Abstract
Current cytogenetic methods (e.g., G-banding and multicolor chromosomal painting) allow detection of translocation events but lack the resolution to (a) locate the breakpoints precisely at the chromosome band level or (b) discriminate balanced translocations from translocations with copy number alterations not previously reported, or imperfectly balanced translocations. In this study, we demonstrate that cytogenetically balanced translocations are in fact frequently associated with segmental gain or loss of DNA. The recent development of a whole genome tiling path BAC array has enabled tiling resolution analysis of genomic segmental copy number status. Combining tiling resolution BAC array comparative genomic hybridization (array CGH) with G-Banding analysis and multicolor chromosomal painting approaches such as spectral karyotyping (SKY) facilitates high-resolution mapping of genomic alterations associated with imperfectly balanced translocations. Using a refined version of our CGH array we have deduced the copy number status throughout the genomes of three cytogenetically well-characterized prostate cancer cell lines (PC3, DU145, LNCaP) to determine whether translocations are associated with focal gains and losses of DNA. At 78 kb tiling resolution we identified the boundaries of 170, 80, and 34 known and novel copy number alterations (CNA) in these cell line genomes, respectively. Thirty-three of the 36 known translocations (92%, P < 0.001) in DU145 were associated with segmental CNA. Likewise, 80% (P < 0.001) of the known translocations showed association in LNCaP. Although many translocation breakpoints exhibit segmental alteration in PC3, the pattern of chromosomal rearrangements is too complex for use in comprehensive association with CNA boundaries. Our results reveal that imperfectly balanced translocations in tumor genomes are a phenomenon that occurs at frequencies much higher than previously demonstrated.
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Au WY, Gascoyne RD, Viswanatha DS, Connors JM, Klasa RJ, Horsman DE (2002) Cytogenetic analysis in mantle cell lymphoma: a review of 214 cases. Leuk Lymphoma 43(4):783–791
Baldwin C, Garnis C, Zhang L, Rosin MP, Lam WL (2005) Multiple microalterations detected at high frequency in oral cancer. Cancer Res 65(17):7561–7567
Beheshti B, Karaskova J, Park PC, Squire JA, Beatty BG (2000) Identification of a high frequency of chromosomal rearrangements in the centromeric regions of prostate cancer cell lines by sequential giemsa banding and spectral karyotyping. Mol Diagn 5(1):23–32
Beheshti B, Park PC, Sweet JM, Trachtenberg J, Jewett MA, Squire JA (2001) Evidence of chromosomal instability in prostate cancer determined by spectral karyotyping (SKY) and interphase fish analysis. Neoplasia 3(1):62–69
Beheshti B, Vukovic B, Marrano P, Squire JA, Park PC (2002) Resolution of genotypic heterogeneity in prostate tumors using polymerase chain reaction and comparative genomic hybridization on microdissected carcinoma and prostatic intraepithelial neoplasia foci. Cancer Genet Cytogenet 137(1):15–22
Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL (2004) SeeGH–a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformat 5(1):13
Ciccone R, Giorda R, Gregato G, Guerrini R, Giglio S, Carrozzo R, Bonaglia MC, Priolo E, Lagana C, Tenconi R, others (2005) Reciprocal translocations: a trap for cytogenetists? Hum Genet 117(6):571–582
Clark J, Edwards S, Feber A, Flohr P, John M, Giddings I, Crossland S, Stratton MR, Wooster R, Campbell C, others (2003) Genome-wide screening for complete genetic loss in prostate cancer by comparative hybridization onto cDNA microarrays. Oncogene 22(8):1247–1252
Ford S, Gray IC, Spurr NK (1998) Rearrangement of the long arm of chromosome 10 in the prostate adenocarcinoma cell line LNCaP. Cancer Genet Cytogenet 102(1):6–11
Gerstein AV, Almeida TA, Zhao G, Chess E, Shih Ie M, Buhler K, Pienta K, Rubin MA, Vessella R, Papadopoulos N (2002) APC/CTNNB1 (beta-catenin) pathway alterations in human prostate cancers. Genes Chromosomes Cancer 34(1):9–16
Gisselsson D, Pettersson L, Hoglund M, Heidenblad M, Gorunova L, Wiegant J, Mertens F, Dal Cin P, Mitelman F, Mandahl N (2000) Chromosomal breakage-fusion-bridge events cause genetic intratumor heterogeneity. Proc Natl Acad Sci USA 97(10):5357–5362
Hermans KG, van Alewijk DC, Veltman JA, van Weerden W, van Kessel AG, Trapman J (2004) Loss of a small region around the PTEN locus is a major chromosome 10 alteration in prostate cancer xenografts and cell lines. Genes Chromosomes Cancer 39(3):171–184
Hu Y, Pang E, Lai PB, Squire JA, MacGregor PF, Beheshti B, Albert M, Leung TW, Wong N (2004) Genetic alterations in doxorubicin-resistant hepatocellular carcinoma cells: a combined study of spectral karyotyping, positional expression profiling and candidate genes. Int J Oncol 25(5):1357–1364
Hughes S, Lim G, Beheshti B, Bayani J, Marrano P, Huang A, Squire JA (2004) Use of whole genome amplification and comparative genomic hybridisation to detect chromosomal copy number alterations in cell line material and tumour tissue. Cytogenet Genome Res 105(1):18–24
Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, others (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36(3):299–303
Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258(5083):818–821
Kennedy MA, Gonzalez-Sarmiento R, Kees UR, Lampert F, Dear N, Boehm T, Rabbitts TH (1991) HOX11, a homeobox-containing T-cell oncogene on human chromosome 10q24) Proc Natl Acad Sci USA 88(20):8900–8904
Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, others (2004) A set of BAC clones spanning the human genome. Nucleic Acids Res 32(12):3651–3660
Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI, Puc J, Miliaresis C, Rodgers L, McCombie R, others (1997) PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275(5308):1943–1947
Lim G, Karaskova J, Vukovic B, Bayani J, Beheshti B, Bernardini M, Squire JA, Zielenska M (2004) Combined spectral karyotyping, multicolor banding, and microarray comparative genomic hybridization analysis provides a detailed characterization of complex structural chromosomal rearrangements associated with gene amplification in the osteosarcoma cell line MG-63) Cancer Genet Cytogenet 153(2):158–164
Mitelman F, Johansson B, Mertens F (2004) Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer. Nat Genet 36(4):331–334
Peehl DM (2005) Primary cell cultures as models of prostate cancer development. Endocr Relat Cancer 12(1):19–47
Shaffer L.G. TN (2005) ISCN (2005):An international system for human cytogenetic nomenclature. Karger, Basel
Steck PA, Pershouse MA, Jasser SA, Yung WK, Lin H, Ligon AH, Langford LA, Baumgard ML, Hattier T, Davis T (1997) Identification of a candidate tumour suppressor gene, MMAC1, at chromosome 10q23.3 that is mutated in multiple advanced cancers. Nat Genet 15(4):356–62
Strefford JC, Lillington DM, Young BD, Oliver RT (2001) The use of multicolor fluorescence technologies in the characterization of prostate carcinoma cell lines: a comparison of multiplex fluorescence in situ hybridization and spectral karyotyping data. Cancer Genet Cytogenet 124(2):112–121
Tyynismaa H, Sembongi H, Bokori-Brown M, Granycome C, Ashley N, Poulton J, Jalanko A, Spelbrink JN, Holt IJ, Suomalainen A (2004) Twinkle helicase is essential for mtDNA maintenance and regulates mtDNA copy number. Hum Mol Genet 13(24):3219–27
Vukovic B (2006) Correlating breakage-fusion-bridge events with the overall chromosomal instability and in vitro karyotypic evolution in prostate cancer. Cytogen Genome Resp
Watson SK, deLeeuw RJ, Ishkanian AS, Malloff CA, Lam WL (2004) Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays. BMC Genomics 5(1):6
Wolf M, Mousses S, Hautaniemi S, Karhu R, Huusko P, Allinen M, Elkahloun A, Monni O, Chen Y, Kallioniemi A, others (2004) High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression. Neoplasia 6(3):240–247
Ylstra B, van den Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA (2006) BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 34(2):445–450
Yoshimoto M, Cutz J-C, Nuin PAS, Joshua AM, Bayani J, Evans AJ, Zielenska M, Squire JA (2006) Interphase fluorescense in situ hybridization analysis of PTEN in histologic sections shows genomic deletions are present in 68% of primary prostate cancer and 23% of high-grade prostatic intra-epithelial neoplasia. Cancer Genet Cytogenet
Zhao H, Kim Y, Wang P, Lapointe J, Tibshirani R, Pollack JR, Brooks JD (2005) Genome-wide characterization of gene expression variations and DNA copy number changes in prostate cancer cell lines. Prostate 63(2):187–197
Zielenska M, Marrano P, Thorner P, Pei J, Beheshti B, Ho M, Bayani J, Liu Y, Sun BC, Squire JA, others (2004) High-resolution cDNA microarray CGH mapping of genomic imbalances in osteosarcoma using formalin-fixed paraffin-embedded tissue. Cytogenet Genome Res 107(1–2):77–82
Acknowledgments
We would like to acknowledge the Lam Lab BAC array group, Ben Beheshti for supplying the cell line DNA, Lindsey Kimm and Miwa Suzuki for technical assistance, and Jana Paderova for editing assistance. Supported by Genome Canada and Genome BC grants.
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Watson, S.K., deLeeuw, R.J., Horsman, D.E. et al. Cytogenetically balanced translocations are associated with focal copy number alterations. Hum Genet 120, 795–805 (2007). https://doi.org/10.1007/s00439-006-0251-9
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DOI: https://doi.org/10.1007/s00439-006-0251-9