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Genetic and epigenetic alterations are essential for the initiation and progression of human cancer. We previously reported that primary human medulloblastomas showed extensive cancer-specific CpG island DNA hypermethylation in critical developmental pathways. To determine whether genetically engineered mouse models (GEMMs) of medulloblastoma have comparable epigenetic changes, we assessed genome-wide DNA methylation in three mouse models of medulloblastoma. In contrast to human samples, very few loci with cancer-specific DNA hypermethylation were detected, and in almost all cases the degree of methylation was relatively modest compared with the dense hypermethylation in the human cancers. To determine if this finding was common to other GEMMs, we examined a Burkitt lymphoma and breast cancer model and did not detect promoter CpG island DNA hypermethylation, suggesting that human cancers and at least some GEMMs are fundamentally different with respect to this epigenetic modification. These findings provide an opportunity to both better understand the mechanism of aberrant DNA methylation in human cancer and construct better GEMMs to serve as preclinical platforms for therapy development.

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.

DT40 presents a unique opportunity to exploit newly available tools for chicken genomic analysis. A 13K chicken cDNA microarray representing 11447 non-overlapping ESTs has been developed. This array detects expression of 7086 DT40 genes of which_644 are over-expressed 3-fold or greater and 1585 are under-expressed 3-fold or greater relative to normal post-hatch bursal cell populations. Changes in RNA expression due to single gene alterations can be detected by expression profiling. For example, by this method, over expression of the oncogenic micro RNA bic up-regulates expression of VBP, a known regulator of Avian Leukosis Virus LTR- driven transcription with very little additional expression change, A degree of cytogenetic abnormality and instability of DT40 cells has been observed, which is characterized at the fine structure level using microarray-based comparative genome hybridization (array-CGH). The relationship between gene copy number and RNA expression levels can be assessed in the same tissue samples using the same microarray. A newly introduced technique for genome-wide analysis of palindrome formation (GAPF) detects long inverted repeats, or palindromes, which are early events in gene amplification and possibly other DNA structural change. Since both array CGH-detected copy number changes and GAPF-detected palindromes are abundant in DT40, these techniques, coupled with targeted gene deletion and replacement, may provide a powerful tool for analysis of genomic instability and its underlying genetic mechanisms.

DT40 presents a unique opportunity to exploit newly available tools for chicken genomic analysis. A 13K chicken cDNA microarray representing 11447 non-overlapping ESTs has been developed. This array detects expression of 7086 DT40 genes of which_644 are over-expressed 3-fold or greater and 1585 are under-expressed 3-fold or greater relative to normal post-hatch bursal cell populations. Changes in RNA expression due to single gene alterations can be detected by expression profiling. For example, by this method, over expression of the oncogenic micro RNA bic up-regulates expression of VBP, a known regulator of Avian Leukosis Virus LTR- driven transcription with very little additional expression change, A degree of cytogenetic abnormality and instability of DT40 cells has been observed, which is characterized at the fine structure level using microarray-based comparative genome hybridization (array-CGH). The relationship between gene copy number and RNA expression levels can be assessed in the same tissue samples using the same microarray. A newly introduced technique for genome-wide analysis of palindrome formation (GAPF) detects long inverted repeats, or palindromes, which are early events in gene amplification and possibly other DNA structural change. Since both array CGH-detected copy number changes and GAPF-detected palindromes are abundant in DT40, these techniques, coupled with targeted gene deletion and replacement, may provide a powerful tool for analysis of genomic instability and its underlying genetic mechanisms.

Genetic instability plays a key role in the formation of naturally occurring cancer. The formation of long DNA palindromes is a rate-limiting step in gene amplification, a common form of tumor-associated genetic instability. Genome-wide analysis of palindrome formation (GAPF) has detected both extensive palindrome formation and gene amplification, beginning early in tumorigenesis, in an experimental Myc-induced model tumor system in the chicken bursa of Fabricius. We determined that GAPF-detected palindromes are abundant and distributed nonrandomly throughout the genome of bursal lymphoma cells, frequently at preexisting short inverted repeats. By combining GAPF with chromatin immunoprecipitation (ChIP), we found a significant association between occupancy of gene-proximal Myc binding sites and the formation of palindromes. Numbers of palindromic loci correlate with increases in both levels of Myc over-expression and ChIP-detected occupancy of Myc binding sites in bursal cells. However, clonal analysis of chick DF-1 fibroblasts suggests that palindrome formation is a stochastic process occurring in individual cells at a small number of loci relative to much larger numbers of susceptible loci in the cell population and that the induction of palindromes is not involved in Myc-induced acute fibroblast transformation. GAPF-detected palindromes at the highly oncogenic bic/miR-155 locus in all of our preneoplastic and neoplastic bursal samples, but not in DNA from normal and other transformed cell types. This finding indicates very strong selection during bursal lymphomagenesis. Therefore, in addition to providing a platform for gene copy number change, palindromes may alter microRNA genes in a fashion that can contribute to cancer development., Author Summary Genetic instability is a key process in the development of naturally occurring cancer. Gene amplification is one important consequence of underlying oncogenic instability. Long DNA palindrome formation is a rate-limiting early step in gene amplification. The development of a new functional genomic tool called genome-wide analysis of palindrome formation (GAPF) led to the recent discovery of the widespread occurrence of such palindromes in both animal tumor models and human tumor cells. Using a Myc oncogene-induced lymphoma model system, this paper describes clustering of tumor-specific palindromes throughout the genome as well as an association of sites of palindrome formation with both preexisting short inverted DNA repeat sequences and occupied Myc DNA-binding sites. We discovered consistent palindrome formation at a cancer-associated microRNA gene called bic/miR-155, beginning at an early stage of tumor development, and without significant further amplification of the locus. Thus, DNA palindromes themselves may directly influence tumorigenesis.