Structural organization of MYCN amplicons of neuroblastoma tumors, xenografts, and cell lines characterized by the sequences encompassing the MYCN amplicons in a human neuroblastoma cell line

Abstract

We characterized differences in the structural organization of the MYCN amplicons of a number of neuroblastomas by analyzing 8 contigs spanning 330 kb cloned from the MYCN amplicon of a neuroblastoma cell line. Some regions were amplified in almost all specimens, the conserved regions (CRs), and others were differentially amplified in some subsets, the non-conserved regions (NCRs). CRs constituted only 20% of the 330 kb region, with the remainder being NCRs. The regions that inevitably co-segregate with the MYCN gene make up the core, whereas flanking regions are retained at random. If a histogram of the frequency with which the amplified NCR sequences from one specimen match those of the cell line MC-NB-I shows a random distribution, the NCRs would co-segregate with MYCN as a result of random events. However, both the tumors and cell lines/xenografts showed a distribution with two distinct peaks; one from a group containing a small number of sequences with a fairly high degree of homology to the NCRs of MC-NB-I, and the other from a group containing a large number of sequences with little homology. These results indicate that the flanking segments are preferentially co-segregated with MYCN by a non-random mechanism.

Integrated Cytogenetic and High-Resolution Array CGH Analysis of Genomic Alterations Associated with <i>MYCN</i> Amplification

“…Most MYCN amplicons contain 50-100 tandem repeats of a unit that is 100 kb to 1 MB in size [Akiyama et al, 1993;Noguchi et al, 1996]. MYCN maps to the central core of amplicons and co-amplified genomic regions vary considerably in size and complexity [Kohl et al, 1983;Schwab et al, 1983Schwab et al, , 1984Pandita et al, 1997].…”

Megabase-scale analysis of the origin of N-myc amplicons in human neuroblastomas

“…In all of the neuroblastoma cell lines, xenografts, and tumor specimens, N-myc was amplified 20 to a few hundred-fold (4, 7, 15, 20, 21, unpublished data). Detailed information on these specimens is given elsewhere (10,11,15).…”

“…The probes used in this experiment came from two different DNA sources; one is from the cell line MC-NB-l (10,15) and the other is from the cell line IMR-32 (3,19), which showed differential amplification among the subsets of the various human neuroblastomas (3, 7,8,10,11,15,16,19). To generate a restriction map, we used the strategy of performing single digests with up to 20 different rare cutting enzymes and hybridizing the resulting fragments with a number of DNA probes ( Fig.…”

“…Analysis of amplified regions in 38 different neuroblastoma tumors, xenografts and cell lines Some of the co-amplification profiles of the DNA probes isolated from the cell lines MC-NB-1 and IMR-32 have been previously described (7, 8, 10, 11,15,16,19). In this study, we completed the co-amplification profiles of the probes used to construct the physical map for the neuroblastoma specimens, which include 14 cell lines, 5 xenografts and 19 tumors.…”

“…Analyses of the structural organization of the amplified DNA show that the amplified region is organized as a tandem repeat of amplicons, called 'N-myc amplicons', each of which contains the N-myc gene along with flanking sequences ranging up to several hundred kilobases in size. This is a consequence of complex rearrangements (8,10,11,12,13,14,15,16,17). These studies lead us to consider the N-myc gene amplification in two contexts: one is rearrangements in the initial stage, that is, either over-replication or excision, and the other is rearrangements during subsequent stages.…”