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Somatic structural rearrangements in genetically engineered mouse mammary tumors

Ignacio Varela1, Christiaan Klijn23, Phillip J Stephens1, Laura J Mudie1, Lucy Stebbings1, Danushka Galappaththige1, Hanneke van der Gulden2, Eva Schut2, Sjoerd Klarenbeek2, Peter J Campbell1, Lodewyk FA Wessels23, Michael R Stratton14*, Jos Jonkers2*, P Andrew Futreal1* and David J Adams1*

Author Affiliations

1 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK

2 Netherlands Cancer Institute, Division of Molecular Biology, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands

3 Delft University of Technology, Delft Bioinformatics Lab., PO Box 5031. 2600 GA, Delft, The Netherlands

4 Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, Surrey, SM2 5NG, UK

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Genome Biology 2010, 11:R100  doi:10.1186/gb-2010-11-10-r100

Published: 13 October 2010

Abstract

Background

Here we present the first paired-end sequencing of tumors from genetically engineered mouse models of cancer to determine how faithfully these models recapitulate the landscape of somatic rearrangements found in human tumors. These were models of Trp53-mutated breast cancer, Brca1- and Brca2-associated hereditary breast cancer, and E-cadherin (Cdh1) mutated lobular breast cancer.

Results

We show that although Brca1- and Brca2-deficient mouse mammary tumors have a defect in the homologous recombination pathway, there is no apparent difference in the type or frequency of somatic rearrangements found in these cancers when compared to other mouse mammary cancers, and tumors from all genetic backgrounds showed evidence of microhomology-mediated repair and non-homologous end-joining processes. Importantly, mouse mammary tumors were found to carry fewer structural rearrangements than human mammary cancers and expressed in-frame fusion genes. Like the fusion genes found in human mammary tumors, these were not recurrent. One mouse tumor was found to contain an internal deletion of exons of the Lrp1b gene, which led to a smaller in-frame transcript. We found internal in-frame deletions in the human ortholog of this gene in a significant number (4.2%) of human cancer cell lines.

Conclusions

Paired-end sequencing of mouse mammary tumors revealed that they display significant heterogeneity in their profiles of somatic rearrangement but, importantly, fewer rearrangements than cognate human mammary tumors, probably because these cancers have been induced by strong driver mutations engineered into the mouse genome. Both human and mouse mammary cancers carry expressed fusion genes and conserved homozygous deletions.