Efficient Recreation of t(11;22) EWSR1-FLI1+ in Human Stem Cells Using CRISPR/Cas9

Abstract

Efficient methodologies for recreating cancer-associated chromosome translocations are in high demand as tools for investigating how such events initiate cancer. The CRISPR/Cas9 system has been used to reconstruct the genetics of these complex rearrangements at native loci while maintaining the architecture and regulatory elements. However, the CRISPR system remains inefficient in human stem cells. Here, we compared three strategies aimed at enhancing the efficiency of the CRISPR-mediated t(11;22) translocation in human stem cells, including mesenchymal and induced pluripotent stem cells: (1) using end-joining DNA processing factors involved in repair mechanisms, or (2) ssODNs to guide the ligation of the double-strand break ends generated by CRISPR/Cas9; and (3) all-in-one plasmid or ribonucleoprotein complex-based approaches. We report that the generation of targeted t(11;22) is significantly increased by using a combination of ribonucleoprotein complexes and ssODNs. The CRISPR/Cas9-mediated generation of targeted t(11;22) in human stem cells opens up new avenues in modeling Ewing sarcoma.

Keywords: CRISPR; Cas9; Ewing sarcoma; MSC; cancer modeling; cancer translocation; disease model; genome engineering; human stem cells; iPSC.

Graphical abstract

Figure 1

Validation of the All-in-One Cas9 CRIPSR Plasmid in HEK293 and hMSCs (A) pLV-U6sgRNA^#1-H1sgRNA^#2-C9G all-in-one plasmid co-expressing sgRNAs targeting introns in EWSR1 (sgE1) and FLI1 (sgF2) and expressing Cas9 protein. The middle schemes show the location of the regions targeted by sgE1 and sgF2 sgRNAs in the t(11;22)/EWSR1-FLI1 chromosomal translocation: EWSR1 intron 7 (sgE1) and FLI1 intron 4 (sgF2). The lower schemes show PCR oligonucleotide positions and PCR product sizes. The U6, H1, and CMV promoters are represented as black arrows. LTR, long terminal repeat; P2A, 2A self-cleaving peptide; EGFP, enhanced green fluorescent protein; WPRE, woodchuck post-transcriptional regulatory element. (B) Representative FISH images obtained with a dual-color dual-fusion probe (EWSR1 in green and FLI1 in red), showing HEK293 and hMSCs positive and negative for t(11;22). Arrows indicate fusion signals corresponding to the junction regions. Interphase nuclei are counterstained with DAPI. Scale bars, 10 μm. (C) Fold change in the number of FISH-identified t(11;22)⁺ HEK293 and hMSCs obtained using the all-in-one plasmid approach (one plasmid) versus the two-plasmid approach. Data are means ± SEM (n = 3 independent experiments); ^∗∗p < 0.01, ^∗∗∗p < 0.001, unpaired Student's t test. (D) Top: agarose gel electrophoresis of translocation-specific PCR products from pooled HEK293 and hMSC samples. Bottom: representative Sanger sequencing chromatogram showing the breakpoint region in the EWSR1-FLI1 fusion gene mapped at der(22) in hMSCs.

Figure 2

FACS Sorting of Cas9-2A-GFP-Transfected Cells Enriches for Efficiently Engineered t(11;22) Translocations (A) Representative EGFP flow cytometry profiles for transfected hMSCs. The percentages of EGFP⁺ cells in the initial population are indicated. (B) Fold-change variation in the number of engineered t(11;22) translocations determined by FISH in hMSCs with or without GFP FACS purification. Data are means ± SEM (n = 3 independent experiments); ^∗p < 0.05. (C) Representative EGFP flow-cytometry profiles for transfected HEK293 cells. The percentages of GFP^low and GFP^high cells in the initial population are indicated. (D) Fold-change variation in the number of engineered t(11;22) translocations evaluated by FISH in HEK293 cells without or with sorting of either GFP^low and GFP^high cells. Data are means ± SEM (n = 3 independent experiments); ^∗∗p < 0.01, unpaired Student's t test.

Figure 3

Effect of Nuclear Localization Signals on Cas9 Protein Function (A) Representative immunofluorescence images of HEK293 and hMSCs transfected with constructs encoding nuclear localization signal (1xNLS or 2xNLS) versions of pLV-U6#1H1#2-C9G stained with anti-Cas9 antibody to visualize Cas9 localization. DNA was counterstained with DAPI. Scale bar, 50 μm. (B) Nuclear/cytoplasm ratio of Cas9 with 1xNLS or 2xNLS signals. n, number of analyzed cells. Data are means ± SEM; ^∗∗p < 0.01, ^∗∗∗p < 0.001, unpaired Student's t test. (C) Representative sgF2 T7 endonuclease I assay in HEK293 cells to determine the targeting activity of 1xNLS or 2xNLS versions of pLV-U6^#1H1^#2-C9G. Cells were either transfected with an empty pLV-U6H1-C9G plasmid (control) or with 1xNLS-pLV-U6#1H1#2-C9G or 2xNLS- pLV-U6#1H1#2-C9G plasmids. Open triangle depicts the full-length PCR product and filled triangles the digestion products. (D) Fold-change variation in the number of engineered t(11;22) translocations evaluated by FISH in HEK293 cells and hMSCs transfected with 1xNLS versus 2xNLS versions of pLV-U6^#1H1^#2-C9G vector. Data are means ± SEM (n = 3 independent experiments); ^∗p < 0.05, unpaired Student's t test.

Figure 4

Contribution of ssODNs and DNA End-Processing Factors to CRISPR/Cas9 Targeting Efficiency (A) ssODN strategy, indicating the sgRNA target loci and the e1f2 and f1e2 ssODNs flanking the breakpoint regions mapping to introns in FLI1 (red) and EWSR1 (blue). The scheme on the right represents the lengths of the e1f2 ssODNs. (B) Influence of ssODN length on the efficiency of t(11;22) translocations in HEK293 cells evaluated by FISH. (C and D) FISH evaluation of the influence of two ssODNs versus one ssODN on the efficiency of t(11;22) generation in HEK293 cells (C) and without ssODNs versus two ssODNs in hMSCs (D). Data are means ± SEM (n = 3 independent experiments); ^∗p < 0.05, ^∗∗p < 0.01, unpaired Student's t test.

Figure 5

Contribution of DNA End-Processing Factors and RNPs to CRISPR/Cas9-Mediated t(11;22) Generation (A and B) Influence of different DNA end-processing factors on the efficiency of t(11;22) translocation in HEK293 cells (A) and hMSCs (B). (C) FISH evaluation of the frequency of t(11;22) translocations engineered with 3xNLS RNP complexes in HEK293 cells and hMSCs. (D) Frequency of engineered t(11;22) translocations evaluated by FISH in hMSCs transfected with Cas9 RNP, ssODNs, and TREX2 and PARP1 factors. Data are means ± SEM (n = 3 independent experiments); ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, unpaired Student's t test.

Figure 6

Induction of Targeted Chromosomal Translocation in hiPSCs (A) Representative sgE1 and sgF2 on-target T7 endonuclease I assay in hiPSCs to determine the targeting activity of RNP complexes. Cells were transfected either with a non-targeting 3xNLS RNP complex (control), with 2xNLS plasmid, or with 3xNLS RNP complexes targeting both breakpoint regions. Open triangles depict the full-length PCR product and filled triangles the digestion products. (B) Agarose gel electrophoresis of translocation-specific PCR products from pooled hiPSC samples. The Sanger sequencing chromatogram shows the breakpoint region in the EWSR1-FLI1 fusion gene mapped at der(22). (C) Representative FISH images obtained with a break-apart EWSR1 probe showing hiPSCs positive and negative for t(11;22) generated with Cas9 RNP and ssODNs. Arrows indicate separated signals corresponding to the der(22) and der(11) breakpoint regions. Interphase nuclei are counterstained with DAPI. Scale bars, 10 μm. (D) Fold-change variation in the number of engineered t(11;22) translocations determined by FISH in hiPSCs transfected with the 2xNLS-pLV-U6#1H1#2-C9G plasmid approach or with the RNP + ssODNs approach. Data are means ± SEM (n = 3 independent experiments); ^∗∗p < 0.01, unpaired Student's t test. (E) Immunostaining of t(11;22) positive and negative hiPSC colonies for the pluripotency markers OCT4 and SSEA4. Scale bars, 200 μm.