosis, detectable as FANCD2-associated chromosomal sites that were transmitted to daughter cells in 53BP1-shielded nuclear bodies. Expression of a catalytically inactive mutant of Pol η increased replication fork stalling and activated the replication checkpoint. These data are consistent with the requirement of Pol η–dependent DNA synthesis during S phase at replication forks stalled in CFS regions to suppress CFS instability by preventing checkpoint-blind under-replicated DNA in mitosis.
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Affiliation(s)
- Valérie Bergoglio
- Equipe labellisée Ligue Contre le Cancer 2013, INSERM Unit 1037, ERL5294 Centre National de la Recherche Scientifique, Cancer Research Center of Toulouse, BP3028, CHU Purpan, 31024 Toulouse, France
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Kuzminov A. Inhibition of DNA synthesis facilitates expansion of low-complexity repeats: is strand slippage stimulated by transient local depletion of specific dNTPs? Bioessays 2013; 35:306-13. [PMID: 23319444 DOI: 10.1002/bies.201200128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Simple DNA repeats (trinucleotide repeats, micro- and minisatellites) are prone to expansion/contraction via formation of secondary structures during DNA synthesis. Such structures both inhibit replication forks and create opportunities for template-primer slippage, making these repeats unstable. Certain aspects of simple repeat instability, however, suggest additional mechanisms of replication inhibition dependent on the primary DNA sequence, rather than on secondary structure formation. I argue that expanded simple repeats, due to their lower DNA complexity, should transiently inhibit DNA synthesis by locally depleting specific DNA precursors. Such transient inhibition would promote formation of secondary structures and would stabilize these structures, facilitating strand slippage. Thus, replication problems at simple repeats could be explained by potentiated toxicity, where the secondary structure-driven repeat instability is enhanced by DNA polymerase stalling at the low complexity template DNA.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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116
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Romano G. Development of safer gene delivery systems to minimize the risk of insertional mutagenesis-related malignancies: a critical issue for the field of gene therapy. ISRN ONCOLOGY 2012; 2012:616310. [PMID: 23209944 PMCID: PMC3512301 DOI: 10.5402/2012/616310] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 10/23/2012] [Indexed: 12/17/2022]
Abstract
Integrating gene delivery systems allow for a more stable transgene expression in mammalian cells than the episomal ones. However, the integration of the shuttle vector within the cellular chromosomal DNA is associated with the risk of insertional mutagenesis, which, in turn, may cause malignant cell transformation. The use of a retroviral-derived vector system was responsible for the development of leukemia in five children, who participated in various clinical trials for the treatment of severe combined immunodeficiency (SCID-X1) in France and in the United Kingdom. Unfortunately, the hematological malignancy claimed the life of one patient in 2004, who was enrolled in the French clinical trial. In addition, adeno-associated-viral-(AAV-) mediated gene transfer induced tumors in animal models, whereas the Sleeping Beauty (SB) DNA transposon system was associated with insertional mutagenesis events in cell culture systems. On these grounds, it is necessary to develop safer gene delivery systems for the genetic manipulation of mammalian cells. This paper discusses the latest achievements that have been reported in the field of vector design.
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Affiliation(s)
- Gaetano Romano
- Department of Biology, College of Science and Technology, Temple University, Bio-Life Science Building, Suite 456, 1900 N. 12th Street, Philadelphia, PA 19122, USA
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117
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Walsh E, Wang X, Lee MY, Eckert KA. Mechanism of replicative DNA polymerase delta pausing and a potential role for DNA polymerase kappa in common fragile site replication. J Mol Biol 2012; 425:232-43. [PMID: 23174185 DOI: 10.1016/j.jmb.2012.11.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Revised: 11/12/2012] [Accepted: 11/12/2012] [Indexed: 11/16/2022]
Abstract
Common fragile sites (CFSs) are hot spots of chromosomal breakage, and CFS breakage models involve perturbations of DNA replication. Here, we analyzed the contribution of specific repetitive DNA sequence elements within CFSs to the inhibition of DNA synthesis by replicative and specialized DNA polymerases (Pols). The efficiency of in vitro DNA synthesis was quantitated using templates corresponding to regions within FRA16D and FRA3B harboring AT-rich microsatellite and quasi-palindrome (QP) sequences. QPs were predicted to form stems of ~75-100% self-homology, separated by 3-9 bases of intervening sequences. Analysis of DNA synthesis progression by human Pol δ demonstrated significant synthesis perturbation both at [A](n) and [TA](n) repeats in a length-dependent manner and at short (<40 base pairs) QP sequences. DNA synthesis by the Y-family polymerase κ was significantly more efficient than Pol δ through both types of repetitive elements. Using DNA trap experiments, we show that Pol δ pauses within CFS sequences are sites of enzyme dissociation, and dissociation was observed in the presence of RFC-loaded PCNA. We propose that enrichment of microsatellite and QP elements at CFS regions contributes to fragility by perturbing replication through multiple mechanisms, including replicative Pol pausing and dissociation. Our finding that Pol δ dissociates at specific CFS sequences is significant, since dissociation of the replication machinery and inability to efficiently recover the replication fork can lead to fork collapse and/or formation of double-strand breaks in vivo. Our biochemical studies also extend the potential involvement of Y-family polymerases in CFS maintenance to include polymerase κ.
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Affiliation(s)
- Erin Walsh
- Cellular and Molecular Biology Graduate Program, Penn State University College of Medicine, Hershey, PA 17033, USA
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118
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Cer RZ, Donohue DE, Mudunuri US, Temiz NA, Loss MA, Starner NJ, Halusa GN, Volfovsky N, Yi M, Luke BT, Bacolla A, Collins JR, Stephens RM. Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools. Nucleic Acids Res 2012; 41:D94-D100. [PMID: 23125372 PMCID: PMC3531222 DOI: 10.1093/nar/gks955] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.
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Affiliation(s)
- Regina Z Cer
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., Frederick, MD 21702, USA
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