Abstract 1213: Endogenous p53 affinity tagging with CRISPR
Authors: Yang Chen , Lawrence Cortney L. , Lyons Charles E. , Taylor Shirley M. , Moran Richard G. 
Published: August 2015

Several antimetabolites used for cancer treatment, including hydroxyurea (HU) and pemetrexed (PTX), stabilize tumor suppressor protein p53, but fail to induce the transcription of p53 downstream target genes. To understand the underlying mechanism for the deficiency of stabilized p53, we are quantitatively characterizing p53 posttranslational modification and its interaction partners with mass spectrometry (MS). To facilitate the purification of endogenous p53, we established an HCT116 human colon carcinoma cell line, in which one allele of endogenous p53 was tagged with a classic Tandem Affinity Tag (TAP) at the C-terminus, using adenovirus associated virus (AAV) mediated homologous recombination (HR). The purification of p53 from this cell exhibited severe losses at each step, compromising analysis by MS. Because of this limited yield from TAP purification, we performed a systematic tagging of p53 with 3xFLAG, Strep-II, and HALO tags, and their combinations, at both N- and C-termini. The latest CRISPR (clustered regularly interspaced short palindromic repeats)/cas9 nuclease system provides major advantages for endogenous gene modification through HR. Efficient site-specific protein tagging (or mutation) requires a DNA break point in the immediate vicinity, limiting the choice of guide DNA (gDNA) positions possible. By extending the complementary sequence between CRISPR targeting RNA (crRNA) and trans-activating crRNA (tracrRNA) in the chimeric single guide RNA (sgRNA), we expanded the essential Protospacer Adjacent Motif (PAM) sequence of the S. pyogenes CRISPR II system from NGG to NAG with equal targeting efficiency. Cas9 nickase (both D10A, and H840A-N854A-N863A) generated more favorable HR rates compared to non-homologous end joining (NHEJ), while mitigating off-target effects, in comparison to wild type cas9. Utilizing our conditions, we achieved 2-8% (for different tags) endogenous p53 tagging in the background of 10-60% NHEJ from wild type cas9 and single sgRNA. With cas9 nickase and two sgRNA, we consistently achieved 0.2-2% specific p53 tagging in the background of 0.01-8% NHEJ, with higher efficiency for 5′ than 3′ single strand overhangs generated. We are currently generating single cell clones, selecting those tags most faithful to natural p53 expression levels, and testing p53 purification efficiencies with different tags. In conclusion, we optimized the CRISPR system, extensively characterized the individual steps in generating single cell clones for endogenous gene tagging, and will apply the optimal tag to purify p53 and its co-eluted binding partners for quantitative MS analysis.

Citation Format: Chen Yang, Cortney L. Lawrence, Charles E. Lyons, Shirley M. Taylor, Richard G. Moran. Endogenous p53 affinity tagging with CRISPR. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1213. doi:10.1158/1538-7445.AM2015-1213