Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors

Y Esther Tak; Gaylor Boulay; Lukuo Lee; Sowmya Iyer; Nicholas T Perry; Hayley T Schultz; Sara P Garcia; Liliane Broye; Joy E Horng; Shruthi Rengarajan; Beverly Naigles; Angela Volorio; Jeffry D Sander; Jingyi Gong; Nicolὸ Riggi; J Keith Joung; Miguel N Rivera

doi:10.1016/j.xgen.2022.100119

Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors

Cell Genom. 2022 Apr 13;2(4):100119. doi: 10.1016/j.xgen.2022.100119.

Authors

Y Esther Tak^{1

2

3}, Gaylor Boulay^{1

3

4}, Lukuo Lee¹, Sowmya Iyer¹, Nicholas T Perry^{1

2}, Hayley T Schultz^{1

2}, Sara P Garcia¹, Liliane Broye⁵, Joy E Horng^{1

2}, Shruthi Rengarajan¹, Beverly Naigles¹, Angela Volorio^{1

5}, Jeffry D Sander^{1

2

3}, Jingyi Gong^{1

2}, Nicolὸ Riggi⁵, J Keith Joung^{1

2

3}, Miguel N Rivera^{1

3

4}

Affiliations

¹ Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA.
² Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA.
³ Department of Pathology, Harvard Medical School, Boston, MA, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁵ Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland.

Abstract

Repeat elements can be dysregulated at a genome-wide scale in human diseases. For example, in Ewing sarcoma, hundreds of inert GGAA repeats can be converted into active enhancers when bound by EWS-FLI1. Here we show that fusions between EWS and GGAA-repeat-targeted engineered zinc finger arrays (ZFAs) can function at least as efficiently as EWS-FLI1 for converting hundreds of GGAA repeats into active enhancers in a Ewing sarcoma precursor cell model. Furthermore, a fusion of a KRAB domain to a ZFA can silence GGAA microsatellite enhancers genome wide in Ewing sarcoma cells, thereby reducing expression of EWS-FLI1-activated genes. Remarkably, this KRAB-ZFA fusion showed selective toxicity against Ewing sarcoma cells compared with non-Ewing cancer cells, consistent with its Ewing sarcoma-specific impact on the transcriptome. These findings demonstrate the value of ZFAs for functional annotation of repeats and illustrate how aberrant microsatellite activities might be regulated for potential therapeutic applications.

Abstract

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