This research was supported by funding from the National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health through grants U01HL099656 (P.G. and D.L.F.) and U01HL134696 (P.G. and D.L.F.).

1. Design and construction of guide RNA (gRNA)
NOTE: Each gRNA is made up of two 60 base pair (bp) oligonucleotides that are annealed to generate a 100 bp double stranded (ds) oligonucleotide (Figure 1A-C). The timeline for gRNA design, generation, and testing cutting efficiency is approximately 2 weeks (Figure 2).
<ol>
	<li>Select the DNA region of interest to be genome edited and identify 3-4 23 bp sequences that ...

<ol>
	<li>Srivastava, D., Dewitt, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Review+In+Vivo+Cellular+Reprogramming:+The+Next+Generation.">Review In Vivo Cellular Reprogramming: The Next Generation.</a> Cell. 166 (6), 1386-1396 (2016).</li><li>Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Review+Modeling+Development+and+Disease+with+Organoids.">Review Modeling Development and Disease with Organoids.</a> Cell. 165 (7), 1586-1597 (2016).</li><li>Murry, C. E., Keller, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differentiation+of+Embryonic+Stem+Cells+to+Relevant+Populations:+Lessons+from+Embryonic+Development.">Differentiation of Embryonic Stem Cells to Relevant Populations: Lessons from Embryonic Development.</a> Cell. 132 (4), 661-680 (2008).</li><li>Liu, C., Oikonomopoulos, A., Sayed, N., Wu, J. 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S., Liu, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetic+Modification+in+Human+Pluripotent+Stem+Cells+by+Homologous+Recombination+and+CRISPR/Cas9+System.">Genetic Modification in Human Pluripotent Stem Cells by Homologous Recombination and CRISPR/Cas9 System.</a> Methods in Molecular Biology. 1307, 173-190 (2014).</li><li>Huang, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Production+of+gene-corrected+adult+beta+globin+protein+in+human+erythrocytes+differentiated+from+patient+iPSCs+after+genome+editing+of+the+sickle+point+mutation.">Production of gene-corrected adult beta globin protein in human erythrocytes differentiated from patient iPSCs after genome editing of the sickle point mutation.</a> Stem Cells. 33 (5), 1470-1479 (2015).</li><li>Wang, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unbiased+detection+of+off-target+cleavage+by+CRISPR-Cas9+and+TALENs+using+integrase-defective+lentiviral+vectors.">Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors.</a> Nature Biotechnology. 33 (2), 175-178 (2015).</li><li>Sim, X., Cardenas-Diaz, F. L., French, D. L., Gadue, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Doxycycline-Inducible+System+for+Genetic+Correction+of+iPSC+Disease+Models.">A Doxycycline-Inducible System for Genetic Correction of iPSC Disease Models.</a> Methods in Molecular Biology. 1353, 13-23 (2015).</li><li>Hockemeyer, D., Jaenisch, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Review+Induced+Pluripotent+Stem+Cells+Meet+Genome+Editing.">Review Induced Pluripotent Stem Cells Meet Genome Editing.</a> Stem Cell. 18 (5), 573-586 (2016).</li><li>Byrne, S. M., Mali, P., Church, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome+editing+in+human+stem+cells.">Genome editing in human stem cells.</a> Methods in Enzymology. 546, 119-138 (2014).</li><li>Zhu, Z., Gonz&#225;lez, F., Huangfu, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+iCRISPR+platform+for+rapid+genome+editing+in+human+pluripotent+stem+cells.">The iCRISPR platform for rapid genome editing in human pluripotent stem cells.</a> Methods in Enzymology. 546, 215-250 (2014).</li><li>Hou, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient+genome+engineering+in+human+pluripotent+stem+cells+using+Cas9+from+Neisseria+meningitidis.">Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis.</a> Proceedings of the National Academy of Sciences of the United States of America. 110 (39), 15644-15649 (2013).</li><li>Cong, L., Zhang, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genome+engineering+using+CRISPR-Cas9+system.">Genome engineering using CRISPR-Cas9 system.</a> Methods in Molecular Biology. 1239, 197-217 (2015).</li><li>Mali, P., Esvelt, K. M., Church, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cas9+as+a+versatile+tool+for+engineering+biology.">Cas9 as a versatile tool for engineering biology.</a> Nature Methods. 10 (10), 957-963 (2013).</li><li>Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L., Corn, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enhancing+homology+directed+genome+editing+by+catalytically+active+and+inactive+CRISPR-Cas9+using+asymmetric+donor+DNA.">Enhancing homology directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA.</a> Nature Biotechnology. 34 (3), 339-344 (2016).</li><li>Maguire, J. A., Cardenas-Diaz, F. L., Gadue, P., French, D. 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The authors have nothing to disclose.

In this protocol, the use of CRISPR-CAS9 along with two ssODN repair templates to generate specific heterozygous or homozygous genome changes is demonstrated in human pluripotent stem cells. This method resulted in the successful generation of isogenic cell lines expressing heterozygous genomic changes with an efficiency close to 10%. This protocol has been optimized for both human ESCs and iPSCs grown on irradiated MEFs which support cell growth and survival after culturing cells at low density after cell sorting. Cell ...

Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) are valuable tools for modeling human disease due to their capacity for renewal, while maintaining the ability to generate cell types of different lineages1,2,3,4. These models open the possibility to interrogate gene function, and understand how specific mutations and phenotypes are related to various diseases5,6. However, to understand how a specific alteration is linked to a particular phenotype, the use of a paired isogenic control and mutant cell lines is important to control for line to line variability7,8. Transcription activator-like effector nucleases (TALENs) and zinc finger nucleases have been used to generate insertion or deletion (indels) mutations in diverse genetic models, including primary cells; but these nucleases can be cumbersome to use and expensive9,10,11,12,13,14. The discovery of the clustered regularly interspaced short palindromic repeat (CRISPR)-CAS9 nuclease has revolutionized the field due to efficiency in indel formation in virtually any region of the genome, simplicity of use, and reduction in cost15,16,17,18,19.
A challenge in using the CRISPR-CAS9 based genome editing technology has been the generation or correction of specific mutations in one allele without creating an indel mutation in the second allele20. The major goal of this protocol is to overcome this challenge by using two single-stranded oligonucleotide (ssODN) repair templates to reduce indel formation in the second allele. Both ssODNs are designed to contain silent mutations to prevent re-cutting by the CAS9 nuclease, but only one contains the alteration of interest. This method increases the efficiency of generating a specific heterozygous genetic modification without inducing indel formation in the second allele. Using this protocol, gene editing experiments in six independent genomic locations demonstrate the precise introduction of the desired genomic change in one allele without indel formation in the second allele and occurs with an overall efficiency of ~10%. The described protocol has been adapted from Maguire et al.21.

<table border="0" cellpadding="0" cellspacing="0" style="width:707px;" width="705">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:375px;">5-ml polystyrene round-bottom tube with cell-strainer cap</td>
			<td style="width:145px;">Corning</td>
			<td style="width:124px;">352235</td>
			<td style="width:63px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">6-well polystyrene tissue culture dishes</td>
			<td>Corning</td>
			<td style="width:124px;">353046</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">AflII restriction endonuclease</td>
			<td>New England Biolabs</td>
			<td style="width:124px;">R0520</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Agarose</td>
			<td>VWR</td>
			<td style="width:124px;">N605</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DMEM/F12 medium</td>
			<td style="width:145px;">ThermoFisher</td>
			<td>11320033</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:375px;">dNTPs</td>
			<td style="width:145px;">Roche</td>
			<td style="width:124px;">11969064001</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fluorescence-activated cell sorter (FACS) apparatus</td>
			<td style="width:145px;"></td>
			<td style="width:124px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gel extraction kit</td>
			<td>Macherey-Nagel</td>
			<td>740609</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Gibson Assembly Kit</td>
			<td>New England Biolabs</td>
			<td>E2611</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">gRNA_Cloning Vector</td>
			<td>Addgene</td>
			<td style="width:124px;">41824</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">LB agar plates containing 50 &#956;g/ml kanamycin</td>
			<td style="width:145px;"></td>
			<td style="width:124px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Lipofectamine Stem Reagent</td>
			<td style="width:145px;">ThermoFisher</td>
			<td style="width:124px;">(STEM00001)</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Matrigel Growth Factor Reduced (GFR)</td>
			<td>Corning</td>
			<td style="width:124px;">354230</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Murine embryonic fibroblasts (MEFs)</td>
			<td style="width:145px;"></td>
			<td style="width:124px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nucleospin Gel Extraction and PCR Clean-up Kit</td>
			<td>Macherey-Nagel</td>
			<td style="width:124px;">740609</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Orbital shaking incubator</td>
			<td style="width:145px;"></td>
			<td style="width:124px;"></td>
			<td></td>
		</tr>
		<tr height="18">
			<td height="18" style="height:19px;">pCas9_GFP vector</td>
			<td style="width:145px;">Addgene</td>
			<td style="width:124px;">44719</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PCR strip tubes</td>
			<td style="width:145px;">USA Scientific</td>
			<td>1402-2900</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Phusion High Fidelity DNA Polymerase and 5&#215; Phusion buffer</td>
			<td>New England Biolabs</td>
			<td>M0530</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PurelinkTM Quick Plasmid Miniprep Kit</td>
			<td>Invitrogen</td>
			<td style="width:124px;">K210011</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Proteinase K</td>
			<td style="width:145px;">Qiagen</td>
			<td style="width:124px;">Qiagen 19133</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">StellarTM electrocompetent Escherichia coli cells</td>
			<td>Takara</td>
			<td style="width:124px;">636763</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SOC medium</td>
			<td>New England Biolabs</td>
			<td>B9020S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">TrypLE Express Enzyme</td>
			<td>ThermoFisher</td>
			<td style="width:124px;">12605036</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Y-27632 dihydrochloride/ROCK inhibitor (ROCKi)</td>
			<td>Tocris</td>
			<td style="width:124px;">1254</td>
			<td></td>
		</tr>
	</tbody>
</table>

generation of defined genomic modifications using crispr-cas9 in human pluripotent stem cells

Human pluripotent stem cells offer a powerful system to study gene function and model specific mutations relevant to disease. The generation of precise heterozygous genetic modifications is challenging due to CRISPR-CAS9 mediated indel formation in the second allele. Here, we demonstrate a protocol to help overcome this difficulty by using two repair templates in which only one expresses the desired sequence change, while both templates contain silent mutations to prevent re-cutting and indel formation. This methodology is most advantageous for gene editing coding regions of DNA to generate isogenic control and mutant human stem cell lines for studying human disease and biology. In addition, optimization of transfection and screening methodologies have been performed to reduce labor and cost of a gene editing experiment. Overall, this protocol is widely applicable to many genome editing projects utilizing the human pluripotent stem cell model.

Generation of gRNAs and screening for indels
Each gRNA will be cloned into a plasmid vector and expressed using the U6 promoter. The AflII restriction enzyme is used to linearize the plasmid (addgene #41824) and is located after the U6 promoter. The 100 bp band generated after annealing the two 60 bp oligos is cloned into the gRNA expression vector using the DNA assembly. Once the gRNA plasmids are generated, they are transfected into hESCs or iPSCs along with a CRISP...

Watch this Scientific Journal Video about Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells at JoVE.com

Generation of Defined Genomic Modifications Using CRISPR-CAS9 in Human Pluripotent Stem Cells

This protocol provides a method to facilitate the generation of defined heterozygous or homozygous nucleotide changes using CRISPR-CAS9 in human pluripotent stem cells.

Human pluripotent stem cells offer a powerful system to study gene function and model specific mutations relevant to disease. The generation of precise ...

The study of gene function and disease are hampered by the outbred nature of the human population. The different genetic backgrounds of patient-specific and control iPS cell lines can affect differentiation efficiency and phenotypes found in a given functional assay. Use of genetically identical or isogenic lines where the only difference is the particular mutation of interest is critical to overcome these issues.Many human diseases are caused by heterozygous mutations, which can be difficult to generate with the CRISPR-Cas9 system. This is due to the generation of indel mutations in the non-targeted allele that can occur at very high frequency. Our technique overcomes this problem by using two repair templates of which only one harbors the mutation of interest.Any investigator trying this technique should be skilled at human pluripotent stem cell culture. The video demonstration of colony picking will be helpful to show correct size and morphology as well as technique used for picking and screening. Demonstrating this procedure will be Leo Cardenas.To begin, plate human ESCs on irradiated MEFs in a 6-well plate. Prepare the transfection master mix. Mix by pipetting and incubate at room temperature for 15 minutes.When the cells reach 70 to 80%confluency, then, add the transfection master mix drop wise to each well with cells and incubate at 37 degrees Celsius for 48 hours. Change the media every 24 hours. To harvest the cells, first, incubate the cells with Triple E for three minutes at room temperature to remove MEFs enzymatically.Add 0.5 milliliters of HESC medium with 10 micromolar ROCK inhibitor. Pellet cells at 300 times g for three minutes and re-suspend in 0.5 milliliters of human ESC medium with 10 micromolar ROCK inhibitor. Filter the cell suspension into a five milliliter tube through a 35 micron cell strainer cap.Using fluorescence-activated cell sorting, gate on live cells and sort the green fluorescent protein-positive cells. Next, transfer a maximum of 1.5 times 10 to the four sorted cells directly into a 10 centimeter dish coated with one to three basement membrane matrix and irradiated MEFs and human ESC medium containing ROCK inhibitor. Change medium daily using the human ESC medium without ROCK inhibitor.After 10 to 15 days, colonies are approximately one to two millimeters in diameter. Under a microscope, use a P200 pipette to carefully scrape a single clone and draw cells into the pipette. Disperse the cells in a well of a 96-well plate by gently pipetting three to four times in the medium drawn up with the colony.Then, pick 20 colonies for each guide RNA and dispense into PCR strip tubes for screening. Pellet the cells by centrifugation at 10, 000 times G for five minutes. Now, incubate cell pellets in 20 microliters of Proteinase K buffer to isolate DNA and vortex vigorously.Centrifuge at 10, 000 times G for five minutes. Next, perform screening PCR of the edited DNA. Add into the tubes 20 microliters of a master mix, including forward and reverse primers, designed to amplify the region of interest, as well as five microliters of the Proteinase K digest.Use genomic DNA isolated from the control iPSC line to confirm a clean amplicon when performing the screening PCR. Evaluate size changes of PCR products following one hour of electrophoresis at 70 to 90 volts on a 2.5%weight by volume agarose gel. Any size difference is indicative of cleavage.To transfect the single strand oligo DNA and the CRISPR-Cas9 plasmids, plate the target cell line in a 6-well dish on irradiated MEFs to reach 70 to 80%confluency after over an overnight incubation. Set up the transfection reaction as described. Mix the reaction by pipetting and incubate for 15 minutes at room temperature.Then, add the transfection reaction mixture drop wise to the cells. After 48 hours, prepare the cells for cell sorting as previously. About 10 days after plating single cells, use a 200 microliter pipette to pick colonies into PCR strip tubes and into a well of a 12-well plate pre-coated with gelatine and MEFs.Transfer 100 microliters of the cells to each well of a 24 or 48-well plate, previously coated with gelatine and irradiated MEFs in human ESC medium with ROCK inhibitor. Use the remaining 100 microliters for DNA isolation. To check for successful integration of the single strand oligo DNA, take five microliters of DNA isolated from each colony to perform PCR using the screening primers previously designed.Purify the PCR products and prepare the 40 microliters of restriction enzyme digestion using the unique enzyme site created in the single strand oligo DNA. Mix the reaction by pipetting and incubate at the manufacturer's recommended temperature for one to three hours. Then, visualize the digested PCR products added with a loading dye on a 1.5%weight by volume ethidium bromide agarose gel, electrophorese at 80 to 100 volts for 40 minutes.If successful integration of the single strand oligo DNA has occurred, sequence specific mutations using a nested primer. In this study, for guide RNA construction, a 100 base pair band was excised from a 1.5%agarose gel. Following cell transfection, validation of guide RNA cutting was visualized using a 2.5%agarose gel.A 180 base pair PCR product showed an uncut control and different clones with band shifts indicating indel formation. Different guide RNAs had different cutting efficiencies. To avoid CRISPR-Cas9 re-cutting of the edited alleles, the PAM sequence was modified using a G to A silent mutation.A silent mutation in the PAM sequence generated a unique restriction site, which helps to screen for successful integration into one or two alleles. Genome edited stem cell lines can be used in downstream differentiations and functional assays to study the effect of a given mutation on human development and disease. This methodology allows the generation of isogenic cell lines with a specific heterozygous or homozygous mutations, implicated in a wide variety of human diseases.These disease models pave the way for the development of new cellular therapies as well as offer platforms for drug discovery.

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8.1K Views.  The Children's Hospital of Philadelphia. The study of gene function and disease are hampered by the outbred nature of the human population. The different genetic backgrounds of patient-specific and control iPS cell lines can affect differentiation efficiency and phenotypes found in a given functional assay. Use of genetically identical or isogenic lines where the only difference is the particular mutation of interest is critical to overcome these issues.Many human diseases are caused by heterozygous mutations, which can be di...