A generic strategy for CRISPR-Cas9-mediated gene tagging

Genome engineering has been greatly enhanced by the availability of Cas9 endonuclease that can be targeted to almost any genomic locus using so called guide RNAs (gRNAs). However, the introduction of foreign DNA sequences to tag an endogenous gene is still cumbersome as it requires the synthesis or cloning of homology templates. Here we present a strategy that enables the tagging of endogenous loci using one generic donor plasmid. It contains the tag of interest flanked by two gRNA recognition sites that allow excision of the tag from the plasmid. Co-transfection of cells with Cas9, a gRNA specifying the genomic locus of interest, the donor plasmid and a cassette-specific gRNA triggers the insertion of the tag by a homology-independent mechanism. The strategy is efficient and delivers clones that display a predictable integration pattern. As showcases we generated NanoLuc luciferase- and TurboGFP-tagged reporter cell lines.

Abstract A148: Modeling patient responses to targeted therapy with rAAV mediated gene editing

Successful drug development in oncology requires a deeper understanding of the functional consequences of the diverse genetic changes observed in human cancers. For example, responses to epidermal growth factor receptor (EGFR) inhibitors are observed in patients whose tumors express EGFR alleles with activating mutations, rather than in tumors overexpressing EGFR. Furthermore, antibodies against EGFR are ineffective in tumors bearing certain activating alleles of KRAS.

Horizon Discovery has used its proprietary rAAV gene engineering technology to generate isogenic cell lines covering a range of mutations commonly found in cancer patients. Use of a non-tumorigenic ‘clean’ cell line background such as MCF10A allows specific evaluation of the mutations without any confounding factors due to the presence of other genetic alterations. Mutations introduced into cancer cell line backgrounds allow the contextual evaluation of a cancer related gene. Here we describe the use of isogenic cell line panels as powerful tools for investigating sensitivity and resistance markers to cancer therapeutics.

Some 50% of human tumors exhibit p53 loss or inactivation. To investigate how p53 loss in combination with other common cancer-driving mutations may influence therapeutic responses, we have generated a suite of MCF10A isogenic cell lines covering some of the major cancer genotypes, either in isolation or on a TP53 (-/-) background. These genotypes include EGFR (delE746-A750/+), EGFR (L858R/+), KRAS (G12V/+), BRAF (V600E/+), BRAF (V600K/+) and PIK3CA (H1047R/+). Thus, we have been able to investigate the interaction effects of discrete mutations in molecularly defined, but more tumor-like cell models.

One data highlight arose from the profiling of the EGFR mutant panel using small molecule EGFR inhibitors; in isolation, the introduction of common activating EGFR mutations L858R or deletion of E746-A750 led to increased sensitivity, recapitulating clinical findings. However, combining EGFR mutation with loss of p53 further enhanced the cell response. Through systematic profiling of this panel to targeted therapeutic agents such as gefinitib, selumetinib, vemurafenib, and pictilisib, we have identified interesting differential sensitivities, which can be directly attributable to introduction of a given mutation.

Results such as these can enable better patient stratification for anticancer agents, and allow incorporation of molecular markers into clinical trial design for personalised therapeutic regimens.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A148.

Citation Format: Annette S. Little, Jessica Hunt, David Hughes, Ruth Feltell, Daniel Gitterman, Rachel Leah, Holly Astley, Ramu Mangena, Kyla Grimshaw, Christopher Torrance. Modeling patient responses to targeted therapy with rAAV mediated gene editing. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A148.

Abstract C119: Identification of gene expression biomarkers that predict sensitivity to the PARP inhibitor olaparib

Background: The oral PARP inhibitor olaparib (AZD2281, KU-0059436) is in Phase II clinical trials in patients with BRCA-mutated breast and ovarian cancer. Early results in these trials have provided positive clinical evidence for the targeted therapy concept of synthetic lethality using PARP inhibitors in molecularly-defined tumors with little effect on normal tissues. However, olaparib offers the potential to treat a broader range of patient tumors and pre-clinical studies have indicated that homologous recombination deficiency (HRD) due to loss of other DNA repair genes or through impaired cell-cycle checkpoints can also lead to sensitivity to PARP inhibitors. The ability to stratify patients whose tumors will respond to treatment will be critical to realise the potential of this targeted therapy approach. In order to identify predictive biomarkers of olaparib response and to provide further insights into mechanisms of olaparib sensitivity a study was undertaken using a panel of cell lines correlating response with molecular profiles.

Methods: A cross tumor-type panel of 95 cell lines (KU-95 panel) representing breast, ovarian, colorectal, lung, head & neck and pancreatic cancers was tested for sensitivity to olaparib using 2D-clonogenic survival assays. Baseline (untreated) gene expression profiles using Affymetrix genome-wide U133A 2.0 arrays together with protein expression and mutational status of genes, such as BRCA1, known to modify of olaparib response were determined for each cell line. Novel statistical, bioinformatics and pathway analysis approaches were used to identify genes that are predictive for olaparib response.

Results: Across the KU-95 cell-line panel, 30 cell lines were highly sensitive to olaparib (IC50 <1 M) treatment and 36 were resistant (IC50 >4 M). Deleterious mutations in BRCA1 or BRCA2 genes were associated with only a small subset of highly sensitive cell lines indicating the presence of other factors able to modulate olaparib responsiveness. Directed analysis of several other DNA repair genes showed correlations with response consistent with previous data. Genome-wide transcriptome and pathway mapping analysis revealed DNA repair and proliferation associated genes to be most consistently correlated with olaparib sensitivity. Based on results from all these approaches a candidate baseline gene expression profile predictive of olaparib response was established.

Conclusions: By profiling a large panel of cell lines we have determined that factors in addition to BRCA mutation can be linked with olaparib sensitivity. A list of candidate gene transcripts was identified that predicts sensitivity to olaparib across a broad range of tumor types in vitro and may have utility as predictive biomarkers in the clinic. Studies are already underway to determine whether this baseline transcript tumor profile can be correlated with patient responses to olaparib.

Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C119.