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E-GEOD-71928 - Induced genomic rearrangements and chromothripsis by micronucleus-mediated chromosome transfer [850K]

Status
Released on 13 August 2015, last updated on 20 August 2015
Organism
Homo sapiens
Samples (4)
Array (1)
Protocols (8)
Description
Chromosome segregation errors have been linked to DNA damage and genomic rearrangements. Accumulating evidence has shown that catastrophic genomic rearrangements, like chromothripsis, can result from lagging chromosomes undergoing aberrant DNA replication and DNA damage in micronuclei. Detailed characterization of genomic rearrangements resulting from DNA damage in micronuclei has been hampered because of difficulties in culturing daughter cells with DNA damage. Here, we employ a method by which a specific single chromosome is trapped in a micronucleus, followed by transfer to an acceptor cell. Next, stably propagating clonal cell lines with an extra chromosome were established and analyzed by copy number profiling and whole genome sequencing. While non-transformed, p53 proficient and telomerase-immortalized RPE1 cells showed a stable genome following addition of the transferred chromosome, we observed frequent de novo genomic rearrangements in cells derived from the HCT116 colorectal cancer cell line after chromosome transfer. The de novo rearrangements varied from simple deletions and duplications to complex rearrangements. Phase-informative SNPs revealed that the rearrangements specifically occurred on the transferred chromosome. We found that the complex rearrangements recapitulated all features of chromothripsis, including massive oscillation between two copy number states, localization to a single chromosome, random joining of chromosome fragments and non-homologous or micro-homologous repair. We describe an approach that enables the isolation of clonal cell lines with genomic rearrangements and chromothripsis on a specific chromosome in p53 proficient cells. The procedure enables further investigation of the exact mechanism leading to chromothripsis and the analysis of its consequences for cell survival (viability) and cancer development. We analyzed 38 cell clones, originating from HCT116 or RPE1 cells respectively, with Illumina beadchip arrays to test for unique de novo copy number variants and to determine the chromosome affacted by the CNAs.
Experiment type
genotyping by array 
Contacts
Wigard Kloosterman <w.kloosterman@umcutrecht.nl>, Aline Campos Sparr, Fenna Kropveld, Ivo Renkens, Karen J Duran, Markus J van Roosmalen, Mirjam S de Pagter, Verena Passerini, Wigard P Kloosterman, Zuzana Storchová
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-71928.idf.txt
Sample and data relationshipE-GEOD-71928.sdrf.txt
Processed data (1)E-GEOD-71928.processed.1.zip
Additional data (1)E-GEOD-71928.additional.1.zip
Array designA-GEOD-19718.adf.txt
Links