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Engineering Human Stem Cell Lines with Inducible Gene Knockout using CRISPR/Cas9

http://www.cell.com/cell-stem-cell/abstract/S1934-5909(15)00261-1?rss=yes by

 

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Figure 1

Generation of FRT Knockin hPSC Lines using Cas9 Nuclease

(A) Schematic diagram of the two-step strategy for generating an iKO hPSC line using PAX6 as an example. The first step is to generate an hPSC line with exons in both alleles flanked by FRT sites using our dual-sgRNA targeting strategy. The second step is to remove the drug-resistance cassette and insert the Flpe-ERT2 expression cassette into the AAVS1 locus to establish the iKO hPSC line. Upon treatment with 4-OHT, Flpe-ERT2 will translocate into the nucleus and recombine the FRT-flanked exons, thus resulting in frame-shift of a protein-coding sequence and KO of the targeted gene. Exons are shown as green or orange boxes, blue triangles represent LoxP sites, and yellow triangles represent FRT sites.

(B) Schematic depiction of the targeting strategy for exon 4 of the PAX6 locus. Vertical arrows indicate sgRNA2 and sgRNA7 targeting sites. Red and blue horizontal arrows indicate PCR genotyping primers for assaying PAX6 locus targeting and homozygosity, respectively. Donor plasmids: PGK, phosphoglycerate kinase promoter; Puro, puromycin-resistance gene.

(C) PCR genotyping of hESC clones targeted by sgRNA2 (first panel), sgRNA7 (second panel), or both sgRNA2 and sgRNA7 (third panel). The expected PCR product for the correctly targeted PAX6 locus is ∼1,800 bp (red arrows). Correctly targeted clones underwent a further homozygosity assay (fourth panel). Clones with the PCR products of ∼700 bp are heterozygous (blue arrow), and those clones without PCR products are homozygous (red asterisk).

(D) Representative sequencing results of targeted heterozygous or homozygous clones in the PAX6 locus using sgRNA2 (heterozygous), sgRNA7 (homozygous), or both sgRNA2 and sgRNA7 (homozygous). The PAM sequences and FRT sequences are labeled in red and yellow, respectively.

(E) OTX2 locus targeting. PCR genotyping of hESC clones targeted by both sgRNA3 and sgRNA5 (left panel) or both sgRNA2 and sgRNA9 (middle panel) is displayed. The expected PCR products for correctly targeted OTX2 locus are ∼1,200 bp (red arrows). Correctly targeted clones underwent a further homozygosity assay (right panel). Those clones with the PCR products of ∼750 bp are heterozygous (blue arrow), and those clones without these PCR products are homozygous (red asterisks).

See also Figures S1 and S2 .

Figure 2

Generation of FRT Knockin hPSC Lines using Cas9 Nickase

(A) Schematic depiction of the targeting strategy for exon 3 of the AGO2 locus. Vertical arrows indicate targeting sites for sgRNApair 7 (sgRNA7+sgRNA9), sgRNApair 14 (sgRNA14+sgRNA17), or sgRNApair 15 (sgRNA15+sgRNA18). PCR genotyping primers for the AGO2 locus targeting test (red arrows) or homozygosity test (blue arrows) are indicated.

(B) PCR genotyping of hESC clones targeted by both sgRNApair 7 and sgRNApair 15 (left panel) or both sgRNApair 7 and sgRNApair 14 (middle panel). Expected PCR products for the correctly targeted AGO2 locus are ∼1,400 bp (red arrows). Correctly targeted clones underwent a further homozygosity assay (right panel). Those clones with the PCR products of about 420 bp are heterozygous (blue arrow), and those without these PCR products are homozygous (red asterisk).

(C) Schematic diagram depicting the targeting strategy for the SOX2 locus using Cas9 nickase. The vertical arrows indicate targeting sites by SOX2 sgRNApair 1A (sgRNA1A+sgRNA1B), sgRNApair 2A (sgRNA2A+sgRNA2B), sgRNApair 5B (sgRNA5A+sgRNA5B), or sgRNApair 6B (sgRNA6A+sgRNA6B). PCR genotyping primers for the SOX2 locus targeting test (red horizontal arrows) or homozygosity test (blue horizontal arrow) are indicated.

(D and E) SOX2 locus targeting. PCR genotyping of hESC clones targeted using Cas9 nickase combined with either sgRNApair 2A and sgRNApair 5B (D) or sgRNApair 1A and sgRNApair 6B (E) is displayed. Expected PCR products for the correctly targeted SOX2 locus are ∼1,700 bp (red arrow). Those clones with the PCR products of about 550 bp are heterozygous (blue arrow), and those clones without these PCR products are homozygous (red asterisks).

See also Figure S3 .

Figure 3

Generation of iKO hPSC Lines

(A) Schematic depiction of the targeting strategy for the AAVS1 locus. Exons are shown as orange boxes. The vertical arrows indicate the targeting site by sgRNA T2 in the AAVS1 locus. The orange horizontal arrows indicate PCR genotyping primers for AAVS1 locus targeting. Donor plasmids: SA-Neo, splice acceptor sequence followed by a T2A self-cleaving peptide sequence and the neomycin resistance gene; CAG, synthetic CAGGS promoter containing the actin enhancer and the cytomegalovirus early promoter; Flpe, enhanced Flp recombinase; ERT2, mutated ligand-binding domain of estrogen receptor (ER).

(B) Genotyping strategy for Cre recombinase-mediated removal of the resistance gene expression cassette in the FRT knockin PAX6 or OTX2 locus. Exons are shown as green boxes, blue triangles represent LoxP sites, and yellow triangles represent FRT sites. The green and black arrows indicate PCR primers for assaying removal of the Cre recombinase-mediated resistance gene expression cassette and homozygosity, respectively.

(C) PCR genotyping of PAX6- or OTX2-iKO hESCs clones. The expected PCR products for the correctly targeted AAVS1 locus are ∼1,000 bp (orange arrows). The expected PCR products for PGK-puromycin (PGK-Puro) removal in the flanked PAX6 or OTX2 locus are ∼700 bp or ∼1,500 bp (green arrows), respectively. Those clones with the positive PCR products of ∼1,800 bp (in FRT knockin PAX6 locus, black arrow) or ∼1,450 bp (in FRT knockin OTX2 locus, black arrow) in the homozygosity test are heterozygous, and those clones without these PCR products are homozygous (PGK-Puro was removed in both targeted alleles). Those clones with the positive PCR products in the homozygosity test are heterozygous. Vertical arrows indicate clones with the correct AAVS1 locus targeting, PGK-Puro removal, and homozygosity of PGK-Puro removal in the FRT knockin PAX6 or OTX2 locus.

(D) Summary of the efficiency of second-step targeting in the hESC line with the exons of PAX6 or OTX2 flanked by FRT sequences.

See also Figure S4 .

Figure 4

Inducible Depletion of OTX2 and Functional Consequences

(A) Schematic depiction of PCR primer sets for genotyping. Blue arrows: external primer pair; red arrows: internal primer pair.

(B–D) Depletion of FRT-flanked exons of OTX2 in a time-dependent (at 2.5 μM, left panel) and dose-dependent (at 72 hr, right panel) manner upon 4-OHT treatment. The expected sizes of PCR products using external primer pairs for un-recombined FRT-flanked exons (blue arrow, upper) or recombined FRT-flanked exons (blue arrow, lower) are ∼1,600 bp or ∼650 bp, respectively. The red arrow indicates the PCR products (∼650 bp) using internal primer pairs. The black arrow indicates PCR products (∼420 bp) amplified from the AGO2 locus, which did not undergo recombination (control). The KO efficiency was plotted in (C) and (D) by calculating the density of PCR products from three or four independent experiments. Data are represented as mean ± SEM.

(E) Depletion of FRT-flanked exons of OTX2 upon 72 hr of treatment with 2.5 μM 4-OHT in OTX2 iKO neuroepithelial cells that underwent neural differentiation for 8 days. The arrows are indicated as in (B).

(F) Western blotting shows depletion of OTX2 protein upon treatment with 1.25 μM 4-OHT for 72 hr in OTX2 iKO and parental hESCs.

(G) Western blotting shows OTX2 protein expression along neural differentiation upon treatment with 1.25 μM 4-OHT at day 3.

(H) Western blotting shows permanent depletion of OTX2 expression upon 4 days of treatment with 1.25 μM 4-OHT commenced 2 days before neural differentiation.

(I) Immunostaining shows depletion of OTX2 protein expression at day 8 following 4 days of treatment with 1.25 μM 4-OHT commenced 2 days before neural differentiation. Scale bar, 20 μM.

(J and K) RT-qPCR shows gene expression after 4 days of treatment with 1.25 μM 4-OHT 2 days before neural differentiation (cells were collected at day 8; J) or 8 days after neural differentiation (cells were collected at day 16; K). Student’s t test. Data are represented as mean ± SEM. p < 0.05; ∗∗p < 0.01; ∗∗∗p < 0.001.

See also Figure S5 , Table S3 , and Table S5 .

Figure 5

Flanking Exons of Multiple Genes in One Step

(A) Schematic overview depicting the strategy for simultaneously targeting both the PAX6 locus and the SOX2 locus. Donor plasmids: Pur, PGK-driven puromycin resistance gene; Neo, PGK-driven neomycin resistance gene.

(B) PCR genotyping of hPSC clones targeted using the SOX2 donor plasmid (Puro), the PAX6 donor plasmid (Neo), WT Cas9, SOX2 targeting sgRNAs (sgRNA1A and sgRNA6B), and PAX6 targeting sgRNAs (sgRNA2 and sgRNA7). Expected PCR products for the correctly targeted SOX2 locus or PAX6 locus are ∼1,700 bp or ∼1,800 bp (red arrows), respectively. The vertical arrows indicate clones with both the SOX2 locus and the PAX6 locus targeted.

(C) Correctly targeted clones in both the SOX2 locus and the PAX6 locus underwent further homozygosity testing in both the SOX2 locus and the PAX6 locus. Those clones without the PCR products of ∼700 bp at the PAX6 locus (blue arrow, upper) and without the PCR products of ∼550 bp at SOX2 locus (blue arrow, lower) are homozygous clones targeted in both the SOX2 locus and the PAX6 locus (vertical arrows).

(D) Summary of the targeting efficiency and homozygous efficiency in both the SOX2 locus and the PAX6 locus.

See also Figure S6 .

Highlights

  • Efficient strategy outlined for engineering clonal inducible gene knockout hPSC lines
  • Dual-sgRNA targeting is essential for precise biallelic knockin of FRT
  • Inducible gene knockout can occur in all cells at any differentiation stages
  • Multiple genes can be targeted for inducible knockout

Summary

Precise temporal control of gene expression or deletion is critical for elucidating gene function in biological systems. However, the establishment of human pluripotent stem cell (hPSC) lines with inducible gene knockout (iKO) remains challenging. We explored building iKO hPSC lines by combining CRISPR/Cas9-mediated genome editing with the Flp/FRT and Cre/LoxP system. We found that “dual-sgRNA targeting” is essential for biallelic knockin of FRT sequences to flank the exon. We further developed a strategy to simultaneously insert an activity-controllable recombinase-expressing cassette and remove the drug-resistance gene, thus speeding up the generation of iKO hPSC lines. This two-step strategy was used to establish human embryonic stem cell (hESC) and induced pluripotent stem cell (iPSC) lines with iKO of SOX2, PAX6, OTX2, and AGO2, genes that exhibit diverse structural layout and temporal expression patterns. The availability of iKO hPSC lines will substantially transform the way we examine gene function in human cells.

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