Cancer translocations in human cells induced by zinc finger and TALE nucleases

Despite the wide range of recurrent chromosomal translocations identified in various cancers (more than 300 genes implicated) (Mitelman et al. 2007), the direct path from translocation formation to tumorigenesis is not always clear. In mouse and human cells, studies are mostly based on either ectopically expressing or silencing the fusion gene induced by the translocation. In the case of fusion protein expression from a cDNA (often randomly integrated into the genome), the choice of the fusion transgenic promoter is crucial because the level of fusion protein expression must often be tightly controlled to recapitulate endogenous levels or risk spurious results from overexpression. And in silencing strategies, even low levels of expression remaining for the fusion protein could mask to some extent the full cellular consequences of the translocation. DNA double-strand breaks (DSBs) are considered to be causative lesions for many genomic rearrangements, including chromosomal translocations (Richardson and Jasin 2000; Mani and Chinnaiyan 2010). With the development of tailored endonucleases like zinc finger nucleases (ZFNs) (Urnov et al. 2010; Carroll 2011) and more recently transcription activator-like effector nucleases (TALENs) (Doyon et al. 2011; Mussolino and Cathomen 2012), it is now possible to create a DSB in the genome of a human cell at any locus of interest for the purposes of gene correction and gene disruption. In addition, contemporaneous expression of two ZFNs targeting loci has led to the induction of translocations at model loci in human multipotent and stem cells (Brunet et al. 2009) and intrachromosomal rearrangements (e.g., deletions) in transformed cell lines (Lee et al. 2010, 2012). This approach to study translocation formation obviates the need for prior genetic manipulation or cloning of cells, significantly expanding the repertoire of human cells that can be interrogated for translocation formation. In this study, we now investigate the formation of two specific translocations, one frequently observed in Ewing sarcoma and one found in anaplastic large cell lymphoma (ALCL) using both types of nucleases (ZFNs and TALENs). Ewing sarcoma is a prototype of a solid tumor carrying a specific chromosomal translocation; it enables the transcription of the EWSR1–FLI1 chimeric protein corresponding to the in-frame fusion of the EWSR1 amino terminus with the FLI1 carboxyl terminus. It is well accepted that the EWSR1–FLI1 fusion protein acts as a transcriptional factor, but target genes induced or repressed by the fusion protein are not fully identified yet (Chansky et al. 2004; Prieur et al. 2004; Smith et al. 2006; Riggi et al. 2010). ALCL is an aggressive T-cell non-Hodgkin lymphoma, accounting for as much as 10%–15% of children with the disease. About half of tumors exhibits the specific translocation t(2;5)(p23;q35) resulting in NPM1–ALK expression and constitutive ALK tyrosine kinase activity (Morris et al. 1994; Elmberger et al. 1995; Kuefer et al. 1997).