Tang and Weintraub were partially supported by NIH-AR070029, NIH-HL086555, NIH-HL134354.

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The authors have nothing to disclose.

Duchenne Muscular Dystrophy (DMD) is a destructive and ultimately fatal hereditary disease characterized by a lack of dystrophin, leading to progressive muscle atrophy1,2. Our results demonstrate the restored dystrophin gene expression in Dmdmdx iPSC-derived myogenic progenitor cells by the approach of CRISPR/Cas9-mediated exon23 deletion. This approach has three advantages.
First, we generated iPSCs from Dmdmdx m...

Duchenne muscular dystrophy (DMD) is one of the most common muscular dystrophies and is characterized by the absence of dystrophin, affecting 1 of approximately 5,000 newborn boys worldwide1. Loss of dystrophin gene function results in structural muscle defects leading to progressive myofibers degeneration1,2. Recombinant adeno-associated virus (rAAV)-mediated gene therapy system has been tested to restore the dystrophin expression and improve muscle function, such as gene replacement using micro-dystrophins (&#181;-Dys). However, the rAAV approach requires repeated injections to sustain expression of the functional protein3,4. Therefore, we need a strategy that can provide effectively and permanently recover dystrophin gene expression in patients with DMD. The&#160;Dmdmdx mouse, a mouse model for DMD, has a point mutation in exon 23 of the&#160;dystrophin&#160;gene that introduces a premature termination codon and results in a non-functional truncated protein lacking the C-terminal dystroglycan binding domain. Recent studies demonstrated the use of CRISPR/Cas9 technology to restore dystrophin gene expression by accurate gene correction or mutant exon deletion in small and large animal5,6,7. Long et al.8 reported the method for correcting the dystrophin gene mutation in Dmdmdx mouse germline by homology-directed repair (HDR) based CRISPR/Cas9 genome editing. El Refaey et al.9 reported that rAAV could efficiently excise the mutant exon 23 in dystrophic mice. In these studies, gRNAs were designed in the introns 20 and 23 to cause double-stranded DNA breaks, which partially restored the dystrophin expression after DNA repair via non-homologous end joining (NHEJ). Even more exciting, Amoasii et al.10 recently reported the efficacy and feasibility of rAAV-mediated CRISPR gene editing in restoring dystrophin expression in canine models, an essential step in future clinical application.
DMD also causes stem cell disorders11. For muscle damage, residential muscle stem cells replenish dying muscle cells after muscle differentiation. However, the consecutive cycles of injury and repair lead to shortening of telomeres in muscle stem cells12, and premature depletion of stem cell pools13,14. Therefore, a combination of autologous stem cell therapy with genome editing to restore dystrophin expression can be a practical approach for treating DMD. The CRISPR/Cas9 technology provides the possibility of generating autologous genetically corrected induced pluripotent stem cells (iPSC) for functional muscle regeneration and prevent further complications of DMD without causing immune rejection. However, iPSCs have a risk of tumor formation, which could be alleviated by the differentiation of iPSC into myogenic progenitor cells.
In this protocol, we describe the use of non-integrating Sendai virus to reprogramming dermal fibroblasts of Dmdmdx mice into iPSCs and then recover dystrophin expression by CRISPR/Cas9 genome deletion. After validation of Exon23 deletion in iPSC by genotyping, we differentiated genome-corrected iPSC into myogenic progenitors (MPC) via MyoD-induced myogenic differentiation.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Surgical Instruments</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>31-gauge needle</td>
			<td>Various&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sharp Incision</td>
			<td>Various&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile Scalpels</td>
			<td>Various&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Tweezers</td>
			<td>Various&#160;</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fibroblast medium (for 100 mL of complete medium)</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Volume</td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol (55 mM)</td>
			<td>Gibco</td>
			<td>21-985-023</td>
			<td>0.1 mL</td>
		</tr>
		<tr>
			<td>Antibiotic Antimycotic Slution 100x</td>
			<td>CORNING</td>
			<td>MT30004CI</td>
			<td>1 mL</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle&#39;s Medium - high glucose</td>
			<td>SIGMA</td>
			<td>D6429</td>
			<td>87 mL</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum Characterized</td>
			<td>HyClone</td>
			<td>SH30396.03</td>
			<td>10 mL</td>
		</tr>
		<tr>
			<td>L-Glutamine solution</td>
			<td>SIGMA</td>
			<td>G7513</td>
			<td>1 mL</td>
		</tr>
		<tr>
			<td>MEM Non-Essential Amino Acids Solution (100x)&#160;</td>
			<td>Gibco</td>
			<td>11140076</td>
			<td>1 mL</td>
		</tr>
		<tr>
			<td>TVP solution (for 500 mL of complete solution)</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Volume</td>
		</tr>
		<tr>
			<td>Chicken Serum</td>
			<td>Gibco</td>
			<td>16110-082</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma-Aldrich</td>
			<td>E6758</td>
			<td>186 mg</td>
		</tr>
		<tr>
			<td>Phosphat-buffered saline</td>
			<td></td>
			<td></td>
			<td>to 500 mL</td>
		</tr>
		<tr>
			<td>Trypsin (2.5%)</td>
			<td>Thermo</td>
			<td>15090046</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td>mES growth medium(for 500 mL of complete solution)</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Volume</td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol (55 mM)</td>
			<td>Gibco</td>
			<td>21-985-023</td>
			<td>0.5 mL</td>
		</tr>
		<tr>
			<td>Antibiotic Antimycotic Slution 100x</td>
			<td>CORNING</td>
			<td>MT30004CI</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle&#39;s Medium - high glucose</td>
			<td>SIGMA</td>
			<td>D6429</td>
			<td>408.5 mL</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum Characterized</td>
			<td>HyClone</td>
			<td>SH30396.03</td>
			<td>75 mL</td>
		</tr>
		<tr>
			<td>L-Glutamine solution</td>
			<td>SIGMA</td>
			<td>G7513</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td>Mouse recombinant Leukemia Inhibitory Factor (LIF), 0.5 x 106 U/mL</td>
			<td>EMD Millipore Corp</td>
			<td>CS210511</td>
			<td>500 &#956;L</td>
		</tr>
		<tr>
			<td>MEK/GS3 Inhibitor Supplement</td>
			<td>EMD Millipore Corp</td>
			<td>CS210510-500UL</td>
			<td>500 &#956;L</td>
		</tr>
		<tr>
			<td>MEM Non-Essential Amino Acids Solution (100x)&#160;</td>
			<td>Gibco</td>
			<td>11140076</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td colspan="4">The ES cell media should not be stored for more than 4 weeks and with inhibitors not more than 2 weeks.</td>
		</tr>
		<tr>
			<td>mES frozen medium(for 50 mL of complete solution)</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>Volume</td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide (DMSO)</td>
			<td>SIGMA</td>
			<td>D2650</td>
			<td>5 mL</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle&#39;s Medium - high glucose</td>
			<td>SIGMA</td>
			<td>D6429</td>
			<td>24.9 mL</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum Characterized</td>
			<td>HyClone</td>
			<td>SH30396.03</td>
			<td>25 mL</td>
		</tr>
		<tr>
			<td>Mouse recombinant Leukemia Inhibitory Factor (LIF), 0.5 x 106 U/mL</td>
			<td>EMD Millipore Corp</td>
			<td>CS210511</td>
			<td>50 &#956;L</td>
		</tr>
		<tr>
			<td>Name of Material/ Equipment</td>
			<td>Company</td>
			<td>Catalog Number</td>
			<td>RRID</td>
		</tr>
		<tr>
			<td>0.05% Trypsin/0.53 mM EDTA</td>
			<td>CORNING</td>
			<td>25-052-CI</td>
			<td></td>
		</tr>
		<tr>
			<td>4% Paraformaldehyde</td>
			<td>Thermo scientific</td>
			<td>J19943-k2</td>
			<td></td>
		</tr>
		<tr>
			<td>Accutase solution</td>
			<td>SIGMA</td>
			<td>A6964</td>
			<td>Cell detachment solution</td>
		</tr>
		<tr>
			<td>AgeI-HF</td>
			<td>NEB</td>
			<td>R3552L</td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa488-conjugated goat-anti-mouse antibody</td>
			<td>Invitrogen</td>
			<td>A32723</td>
			<td>AB_2633275</td>
		</tr>
		<tr>
			<td>Alexa488-conjugated goat-anti-rabbit antibody</td>
			<td>Invitrogen</td>
			<td>A32731</td>
			<td>AB_2633280</td>
		</tr>
		<tr>
			<td>Alexa555-conjugated goat-anti-rabbit antibody</td>
			<td>Invitrogen</td>
			<td>A32732</td>
			<td>AB_2633281</td>
		</tr>
		<tr>
			<td>anti-AFP</td>
			<td>Thermo scientific</td>
			<td>RB-365-A1</td>
			<td>AB_59574</td>
		</tr>
		<tr>
			<td>anti-&#945;-Smooth Muscle Actin (D4K9N) XP</td>
			<td>CST</td>
			<td>19245S</td>
			<td>AB_2734735</td>
		</tr>
		<tr>
			<td>anti-Dystrophin</td>
			<td>Thermo</td>
			<td>PA5-32388</td>
			<td>AB_2549858</td>
		</tr>
		<tr>
			<td>anti-LIN28A (D1A1A) XP&#160;&#160;&#160;</td>
			<td>CST</td>
			<td>8641S</td>
			<td>AB_10997528</td>
		</tr>
		<tr>
			<td>anti-MYH2</td>
			<td>DSHB</td>
			<td>mAb2F7</td>
			<td>AB_1157865</td>
		</tr>
		<tr>
			<td>anti-Nanog-XP</td>
			<td>CST</td>
			<td>8822S</td>
			<td>AB_11217637</td>
		</tr>
		<tr>
			<td>anti-Oct-4A (D6C8T)</td>
			<td>CST</td>
			<td>83932S</td>
			<td>AB_2721046</td>
		</tr>
		<tr>
			<td>anti-Sox2</td>
			<td>abcam</td>
			<td>ab97959</td>
			<td>AB_2341193</td>
		</tr>
		<tr>
			<td>anti-SSEA1(MC480)&#160;</td>
			<td>CST</td>
			<td>4744s</td>
			<td>AB_1264258</td>
		</tr>
		<tr>
			<td>anti-TH (H-196)</td>
			<td>SANTA CRUZ&#160;</td>
			<td>sc-14007</td>
			<td>AB_671397</td>
		</tr>
		<tr>
			<td>Alkaline Phosphatase Live Stain (500x)</td>
			<td>Thermo</td>
			<td>A14353</td>
			<td></td>
		</tr>
		<tr>
			<td>Blasticidin S</td>
			<td>Sigma-Aldrich</td>
			<td>203350</td>
			<td></td>
		</tr>
		<tr>
			<td>BsmBI/Esp3I</td>
			<td>NEB</td>
			<td>R0580L/R0734L</td>
			<td></td>
		</tr>
		<tr>
			<td>Carbenicillin</td>
			<td>Millipore</td>
			<td>205805-250MG</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagenase IV&#160;</td>
			<td>Worthington Biochemical Corporation</td>
			<td>LS004189</td>
			<td></td>
		</tr>
		<tr>
			<td>Competent Cells</td>
			<td>TakaRa</td>
			<td>636763</td>
			<td></td>
		</tr>
		<tr>
			<td>CutSmart&#160;</td>
			<td>NEB</td>
			<td>B7204S</td>
			<td></td>
		</tr>
		<tr>
			<td>CytoTune-iPS 2.0 Sendai Reprogramming Kit</td>
			<td>Thermo</td>
			<td>A16517</td>
			<td></td>
		</tr>
		<tr>
			<td>DirectPCR Lysis Reagent (cell)</td>
			<td>VIAGEN BIOTECH</td>
			<td>302-C</td>
			<td></td>
		</tr>
		<tr>
			<td>Dispase (1 U/mL)</td>
			<td>STEMCELL Technologies</td>
			<td>7923</td>
			<td></td>
		</tr>
		<tr>
			<td>Doxycycline Hydrochloride</td>
			<td>Fisher BioReagents</td>
			<td>BP26535</td>
			<td></td>
		</tr>
		<tr>
			<td>EcoRI-HF</td>
			<td>NEB</td>
			<td>R3101L</td>
			<td></td>
		</tr>
		<tr>
			<td>Fibronectin bovine plasma</td>
			<td>SIGMA</td>
			<td>F1141</td>
			<td></td>
		</tr>
		<tr>
			<td>&#160; 
			QIAEX II Gel Extraction Kit (500)</td>
			<td>QIAGEN</td>
			<td>20051</td>
			<td></td>
		</tr>
		<tr>
			<td>Gelatin from porcine skin, type A</td>
			<td>SIGMA</td>
			<td>G1890</td>
			<td></td>
		</tr>
		<tr>
			<td>HardSet Antifade Mounting Medium with DAPI</td>
			<td>Vector</td>
			<td>H-1500</td>
			<td></td>
		</tr>
		<tr>
			<td>Hygromycin B (50 mg/mL)</td>
			<td>Invitrogen</td>
			<td>10687010</td>
			<td></td>
		</tr>
		<tr>
			<td>Ketamine HCL Injection</td>
			<td>HENRY SCHEIN ANIMAL HEALTH</td>
			<td>45822</td>
			<td></td>
		</tr>
		<tr>
			<td>KpnI-HF</td>
			<td>NEB</td>
			<td>R3142L</td>
			<td></td>
		</tr>
		<tr>
			<td>lenti-CRISPRv2-blast</td>
			<td>Addgene</td>
			<td>83480</td>
			<td></td>
		</tr>
		<tr>
			<td>lenti-Guide-Hygro-iRFP670</td>
			<td>Addgene</td>
			<td>99377</td>
			<td></td>
		</tr>
		<tr>
			<td>Lipofectamin 3000 Transfection Kit</td>
			<td>Invitrogen</td>
			<td>L3000015</td>
			<td></td>
		</tr>
		<tr>
			<td>LV-TRE-VP64-mouse MyoD-T2A-dsRedExpress2&#160;&#160;</td>
			<td>Addgene</td>
			<td>60625</td>
			<td></td>
		</tr>
		<tr>
			<td>LV-TRE-VP16 mouse MyoD-T2A-dsRedExpress2</td>
			<td>Addgene</td>
			<td>60626</td>
			<td></td>
		</tr>
		<tr>
			<td>Mouse on Mouse (M.O.M.) Basic Kit</td>
			<td>Vector</td>
			<td>BMK-2202</td>
			<td></td>
		</tr>
		<tr>
			<td>NotI-HF</td>
			<td>NEB</td>
			<td>R3189L</td>
			<td></td>
		</tr>
		<tr>
			<td>Opti-MEM I Reduced Serum Media</td>
			<td>ThermoFisher</td>
			<td>31985070</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyethylene glycol 4,000</td>
			<td>Alfa Aesar</td>
			<td>AAA161510B</td>
			<td></td>
		</tr>
		<tr>
			<td>Polybrene</td>
			<td>SIGMA</td>
			<td>TR1003</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning&#160;BioCoat Poly-D-Lysine/Laminin Culture Slide</td>
			<td>CORNING</td>
			<td>CB354688</td>
			<td></td>
		</tr>
		<tr>
			<td>PowerUp SYBR Green Master Mix</td>
			<td>ThermoFisher</td>
			<td>A25742</td>
			<td></td>
		</tr>
		<tr>
			<td>PrimeSTAR Max Premix</td>
			<td>TakaRa</td>
			<td>R045</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>VIAGEN BIOTECH</td>
			<td>507-PKP</td>
			<td></td>
		</tr>
		<tr>
			<td>Puromycin Dihydrochloride</td>
			<td>MP Biomedicals</td>
			<td>ICN19453980</td>
			<td></td>
		</tr>
		<tr>
			<td>qPCR Lentivirus Titration Kit</td>
			<td>abm</td>
			<td>LV900</td>
			<td></td>
		</tr>
		<tr>
			<td>Quick ligation kit</td>
			<td>NEB</td>
			<td>M2200S</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAprep Spin Miniprep Kit (250)</td>
			<td>QIAGEN</td>
			<td>27106</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAGEN Plasmid Plus Midi Kit (100)</td>
			<td>QIAGEN</td>
			<td>12945</td>
			<td></td>
		</tr>
		<tr>
			<td>RevertAid RT Reverse Transcription Kit</td>
			<td>Thermo scientific</td>
			<td>K1691</td>
			<td></td>
		</tr>
		<tr>
			<td>RNAzol RT</td>
			<td>Molecular Research Center, INC</td>
			<td>RN 190</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA Ligase Reaction Buffer</td>
			<td>NEB</td>
			<td>B0202S</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 Polynucleotide Kinase</td>
			<td>NEB</td>
			<td>M0201S</td>
			<td></td>
		</tr>
		<tr>
			<td>Terrific Broth Modified</td>
			<td>Fisher BioReagents</td>
			<td>BP9729-600</td>
			<td></td>
		</tr>
		<tr>
			<td>ViralBoost Reagent (500x)</td>
			<td>ALSTEM</td>
			<td>VB100</td>
			<td></td>
		</tr>
	</tbody>
</table>

crispr/cas9 technology in restoring dystrophin expression in ipsc-derived muscle progenitors

Duchenne muscular dystrophy (DMD) is a severe progressive muscle disease caused by mutations in the dystrophin gene, which ultimately leads to the exhaustion of muscle progenitor cells. Clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) gene editing has the potential to restore the expression of the dystrophin gene. Autologous induced pluripotent stem cells (iPSCs)-derived muscle progenitor cells (MPC) can replenish the stem/progenitor cell pool, repair damage, and prevent further complications in DMD without causing an immune response. In this study, we introduce a combination of CRISPR/Cas9 and non-integrated iPSC technologies to obtain muscle progenitors with recovered dystrophin protein expression. Briefly, we use a non-integrating Sendai vector to establish an iPSC line from dermal fibroblasts of Dmdmdx mice. We then use the CRISPR/Cas9 deletion strategy to restore dystrophin expression through a non-homologous end joining of the reframed dystrophin gene. After PCR validation of exon23 depletion in three colonies from 94 picked iPSC colonies, we differentiate iPSC into MPC by doxycycline (Dox)-induced expression of MyoD, a key transcription factor playing a significant role in regulating muscle differentiation. Our results show the feasibility of using CRISPR/Cas9 deletion strategy to restore dystrophin expression in iPSC-derived MPC, which has significant potential for developing future therapies for the treatment of DMD.

Establishment of Dmdmdx skin fibroblasts derived iPSC. We demonstrated the efficiency of generating mouse iPSCs from Dmdmdx mice derived skin fibroblast using the integration-free reprogramming vectors. Figure 1A demonstrated that the appearance of embryonic stem cell (ESC)-like colonies at three weeks after infection. We evaluate the efficiency of iPSC induction by live alkaline phosphatase (AP) stain; Figure 1B s...

Watch this Scientific Journal Video about CRISPR/Cas9 Technology in Restoring Dystrophin Expression in iPSC-Derived Muscle Progenitors at JoVE.com

CRISPR/Cas9 Technology in Restoring Dystrophin Expression in iPSC-Derived Muscle Progenitors

Here, we present a Cas9-based exon23 deletion protocol to restore dystrophin expression in iPSC from Dmdmdx mouse-derived skin fibroblasts and directly differentiate iPSCs into myogenic progenitor cells (MPC) using the Tet-on MyoD activation system.

Duchenne muscular dystrophy (DMD) is a severe progressive muscle disease caused by mutations in the dystrophin gene, which ultimately leads to the ...

crisprcas9-technology-restoring-dystrophin-expression-ipsc-derived

Research

JoVE Journal

Developmental Biology

8.2K Views.  Augusta University. Here, we present a Cas9-based exon23 deletion protocol to restore dystrophin expression in iPSC from Dmdmdx mouse-derived skin fibroblasts and directly differentiate iPSCs into myogenic progenitor cells (MPC) using the Tet-on MyoD activation system.

Video: CRISPR/Cas9 Technology in Restoring Dystrophin Expression in iPSC-Derived Muscle Progenitors

Analysis of Zebrafish Larvae Skeletal Muscle Integrity with Evans Blue Dye

The zebrafish model is an emerging system for the study of neuromuscular disorders. In the study of neuromuscular diseases, the integrity of the muscle membrane is a critical disease determinant. To date, numerous neuromuscular conditions display degenerating muscle fibers with abnormal membrane integrity; this is most commonly observed in muscular dystrophies. Evans Blue Dye (EBD) is a vital, cell permeable dye that is rapidly taken into degenerating, damaged, or apoptotic cells; in contrast, it is not taken up by cells with an intact membrane. EBD injection is commonly employed to ascertain muscle integrity in mouse models of neuromuscular diseases. However, such EBD experiments require muscle dissection and/or sectioning prior to analysis. In contrast, EBD uptake in zebrafish is visualized in live, intact preparations. Here, we demonstrate a simple and straightforward methodology for performing EBD injections and analysis in live zebrafish. In addition, we demonstrate a co-injection strategy to increase efficacy of EBD analysis. Overall, this video article provides an outline to perform EBD injection and characterization in zebrafish models of neuromuscular disease.

In this study, we describe a straightforward method to perform Evans Blue Dye (EBD) analysis on zebrafish larvae. This technique is a powerful tool for the characterization of skeletal muscle integrity and delineation of zebrafish models of muscular dystrophy, and is a valuable method for the development of novel therapeutics.

The zebrafish model is an emerging system for the study of neuromuscular disorders.  In the study of neuromuscular diseases, the integrity of the muscle ...

Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells

Enhancers control cell identity by regulating tissue-specific gene expression in a position and orientation independent manner. These enhancers are often located distally from the regulated gene in intergenic regions or even within the body of another gene. The position independent nature of enhancer activity makes it difficult to match enhancers with the genes they regulate. Deletion of an enhancer region provides direct evidence for enhancer activity and is the gold standard to reveal an enhancer's role in endogenous gene transcription. Conventional homologous recombination based deletion methods have been surpassed by recent advances in genome editing technology which enable rapid and precisely located changes to the genomes of numerous model organisms. CRISPR/Cas9 mediated genome editing can be used to manipulate the genome in many cell types and organisms rapidly and cost effectively, due to the ease with which Cas9 can be targeted to the genome by a guide RNA from a bespoke expression plasmid. Homozygous deletion of essential gene regulatory elements might lead to lethality or alter cellular phenotype whereas monoallelic deletion of transcriptional enhancers allows for the study of cis-regulation of gene expression without this confounding issue. Presented here is a protocol for CRISPR/Cas9 mediated deletion in F1 mouse embryonic stem (ES) cells (Mus musculus129 x Mus castaneus). Monoallelic deletion, screening and expression analysis is facilitated by single nucleotide polymorphisms (SNP) between the two alleles which occur on average every 125 bp in these cells.

Experimental validation of enhancer activity is best approached by loss-of-function analysis. Presented here is an efficient protocol that uses CRISPR/Cas9 mediated deletion to study allele-specific regulation of gene transcription in F1 ES cells which contain a hybrid genome (Mus musculus129 x Mus castaneus).

Enhancers control cell identity by regulating tissue-specific gene expression in a position and orientation independent manner. These enhancers are often ...

Directed Differentiation of Primitive and Definitive Hematopoietic Progenitors from Human Pluripotent Stem Cells

One of the major goals for regenerative medicine is the generation and maintenance of hematopoietic stem cells (HSCs) derived from human pluripotent stem cells (hPSCs). Until recently, efforts to differentiate hPSCs into HSCs have predominantly generated hematopoietic progenitors that lack HSC potential, and instead resemble yolk sac hematopoiesis.&#160;These resulting hematopoietic progenitors may have limited utility for in vitro disease modeling of various adult hematopoietic disorders, particularly those of the lymphoid lineages. However, we have recently described methods to generate erythro-myelo-lymphoid multilineage definitive hematopoietic progenitors from hPSCs using a stage-specific directed differentiation protocol, which we outline here. Through enzymatic dissociation of hPSCs on basement membrane matrix-coated plasticware, embryoid bodies (EBs) are formed. EBs are differentiated to mesoderm by recombinant BMP4, which is subsequently specified to the definitive hematopoietic program by the GSK3&#946; inhibitor, CHIR99021. Alternatively, primitive hematopoiesis is specified by the PORCN inhibitor, IWP2. Hematopoiesis is further driven through the addition of recombinant VEGF and supportive hematopoietic cytokines. The resulting hematopoietic progenitors generated using this method have the potential to be used for disease and developmental modeling, in vitro.

Here, we present human pluripotent stem cell (hPSC) culture protocols, used to differentiate hPSCs into CD34+ hematopoietic progenitors. This method uses stage-specific manipulation of canonical WNT signaling to specify cells exclusively to either the definitive or primitive hematopoietic program.

One of the major goals for regenerative medicine is the generation and maintenance of hematopoietic stem cells (HSCs) derived from human pluripotent stem ...

Generation of iPSC-derived Human Brain Organoids to Model Early Neurodevelopmental Disorders

The restricted availability of suitable in vitro models that can reliably represent complex human brain development is a significant bottleneck that limits the translation of basic brain research into clinical application. While induced pluripotent stem cells (iPSCs) have replaced the ethically questionable human embryonic stem cells, iPSC-based neuronal differentiation studies remain descriptive at the cellular level but fail to adequately provide the details that could be derived from a complex, 3D human brain tissue. 
This gap is now filled through the application of iPSC-derived, 3D brain organoids, "Brains in a dish," that model many features of complex human brain development. Here, a method for generating iPSC-derived, 3D brain organoids is described. The organoids can help with modeling autosomal recessive primary microcephaly (MCPH), a rare human neurodevelopmental disorder. A widely accepted explanation for the brain malformation in MCPH is a depletion of the neural stem cell pool during the early stages of human brain development, a developmental defect that is difficult to recreate or prove in vitro. 
To study MCPH, we generated iPSCs from patient-derived fibroblasts carrying a mutation in the centrosomal protein CPAP. By analyzing the ventricular zone of microcephaly 3D brain organoids, we showed the premature differentiation of neural progenitors. These 3D brain organoids are a powerful in vitro system that will be instrumental in modeling congenital brain disorders induced by neurotoxic chemicals, neurotrophic viral infections, or inherited genetic mutations.

Modeling human brain development has been hindered due to the unprecedented complexity of neural epithelial tissue. Here, a method for the robust generation of brain organoids to delineate early events of human brain development and to model microcephaly in vitro is described.

The restricted availability of suitable in vitro models that can reliably represent complex human brain development is a significant bottleneck that ...

In Vivo Imaging of Transgenic Gene Expression in Individual Retinal Progenitors in Chimeric Zebrafish Embryos to Study Cell Nonautonomous Influences

The genetic and technical strengths have made the zebrafish vertebrate a key model organism in which the consequences of gene manipulations can be traced in vivo throughout the rapid developmental period. Multiple processes can be studied including cell proliferation, gene expression, cell migration and morphogenesis. Importantly, the generation of chimeras through transplantations can be easily performed, allowing mosaic labeling and tracking of individual cells under the influence of the host environment. For example, by combining functional gene manipulations of the host embryo (e.g., through morpholino microinjection) and live imaging, the effects of extrinsic, cell nonautonomous signals (provided by the genetically modified environment) on individual transplanted donor cells can be assessed. Here we demonstrate how this approach is used to compare the onset of fluorescent transgene expression as a proxy for the timing of cell fate determination in different genetic host environments.
In this article, we provide the protocol for microinjecting zebrafish embryos to mark donor cells and to cause gene knockdown in host embryos, a description of the transplantation technique used to generate chimeric embryos, and the protocol for preparing and running in vivo time-lapse confocal imaging of multiple embryos. In particular, performing multiposition imaging is crucial when comparing timing of events such as the onset of gene expression. This requires data collection from multiple control and experimental embryos processed simultaneously. Such an approach can easily be extended for studies of extrinsic influences in any organ or tissue of choice accessible to live imaging, provided that transplantations can be targeted easily according to established embryonic fate maps.

In Vivo Imaging of Transgenic Gene Expression in Individual Retinal Progenitors in Chimeric Zebrafish Embryos to Study Cell Nonautonomous Influences

Live tracking of individual WT retinal progenitors in distinct genetic backgrounds allows for the assessment of the contribution of cell non-autonomous signaling during neurogenesis. Here, a combination of gene knockdown, chimera generation via embryo transplantation and in vivo time-lapse confocal imaging was utilized for this purpose.

The genetic and technical strengths have made the zebrafish vertebrate a key model organism in which the consequences of gene manipulations can be traced ...

Application of RNAi and Heat-shock-induced Transcription Factor Expression to Reprogram Germ Cells to Neurons in C. elegans

Studying the cell biological processes during converting the identities of specific cell types provides important insights into mechanism that maintain and protect cellular identities. The conversion of germ cells into specific neurons in the nematode Caenorhabditis elegans (C. elegans) is a powerful tool for performing genetic screens in order to dissect regulatory pathways that safeguard established cell identities. Reprogramming of germ cells to a specific type of neurons termed ASE requires transgenic animals that allow broad over-expression of the Zn-finger transcription factor (TF) CHE-1. Endogenous CHE-1 is expressed exclusively in two head neurons and is required to specify the glutamatergic ASE neurons fate, which can easily be visualized by the gcy-5prom::gfp reporter. A trans gene containing the heat-shock promoter-driven che-1 gene expression construct allows broad mis-expression of CHE-1 in the entire animal upon heat-shock treatment. The combination of RNAi against the chromatin-regulating factor LIN-53 and heat-shock-induced che-1 over-expression leads to reprogramming of germ cell into ASE neuron-like cells. We describe here the specific RNAi procedure and appropriate conditions for heat-shock treatment of transgenic animals in order to successfully induce germ cell to neuron conversion.

Application of RNAi and Heat-shock-induced Transcription Factor Expression to Reprogram Germ Cells to Neurons in C. elegans

This protocol describes how to study cellular processes during cell fate conversion in Caenorhabditis elegans in vivo. Using transgenic animals, allowing heat-shock promoter-driven overexpression of the neuron fate-inducing transcription factor CHE-1 and RNAi-mediated depletion of the chromatin-regulating factor LIN-53 germ cell to neuron reprogramming can be observed in vivo.

Studying the cell biological processes during converting the identities of specific cell types provides important insights into mechanism that maintain ...

In Vivo Imaging of Muscle-tendon Morphogenesis in Drosophila Pupae

Muscles together with tendons and the skeleton enable animals including humans to move their body parts. Muscle morphogenesis is highly conserved from animals to humans. Therefore, the powerful Drosophila model system can be used to study concepts of muscle-tendon development that can also be applied to human muscle biology. Here, we describe in detail how morphogenesis of the adult muscle-tendon system can be easily imaged in living, developing Drosophila pupae. Hence, the method allows investigating proteins, cells and tissues in their physiological environment. In addition to a step-by-step protocol with helpful tips, we provide a comprehensive overview of fluorescently tagged marker proteins that are suitable for studying the muscle-tendon system. To highlight the versatile applications of the protocol, we show example movies ranging from visualization of long-term morphogenetic events &#8211; occurring on the time scale of hours and days &#8211; to visualization of short-term dynamic processes like muscle twitching occurring on time scale of seconds. Taken together, this protocol should enable the reader to design and perform live-imaging experiments for investigating muscle-tendon morphogenesis in the intact organism.

In Vivo Imaging of Muscle-tendon Morphogenesis in Drosophila Pupae

Here, we present an easy-to-use and versatile method to perform live imaging of developmental processes in general and muscle-tendon morphogenesis in particular in living Drosophila pupae.

Muscles together with tendons and the skeleton enable animals including humans to move their body parts. Muscle morphogenesis is highly conserved from ...

Generation of Scaffold-free, Three-dimensional Insulin Expressing Pancreatoids from Mouse Pancreatic Progenitors In Vitro

The pancreas is a complex organ composed of many different cell types that work together to regulate blood glucose homeostasis and digestion. These cell types include enzyme-secreting acinar cells, an arborized ductal system responsible for the transportation of enzymes to the gut, and hormone-producing endocrine cells. 
Endocrine beta-cells are the sole cell type in the body that produce insulin to lower blood glucose levels. Diabetes, a disease characterized by a loss or the dysfunction of beta-cells, is reaching epidemic proportions. Thus, it is essential to establish protocols to investigate beta-cell development that can be used for screening purposes to derive the drug and cell-based therapeutics. While the experimental investigation of mouse development is essential, in vivo studies are laborious and time-consuming. Cultured cells provide a more convenient platform for screening; however, they are unable to maintain the cellular diversity, architectural organization, and cellular interactions found in vivo. Thus, it is essential to develop new tools to investigate pancreatic organogenesis and physiology.
Pancreatic epithelial cells develop in the close association with mesenchyme from the onset of organogenesis as cells organize and differentiate into the complex, physiologically competent adult organ. The pancreatic mesenchyme provides important signals for the endocrine development, many of which are not well understood yet, thus difficult to recapitulate during the in vitro culture. Here, we describe a protocol to culture three-dimensional, cellular complex mouse organoids that retain mesenchyme, termed pancreatoids. The e10.5 murine pancreatic bud is dissected, dissociated, and cultured in a scaffold-free environment. These floating cells self-assemble with mesenchyme enveloping the developing pancreatoid and a robust number of endocrine beta-cells developing along with the acinar and the duct cells. This system can be used to study the cell fate determination, structural organization, and morphogenesis, cell-cell interactions during organogenesis, or for the drug, small molecule, or genetic screening.

Generation of Scaffold-free, Three-dimensional Insulin Expressing Pancreatoids from Mouse Pancreatic Progenitors In Vitro

Here, we present a protocol to generate insulin expressing 3D murine pancreatoids from free-floating e10.5 dissociated pancreatic progenitors and the associated mesenchyme.

The pancreas is a complex organ composed of many different cell types that work together to regulate blood glucose homeostasis and digestion. These cell ...

An In Vitro 3D Model and Computational Pipeline to Quantify the Vasculogenic Potential of iPSC-Derived Endothelial Progenitors

Induced pluripotent stem cells (iPSCs) are a patient-specific, proliferative cell source that can differentiate into any somatic cell type. Bipotent endothelial progenitors (EPs), which can differentiate into the cell types necessary to assemble mature, functional vasculature, have been derived from both embryonic and induced pluripotent stem cells. However, these cells have not been rigorously evaluated in three-dimensional environments, and a quantitative measure of their vasculogenic potential remains elusive. Here, the generation and isolation of iPSC-EPs via fluorescent-activated cell sorting are first outlined, followed by a description of the encapsulation and culture of iPSC-EPs in collagen hydrogels. This extracellular matrix (ECM)-mimicking microenvironment encourages a robust vasculogenic response; vascular networks form after a week of culture. The creation of a computational pipeline that utilizes open-source software to quantify this vasculogenic response is delineated. This pipeline is specifically designed to preserve the 3D architecture of the capillary plexus to robustly identify the number of branches, branching points, and the total network length with minimal user input.

Endothelial progenitors derived from induced pluripotent stem cells (iPSC-EPs) have the potential to revolutionize cardiovascular disease treatments and to enable the creation of more faithful cardiovascular disease models. Herein, the encapsulation of iPSC-EPs in three-dimensional (3D) collagen microenvironments and a quantitative analysis of these cells&#8217; vasculogenic potential are described.

Induced pluripotent stem cells (iPSCs) are a patient-specific, proliferative cell source that can differentiate into any somatic cell type. Bipotent ...

Performing Human Skeletal Muscle Xenografts in Immunodeficient Mice

Treatment effects observed in animal studies often fail to be recapitulated in clinical trials. While this problem is multifaceted, one reason for this failure is the use of inadequate laboratory models. It is challenging to model complex human diseases in traditional laboratory organisms, but this issue can be circumvented through the study of human xenografts. The surgical method we describe here allows for the creation of human skeletal muscle xenografts, which can be used to model muscle disease and to carry out preclinical therapeutic testing. Under an Institutional Review Board (IRB)-approved protocol, skeletal muscle specimens are acquired from patients and then transplanted into NOD-Rag1null IL2r&gamma;null (NRG) host mice. These mice are ideal hosts for transplantation studies due to their inability to make mature lymphocytes and are thus unable to develop cell-mediated and humoral adaptive immune responses. Host mice are anaesthetized with isoflurane, and the mouse tibialis anterior and extensor digitorum longus muscles are removed. A piece of human muscle is then placed in the empty tibial compartment and sutured to the proximal and distal tendons of the peroneus longus muscle. The xenografted muscle is spontaneously vascularized and innervated by the mouse host, resulting in robustly regenerated human muscle that can serve as a model for preclinical studies.

Complex human diseases can be challenging to model in traditional laboratory model systems. Here, we describe a surgical approach to model human muscle disease through the transplantation of human skeletal muscle biopsies into immunodeficient mice.

Treatment effects observed in animal studies often fail to be recapitulated in clinical trials. While this problem is multifaceted, one reason for this ...