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

  1. Erika Brunet1,7
  1. 1Museum National d’Histoire Naturelle, CNRS UMR7196, Inserm U565, 75005 Paris, France;
  2. 2INSERM U978, Université Paris 13, Sorbonne Paris Cité, Labex “Inflamex,” 93017 Bobigny, France;
  3. 3Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA;
  4. 4Sangamo BioSciences, Inc., Point Richmond Tech Center, Richmond, California 94804, USA;
  5. 5Institut Cochin, Universite Paris Descartes, CNRS UMR 8104, Inserm U1016, 75014 Paris, France
    1. 6 These authors contributed equally to this work.

    Abstract

    Chromosomal translocations are signatures of numerous cancers and lead to expression of fusion genes that act as oncogenes. The wealth of genomic aberrations found in cancer, however, makes it challenging to assign a specific phenotypic change to a specific aberration. In this study, we set out to use genome editing with zinc finger (ZFN) and transcription activator-like effector (TALEN) nucleases to engineer, de novo, translocation-associated oncogenes at cognate endogenous loci in human cells. Using ZFNs and TALENs designed to cut precisely at relevant translocation breakpoints, we induced cancer-relevant t(11;22)(q24;q12) and t(2;5)(p23;q35) translocations found in Ewing sarcoma and anaplastic large cell lymphoma (ALCL), respectively. We recovered both translocations with high efficiency, resulting in the expression of the EWSR1–FLI1 and NPM1–ALK fusions. Breakpoint junctions recovered after ZFN cleavage in human embryonic stem (ES) cell–derived mesenchymal precursor cells fully recapitulated the genomic characteristics found in tumor cells from Ewing sarcoma patients. This approach with tailored nucleases demonstrates that expression of fusion genes found in cancer cells can be induced from the native promoter, allowing interrogation of both the underlying mechanisms and oncogenic consequences of tumor-related translocations in human cells. With an analogous strategy, the ALCL translocation was reverted in a patient cell line to restore the integrity of the two participating chromosomes, further expanding the repertoire of genomic rearrangements that can be engineered by tailored nucleases.

    Footnotes

    • 7 Corresponding authors

      E-mail m-jasin{at}ski.mskcc.org

      E-mail ebrunet{at}mnhn.fr

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.147314.112.

      Freely available online through the Genome Research Open Access option.

    • Received August 3, 2012.
    • Accepted April 3, 2013.

    This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.

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