Genomic instability during Myc-induced lymphomagenesis in the bursa of Fabricius View Full Text


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Article Info

DATE

2006-05-01

AUTHORS

P E Neiman, R Kimmel, A Icreverzi, K Elsaesser, S-J Bowers, J Burnside, J Delrow

ABSTRACT

Retroviral vector-mediated overexpression of c-myc in embryonic bursal precursors induces multi-staged tumorigenesis beginning with preneoplastic-transformed follicles (TF) and progressing to clonal metastatic B-cell lymphomas. Using a 13K chicken cDNA microarray, specifically enriched for chicken immune system expressed sequence tagged (ESTs), we carried out array-based comparative genomic hybridization (array-CGH) and detected significant DNA copy number change at many loci on most or all chromosomes in both early TF and end-stage lymphomas. Formation of long palindromes, through breakage–fusion–bridge cycles, is thought to play an early role in gene amplification. Employing genome-wide analysis of palindrome formation (GAPF), we detected extensive palindrome formation in early TF and end-stage lymphomas. The population of loci showing amplification by array-CGH was enriched for palindromes detected by GAPF providing strong evidence for genetic instability early in Myc-induced tumorigenesis and further support for the role of palindromes in gene amplification. Comparing gene copy number change and RNA expression changes profiled on the same cDNA array, we detected very little consistent contribution of gene copy number change to RNA expression changes. Palindromic loci in TF and tumors, however, were expressed, many at high levels, suggesting an abundance of RNA species with long double-stranded segments generated during tumorigenesis. More... »

PAGES

6325-6335

References to SciGraph publications

  • 2005-06. c-Myc-regulated microRNAs modulate E2F1 expression in NATURE
  • 2003-02-19. Functional genomic analysis reveals distinct neoplastic phenotypes associated with c-myb mutation in the bursa of Fabricius in ONCOGENE
  • 1999-09. Genome-wide analysis of DNA copy-number changes using cDNA microarrays in NATURE GENETICS
  • 2004-12. An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division in NATURE
  • 2000-05-25. Angiogenesis is an early event in the generation of myc-induced lymphomas in ONCOGENE
  • 2005-06. MicroRNA expression profiles classify human cancers in NATURE
  • 1996-08. Genomic instability in MycER-activated Rat1A-MycER cells in CHROMOSOME RESEARCH
  • 1998-12. Genetic instabilities in human cancers in NATURE
  • 2004-12-09. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution in NATURE
  • 2004-04. Karyotype stability of the DT40 chicken B cell line: Macrochromosome variation and cytogenetic mosaicism in CHROMOSOME RESEARCH
  • 2005-02-13. Widespread and nonrandom distribution of DNA palindromes in cancer cells provides a structural platform for subsequent gene amplification in NATURE GENETICS
  • 2003-09-11. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets in GENOME BIOLOGY
  • 2005-02-04. Development of a cDNA array for chicken gene expression analysis in BMC GENOMICS
  • 1998-11-24. Chimeric amplicons containing the c-myc gene in HL60 cells in ONCOGENE
  • 1997. Genomic Instability and Its Role in Neoplasia in GENETIC INSTABILITY AND TUMORIGENESIS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/sj.onc.1209646

    DOI

    http://dx.doi.org/10.1038/sj.onc.1209646

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1009605128

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16652139


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