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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Love C, Sun Z, Jima D, Li G, Zhang J, Miles R, Richards KL, Dunphy CH, Choi WWL, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Chadburn A, Gordon LI, Czader MB, Gill JI, Hsi ED, Greenough A, Moffitt AB, McKinney M, Banerjee A, Grubor V, Levy S, Dunson DB, Dave SS. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet 2012; 44:1321-5. [PMID: 23143597 DOI: 10.1038/ng.2468] [Citation(s) in RCA: 431] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/17/2012] [Indexed: 12/13/2022]
Abstract
Burkitt lymphoma is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. Here, we describe the first completely sequenced genome from a Burkitt lymphoma tumor and germline DNA from the same affected individual. We further sequenced the exomes of 59 Burkitt lymphoma tumors and compared them to sequenced exomes from 94 diffuse large B-cell lymphoma (DLBCL) tumors. We identified 70 genes that were recurrently mutated in Burkitt lymphomas, including ID3, GNA13, RET, PIK3R1 and the SWI/SNF genes ARID1A and SMARCA4. Our data implicate a number of genes in cancer for the first time, including CCT6B, SALL3, FTCD and PC. ID3 mutations occurred in 34% of Burkitt lymphomas and not in DLBCLs. We show experimentally that ID3 mutations promote cell cycle progression and proliferation. Our work thus elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a new tumor suppressor gene.
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Affiliation(s)
- Cassandra Love
- Duke Institute for Genome Sciences and Policy, Duke University, Durham, NC, USA
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Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Miezcowski P, Dunphy CH, Choi WWL, Auv WY, Srivastava G, Lugar PL, Rizzieri DA, Lagoo AS, Bernal-Mizrachi L, Mann KP, Flowers CR, Naresh KN, Evens AM, Gordon LI, Czader MB, Gill JI, Hsi ED, Liu Q, Fan A, Walsh K, Jima DD, Luftig M, Ni T, Zhu J, Chadburn A, Levy S, Dunson DB, Dave SS. 13th International Conference on Malignancies in AIDS and Other Acquired Immunodeficiencies (ICMAOI) Bethesda, MD, USA. 7-8 November 2011. Abstracts. Infect Agent Cancer 2012; 7 Suppl 1:O1-P49. [PMID: 22551362 PMCID: PMC3330083 DOI: 10.1186/1750-9378-7-s1-o1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M. Inferring tumor progression from genomic heterogeneity. Genome Res 2009; 20:68-80. [PMID: 19903760 DOI: 10.1101/gr.099622.109] [Citation(s) in RCA: 367] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that heterogeneity can be ascribed to a few clonal subpopulations, rather than a series of gradual intermediates. By comparing multiple subpopulations from different anatomic locations, we have inferred pathways of cancer progression and the organization of tumor growth.
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Affiliation(s)
- Nicholas Navin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Børresen-Dale AL, Naume B, Schlicting E, Norton L, Hägerström T, Skoog L, Auer G, Månér S, Lundin P, Zetterberg A. Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 2007; 16:1465-79. [PMID: 17142309 PMCID: PMC1665631 DOI: 10.1101/gr.5460106] [Citation(s) in RCA: 271] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Representational Oligonucleotide Microarray Analysis (ROMA) detects genomic amplifications and deletions with boundaries defined at a resolution of approximately 50 kb. We have used this technique to examine 243 breast tumors from two separate studies for which detailed clinical data were available. The very high resolution of this technology has enabled us to identify three characteristic patterns of genomic copy number variation in diploid tumors and to measure correlations with patient survival. One of these patterns is characterized by multiple closely spaced amplicons, or "firestorms," limited to single chromosome arms. These multiple amplifications are highly correlated with aggressive disease and poor survival even when the rest of the genome is relatively quiet. Analysis of a selected subset of clinical material suggests that a simple genomic calculation, based on the number and proximity of genomic alterations, correlates with life-table estimates of the probability of overall survival in patients with primary breast cancer. Based on this sample, we generate the working hypothesis that copy number profiling might provide information useful in making clinical decisions, especially regarding the use or not of systemic therapies (hormonal therapy, chemotherapy), in the management of operable primary breast cancer with ostensibly good prognosis, for example, small, node-negative, hormone-receptor-positive diploid cases.
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Affiliation(s)
- James Hicks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
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Hicks J, Muthuswamy L, Krasnitz A, Navin N, Riggs M, Grubor V, Esposito D, Alexander J, Troge J, Wigler M, Maner S, Lundin P, Zetterberg A. High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol 2006; 70:51-63. [PMID: 16869738 DOI: 10.1101/sqb.2005.70.055] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Combining representational oligonucleotide microarray analysis (ROMA) of tumor DNA with fluorescence in situ hybridization (FISH) of individual tumor cells provides the opportunity to detect and validate a wide range of amplifications, deletions, and rearrangements directly in frozen tumor samples. We have used these combined techniques to examine 101 aneuploid and diploid breast tumors for which long-term follow-up and detailed clinical information were available. We have determined that ROMA provides accurate and sensitive detection of duplications, amplifications, and deletions and yields defined boundaries for these events with a resolution of <50 kbp in most cases. We find that diploid tumors exhibit fewer rearrangements on average than aneuploids, but rearrangements occur at the same locations in both types. Diploid tumors reflect at least three consistent patterns of rearrangement. The reproducibility and frequency of these events, especially in very early stage tumors, provide insight into the earliest chromosomal events in breast cancer. We have also identified correlations between certain sets of rearrangement events and clinically relevant parameters such as long-term survival. These correlations may enable novel prognostic indicators for breast and other cancers as more samples are analyzed.
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Affiliation(s)
- J Hicks
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, New York 11724, USA
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Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Månér S, Sebat J, Zetterberg A, Wigler M. PROBER: oligonucleotide FISH probe design software. Bioinformatics 2006; 22:2437-8. [PMID: 16740623 DOI: 10.1093/bioinformatics/btl273] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10-100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors. AVAILABILITY http://prober.cshl.edu
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Affiliation(s)
- Nicholas Navin
- Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA.
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Hicks J, Grubor V, Navin N, Lundin P, Månér S, Hägerström T, Skoog L, Wigler M, Zetterberg A. High-resolution representational oligonucleotide microarray analysis and fluorescence in situ hybridization analysis of aneuploid and diploid breast tumors. Breast Cancer Res 2005. [PMCID: PMC4233490 DOI: 10.1186/bcr1069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Jackson Behan K, Fair J, Singh S, Bogwitz M, Perry T, Grubor V, Cunningham F, Nichols CD, Cheung TL, Batterham P, Pollock JA. Alternative splicing removes an Ets interaction domain from Lozenge during Drosophila eye development. Dev Genes Evol 2005; 215:423-35. [PMID: 15868204 DOI: 10.1007/s00427-005-0490-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 04/08/2005] [Indexed: 10/25/2022]
Abstract
Physical and functional characteristics of the RUNX family of transcription factors are conserved between vertebrates and the Drosophila protein Lozenge. The runt-homology domain responsible for DNA binding and also the C-terminus are both nearly identical between the two proteins. The mammalian and fly proteins heterodimerize with a non-DNA binding partner protein to form a core binding factor essential for gene regulation during cell differentiation. The mammalian protein RUNX1 (AML1/PEBP2alphaB) interacts with the transcription factor Ets-1 to increase DNA binding and transactivation potential. Alternative splicing of the mammalian RUNX1 removes a domain required for this cooperative transactivation. In this work we determine the structure of the lozenge transcription unit and map 21 mutations. We show that the lozenge transcript is alternatively spliced during eye development to remove an Ets interaction domain. Emphasis is placed on Pointed the Drosophila homolog of the vertebrate Ets-1 protein; both Lozenge and Pointed proteins are needed for the activation of prospero expression. We use site-directed mutagenesis and yeast two-hybrid analysis to show that conserved amino acids within the alternate Lozenge exon are important for interaction with Pointed. Furthermore, the ectopic expression of Lozenge is sufficient to rescue Prospero expression in the presence of the Pointed competitor, Yan(ACT). We show that both lozenge isoforms are expressed during eye development and that the relative ratio of the transcripts for the two isoforms is sensitive to changes in Ras activity. We suggest that during eye development, Lozenge isoforms function in divergent roles, either interacting with Pointed on downstream targets or by functioning independently to establish distinct cell fates.
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