Abstract 409: Genome engineering to generate models of chromosome arm-level aneuploidies in lung carcinoma

Abstract

Abstract Almost 90% of tumors are aneuploid and have arm- or whole- chromosome level copy number changes. Arm-level copy number alterations cluster by tumor type, suggesting that specific arm-level changes are influenced by cell type. Systematic methods of generating copy number changes on a particular chromosome have not been tested, leaving the effects of specific aneuploidies in cancer unclear. The most frequent genomic alteration in lung squamous cell carcinomas (SCCs) is loss of chromosome 3p. This alteration occurs in 90% of lung SCCs, and covers the entire length of the chromosome arm. Over two-thirds of 3p genes show significantly decreased expression. However, the phenotypic effects of 3p loss in tumorigenesis are not known. We used the CRISPR-Cas9 system to generate double-strand breaks (DSBs) and produce partial aneuploidies of arm-level loss. We have targeted guide RNAs adjacent to centromeric satellite-repeat sequences on chromosome arm 3p. At this location, we induced homologous recombination with a selection cassette and artificial telomere. We have successfully isolated almost 90 clones of immortalized lung epithelial cells with deletion of the 3p arm, with 8 validated by whole genome sequencing. Consistent with patient data, expression of 3p genes is also decreased upon deletion. Phenotypic characterization revealed that cells with chromosome 3p deletion proliferate more slowly than their siblings. 3p deleted cells show increased G1 arrest, but do not undergo increased apoptosis or cell death. We are currently testing 3p loss in combination with other frequent SCC alterations, such as SOX2 and TP63 gain. We have also identified expression changes in trans, outside of chromosome 3p. These studies provide a robust model that will address a gap in our understanding of aneuploidy in cancer by using targeted endonuclease technology to create models of partial aneuploidies. Future work will include investigation of how different chromosomal changes contribute to cancer formation, which will have implications on our understanding of tumorigenesis. Citation Format: Alison M. Taylor, Gavin Ha, Juliann Shih, Xiaoyang Zhang, Joshua M. Francis, Matthew Meyerson. Genome engineering to generate models of chromosome arm-level aneuploidies in lung carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 409. doi:10.1158/1538-7445.AM2017-409