Gene amplification as double minutes or homogeneously staining regions in solid tumors: origin and structure.

Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model). In the present paper we investigated 10 cell lines from solid tumors showing MYCN amplification as dmin or hsr. Particularly revealing results were provided by the two subclones of the neuroblastoma cell line STA-NB-10, one showing dmin-only and the second hsr-only amplification. Both subclones showed a deletion, at 2p24.3, whose extension matched the amplicon extension. Additionally, the amplicon structure of the dmin and hsr forms was identical. This strongly argues that the episome model, already demonstrated in leukemias, applies to solid tumors as well, and that dmin and hsr are two faces of the same coin. The organization of the duplicated segments varied from very simple (no apparent changes from the normal sequence) to very complex. MYCN was always overexpressed (significantly overexpressed in three cases). The fusion junctions, always mediated by nonhomologous end joining, occasionally juxtaposed truncated genes in the same transcriptional orientation. Fusion transcripts involving NBAS (also known as NAG), FAM49A, BC035112 (also known as NCRNA00276), and SMC6 genes were indeed detected, although their role in the context of the tumor is not clear.

[1]  P. Hupé,et al.  Extrachromosomal amplification mechanisms in a glioma with amplified sequences from multiple chromosome loci. , 2010, Human molecular genetics.

[2]  M. Rocchi,et al.  Bone marrow ectopic expression of a non-coding RNA in childhood T-cell acute lymphoblastic leukemia with a novel t(2;11)(q11.2;p15.1) translocation , 2008, Molecular Cancer.

[3]  O. Delattre,et al.  Characterization of amplicons in neuroblastoma: High‐resolution mapping using DNA microarrays, relationship with outcome, and identification of overexpressed genes , 2008, Genes, chromosomes & cancer.

[4]  H. Carén,et al.  High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: Four cases of homozygous deletions of the CDKN2A gene , 2008, BMC Genomics.

[5]  Antony V. Cox,et al.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing , 2008, Nature Genetics.

[6]  A. Bellacosa,et al.  VILIP-1 Downregulation in Non-Small Cell Lung Carcinomas: Mechanisms and Prediction of Survival , 2008, PloS one.

[7]  F. Watzinger,et al.  Genes proximal and distal to MYCN are highly expressed in human neuroblastoma as visualized by comparative expressed sequence hybridization. , 2008, The American journal of pathology.

[8]  Z. Nawaz,et al.  Long-range activation of GREB1 by estrogen receptor via three distal consensus estrogen-responsive elements in breast cancer cells. , 2007, Molecular endocrinology.

[9]  N. Shimizu,et al.  Nonselective DNA damage induced by a replication inhibitor results in the selective elimination of extrachromosomal double minutes from human cancer cells , 2007, Genes, chromosomes & cancer.

[10]  Andrew Menzies,et al.  Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. , 2007, Genome research.

[11]  P. Ambros,et al.  Induction of senescence in MYCN amplified neuroblastoma cell lines by hydroxyurea , 2007, Genes, chromosomes & cancer.

[12]  S. Knuutila,et al.  Specificity, selection and significance of gene amplifications in cancer. , 2007, Seminars in cancer biology.

[13]  J. Squire,et al.  Correlating breakage-fusion-bridge events with the overall chromosomal instability and in vitro karyotype evolution in prostate cancer , 2007, Cytogenetic and Genome Research.

[14]  E. Feingold,et al.  Inverted duplication pattern in anaphase bridges confirms the breakage-fusion-bridge (BFB) cycle model for 11q13 amplification , 2007, Cytogenetic and Genome Research.

[15]  J. Fridlyand,et al.  Genome position and gene amplification , 2007, Genome Biology.

[16]  K. Kok,et al.  High-resolution mapping identifies a commonly amplified 11q13.3 region containing multiple genes flanked by segmental duplications , 2007, Human Genetics.

[17]  J. Squire,et al.  The breakage–fusion–bridge (BFB) cycle as a mechanism for generating genetic heterogeneity in osteosarcoma , 2006, Chromosoma.

[18]  D. Albertson,et al.  Gene amplification in cancer. , 2006, Trends in genetics : TIG.

[19]  M. Rocchi,et al.  MYC-containing double minutes in hematologic malignancies: evidence in favor of the episome model and exclusion of MYC as the target gene. , 2006, Human molecular genetics.

[20]  Frank Speleman,et al.  Translocation–excision–deletion–amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1 , 2006, Genes, chromosomes & cancer.

[21]  R. Gascoyne,et al.  Amplification of IGH/MYC fusion in clinically aggressive IGH/BCL2‐positive germinal center B‐cell lymphomas , 2005, Genes, chromosomes & cancer.

[22]  J. Chernoff,et al.  Visinin-like protein-1 is a potent inhibitor of cell adhesion and migration in squamous carcinoma cells , 2005, Oncogene.

[23]  A. Ferrando,et al.  Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia , 2004, Nature Genetics.

[24]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[25]  B. Johansson,et al.  Fusion genes and rearranged genes as a linear function of chromosome aberrations in cancer , 2004, Nature Genetics.

[26]  Christina A. Cuomo,et al.  The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats. , 2004, American journal of human genetics.

[27]  J. Lunec,et al.  Genes co-amplified with MYCN in neuroblastoma: silent passengers or co-determinants of phenotype? , 2003, Cancer letters.

[28]  J. Abgrall,et al.  Double minutes containing amplified bcr‐abl fusion gene in a case of chronic myeloid leukemia treated by imatinib , 2003, European journal of haematology.

[29]  J. Squire,et al.  Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization. , 2003, Neoplasia.

[30]  G. Horgan,et al.  Relative expression software tool (REST©) for group-wise comparison and statistical analysis of relative expression results in real-time PCR , 2002 .

[31]  David I. Smith,et al.  A role for common fragile site induction in amplification of human oncogenes. , 2002, Cancer cell.

[32]  J. Bullerdiek,et al.  Translocation, deletion/amplification, and expression of HMGIC and MDM2 in a carcinoma ex pleomorphic adenoma. , 2002, The American journal of pathology.

[33]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[34]  B. Schafer,et al.  Concomitant amplification and expression of PAX7-FKHR and MYCN in a human rhabdomyosarcoma cell line carrying a cryptic t(1;13)(p36;q14). , 2000, Cancer genetics and cytogenetics.

[35]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[36]  M. L. Lee,et al.  MYCN gene amplification. Identification of cell populations containing double minutes and homogeneously staining regions in neuroblastoma tumors. , 1999, The American journal of pathology.

[37]  N. Kamada,et al.  Jumping translocation of homogeneously staining region and tetraploidy with double minutes in acute myelomonocytic leukemia. , 1999, Cancer genetics and cytogenetics.

[38]  M. Drumm.  in vivo. , 1999 .

[39]  F. Toledo,et al.  A new role for hypoxia in tumor progression: induction of fragile site triggering genomic rearrangements and formation of complex DMs and HSRs. , 1998, Molecular cell.

[40]  H. Kovar,et al.  Neuroblastoma cells can actively eliminate supernumerary MYCN gene copies by micronucleus formation--sign of tumour cell revertance? , 1997, European journal of cancer.

[41]  J. Biegel,et al.  In vivo amplification of the PAX3-FKHR and PAX7-FKHR fusion genes in alveolar rhabdomyosarcoma. , 1996, Human molecular genetics.

[42]  C. Fegan,et al.  C‐myc amplification, double minutes and homogenous staining regions in a case of AML , 1995, British journal of haematology.

[43]  M. Schwab,et al.  Cytogenetic evolution of MYCN and MDM2 amplification in the neuroblastoma LS tumour and its cell line. , 1995, European journal of cancer.

[44]  G. Krystal,et al.  Isolation and characterization of complementary DNA for N-cym, a gene encoded by the DNA strand opposite to N-myc. , 1992, Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research.

[45]  J. Osinga,et al.  Localization of amplified c-myc and n-myc in small cell lung cancer cell lines. , 1989, Cancer genetics and cytogenetics.

[46]  G. Wahl,et al.  Double minute chromosomes can be produced from precursors derived from a chromosomal deletion , 1988, Molecular and cellular biology.

[47]  G. Levan,et al.  Methotrexate resistance and double minutes in a cell line from the SEWA mouse ascites tumor. , 2008, Hereditas.

[48]  D. George,et al.  Amplified DNA sequences in Y1 mouse adrenal tumor cells: association with double minutes and localization to a homogeneously staining chromosomal region. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[49]  U. Francke,et al.  Homogeneously staining chromosome regions and double minutes in a mouse adrenocortical tumor cell line. , 1980, Cytogenetics and cell genetics.

[50]  G. Moore,et al.  Cell lines from human colon carcinoma with unusual cell products, double minutes, and homogeneously staining regions. , 1979, Cancer research.

[51]  F. Gilbert,et al.  Double minute chromosomes and the homogeneously staining regions in chromosomes of a human neuroblastoma cell line. , 1977, Science.

[52]  B. Spengler,et al.  A novel chromosome abnormality in human neuroblastoma and antifolate-resistant Chinese hamster cell lives in culture. , 1976, Journal of the National Cancer Institute.

[53]  B. Mcclintock,et al.  Chromosome organization and genic expression. , 1951, Cold Spring Harbor symposia on quantitative biology.