The authors thank Chad MacArthur for helpful discussions.

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All of the authors [RHQ, JSTA, KS, and UL] are employees of Thermo Fisher Scientific, which produces some of the reagents and instruments used in this article.

This study provides strategies for monitoring and tracking of the reprogramming process using flow cytometry and real-time imaging-based analysis. The critical steps in the protocol are initiating reprogramming, measuring reprogramming progression based on marker expression and real-time monitoring of reprogramming. Any reprogramming method of choice can be used but here we focus on Sendai based reprogramming of human fibroblasts. The advantage of this method is the ease of use and consistent high efficiency of reprogram...

Patient-derived induced pluripotent stem cells (iPSCs) are promising tools for cell therapy and drug screening. They provide an autologous source of cells for therapy. In addition, they encompass a very broad set of genetic backgrounds, enabling a detailed in vitro analysis of genetic diseases beyond what current embryonic stem cell (ESC) lines would allow. Recent advances have led to the development of several methods for generating iPSCs, including reprogramming with Sendai virus, episomal plasmids or mRNAs 1,2. Notably, different reprogramming methods are associated with varying levels of efficiency and safety, and are likely to differ in other ways that influence their appropriateness for various applications. With the availability of a variety of reprogramming technologies, it has become important to develop methods for assessing the reprogramming process. Most existing methods rely on the qualitative inspection of morphology or staining with stem cell-specific dyes and antibodies. One recently developed method makes use of lentiviral fluorescence reporters that are sensitive to PSC-specific miRNAs or differentiated cell-specific mRNAs 3. Such monitoring methods facilitate the selection and optimization of reprogramming techniques for different situations. For example, CDy1 has been used as a fluorescent probe for early iPSCs in order to screen for reprogramming modulators 4. The ability to observe and compare different reprogramming experiments is also critical for gaining a better understanding of the process itself. For instance, it is now known that some somatic cell types are easier to reprogram than others 5, and that cells go through intermediate states during reprogramming 6-8. Unfortunately, the mechanisms underlying the reprogramming process are still not completely understood and consequently, the exact differences between reprogramming methods also remain to be defined. Thus, methods for monitoring, assessing, and comparing reprogramming events continue to be critical for the stem cell field.
The methods described in this protocol permit the monitoring and assessing of the reprogramming process and illustrate how these techniques can be used to compare different sets of reprogramming reagents. The first approach involves flow cytometry analyses using combinations of antibodies against positive and negative pluripotent stem cell (PSC) markers. The second approach couples real-time imaging and the measurement of total confluence (the percent surface area covered by the cells) and confluence of marker signals (the percent surface area covered by the fluorescent signals).

<table border="0" cellpadding="0" cellspacing="0" width="795">
	<tbody>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">DMEM, high glucose, GlutaMAXSupplement, pyruvate</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">10569-010</td>
			<td style="width:88px;"></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Fetal Bovine Serum, embryonic stem cell-qualified, US origin</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">16141-061</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">MEM Non-Essential Amino Acids Solution (100X)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">11140-050</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Trypsin-EDTA (0.05%), phenol red&#160;</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">25300-054</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Mouse (ICR) Inactivated Embryonic Fibroblasts</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A24903</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Attachment Factor Protein (1X)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">S-006-100</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">DMEM/F-12, GlutaMAX supplement</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">10565-018</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">KnockOut Serum Replacement</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td align="right" style="width:147px;">10828010</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">2-Mercaptoethanol (55 mM)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">21985-023</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Collagenase, Type IV, powder</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">17104-019</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">TrypLE Select Enzyme (1X), no phenol red&#160;</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">12563-011</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">DPBS, no calcium, no magnesium&#160;</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">14190-144</td>
			<td></td>
		</tr>
		<tr height="61">
			<td height="61" style="height:61px;width:297px;">Geltrex LDEV-Free, hESC-Qualified, Reduced Growth Factor Basement Membrane Matrix</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A1413302</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Essential 8 Medium</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A1517001</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">FGF-Basic (AA 1-155) Recombinant Human Protein</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">PHG0264</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">UltraPure 0.5M EDTA, pH 8.0</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">15575-020</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Bovine Albumin Fraction V (7.5% solution)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">15260-037</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">HEPES (1 M)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">15630-080</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Penicillin-Streptomycin (10,000 U/mL)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">15140-122</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">InSolution Y-27632</td>
			<td style="width:263px;">EMD Millipore</td>
			<td align="right" style="width:147px;">688001</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">CytoTune-iPS Sendai Reprogramming Kit</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A1378001</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">CytoTune-iPS 2.0 Sendai Reprogramming Kit</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A16517</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Countess II Automated Cell Counter</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">AMQAX1000</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Countess Cell Counting Chamber Slides</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">C10228</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">BJ ATCC Human Foreskin Fibroblasts, Neonatal</td>
			<td style="width:263px;">ATCC</td>
			<td style="width:147px;">CRL-2522</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">DF1 Adult Human Dermal Fibroblast</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">N/A</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">BG01V/hOG Cells Variant hESC hOct4-GFP Reporter Cells</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">R7799-105</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">IncuCyte ZOOM</td>
			<td style="width:263px;">Essen BioScience</td>
			<td style="width:147px;"></td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">SSEA-4 Antibody, Alexa Fluor 647 conjugate (MC813-70)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">SSEA421</td>
			<td></td>
		</tr>
		<tr height="61">
			<td height="61" style="height:61px;width:297px;">SSEA-4 Antibody, Alexa Fluor 488 conjugate (eBioMC-813-70 (MC-813-70))</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A14810</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">SSEA-4 Antibody (MC813-70)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">41-4000</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">TRA-1-60 Antibody (cl.A)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">&#160;41-1000</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">CD44 Rat Anti-Human/Mouse mAb (clone IM7), PE-Cy5 conjugate</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A27094</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">CD44 Alexa Fluor 488 Conjugate Kit for Live Cell Imaging</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A25528</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">CD44 Rat Anti-Human/Mouse mAb (Clone IM7)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">RM-5700 (no longer available)</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Goat anti-Mouse IgG (H+L) Secondary Antibody, Alexa Fluor 488 conjugate</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">&#160;A-11029</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Goat anti-Rat IgG (H+L) Secondary Antibody, Alexa Fluor 594 conjugate</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">&#160;A-11007</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Alkaline Phosphatase Live Stain</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A14353</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">TRA-1-60 Alexa Fluor 488 Conjugate Kit for Live Cell Imaging</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A25618</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">CD24 Mouse Anti-Human mAb (clone SN3), FITC conjugate</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">MHCD2401</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">beta-2 Microglobulin Antibody, FITC conjugate (B2M-01)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A15737</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">EpCAM / CD326 Antibody, FITC conjugate (VU-1D9)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">A15755</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">CD73 / NT5E Antibody (7G2)</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">41-0200</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">VECTOR Red Alkaline Phosphatase (AP) Substrate Kit</td>
			<td style="width:263px;">Vector Laboratories</td>
			<td style="width:147px;">SK-5100</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Zeiss Axio Observer.Z1 microscope&#160;</td>
			<td style="width:263px;">Carl Zeiss</td>
			<td style="width:147px;">491912-0003-000</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">FlowJo Data Analysis Software</td>
			<td style="width:263px;">FLOJO, LLC</td>
			<td style="width:147px;">N/A</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Attune Accoustic Focusing Cytometer, Blue/Red Laser</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
			<td style="width:147px;">Use Attune NXT&#160;</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">S3e\ Cell Sorter (488/561 nm)</td>
			<td style="width:263px;">BIO-RAD</td>
			<td align="right" style="width:147px;">1451006</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Falcon 12 x 75 mm Tube with Cell Strainer Cap</td>
			<td style="width:263px;">Corning</td>
			<td align="right" style="width:147px;">352235</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:297px;">Falcon 15 mL, high-clarity, dome-seal screw cap</td>
			<td style="width:263px;">Corning</td>
			<td align="right" style="width:147px;">352097</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:297px;">Falcon T-75 Flask</td>
			<td style="width:263px;">Corning</td>
			<td align="right" style="width:147px;">353136</td>
			<td></td>
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			<td height="22" style="height:22px;width:297px;">Falcon T-175 Flask</td>
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			<td height="22" style="height:22px;width:297px;">Falcon 6-well dish</td>
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			<td height="41" style="height:41px;width:297px;">HERAEUS HERACELL CO2 ROLLING INCUBATOR</td>
			<td style="width:263px;">Thermo Fisher Scientific</td>
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			<td height="41" style="height:41px;width:297px;">Nonstick, RNase-free Microfuge Tubes, 1.5 mL</td>
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			<td style="width:147px;">AM12450</td>
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		<tr height="22">
			<td height="22" style="height:22px;width:297px;">HulaMixer Sample Mixer</td>
			<td style="width:263px;"></td>
			<td style="width:147px;">15920D</td>
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kinetic measurement and real time visualization of somatic reprogramming

Somatic reprogramming has enabled the conversion of adult cells to induced pluripotent stem cells (iPSC) from diverse genetic backgrounds and disease phenotypes. Recent advances have identified more efficient and safe methods for introduction of reprogramming factors. However, there are few tools to monitor and track the progression of reprogramming. Current methods for monitoring reprogramming rely on the qualitative inspection of morphology or staining with stem cell-specific dyes and antibodies. Tools to dissect the progression of iPSC generation can help better understand the process under different conditions from diverse cell sources. 
This study presents key approaches for kinetic measurement of reprogramming progression using flow cytometry as well as real-time monitoring via imaging. To measure the kinetics of reprogramming, flow analysis was performed at discrete time points using antibodies against positive and negative pluripotent stem cell markers. The combination of real-time visualization and flow analysis enables the quantitative study of reprogramming at different stages and provides a more accurate comparison of different systems and methods. Real-time, image-based analysis was used for the continuous monitoring of fibroblasts as they are reprogrammed in a feeder-free medium system. The kinetics of colony formation was measured based on confluence in the phase contrast or fluorescence channels after staining with live alkaline phosphatase dye or antibodies against SSEA4 or TRA-1-60. The results indicated that measurement of confluence provides semi-quantitative metrics to monitor the progression of reprogramming.

Monitoring Reprogramming Kinetics Using Flow Cytometry
CD44 is a fibroblast marker while SSEA4 is a PSC marker 6,10. As expected from this expression pattern, flow cytometry of BJ fibroblasts shows an SSEA4- CD44+ population that facilitates the creation of quadrant gates in combination with the unstained sample. During reprogramming of DF1 fibroblasts with the Sendai viruses, CD44 is gr...

Watch this Scientific Journal Video about Kinetic Measurement and Real Time Visualization of Somatic Reprogramming at JoVE.com

Kinetic Measurement and Real Time Visualization of Somatic Reprogramming

The protocol presented in this study describes methods for the real-time monitoring of reprogramming progression via the kinetic measurement of positive and negative pluripotent stem cell markers using flow cytometry analysis. The protocol also includes the imaging-based assessment of morphology, and marker or reporter expression during iPSC generation.

Somatic reprogramming has enabled the conversion of adult cells to induced pluripotent stem cells (iPSC) from diverse genetic backgrounds and disease ...

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JoVE Journal

Developmental Biology

6.6K Views.  Thermo Fisher Scientific. The protocol presented in this study describes methods for the real-time monitoring of reprogramming progression via the kinetic measurement of positive and negative pluripotent stem cell markers using flow cytometry analysis. The protocol also includes the imaging-based assessment of morphology, and marker or reporter expression during iPSC generation.

Video: Kinetic Measurement and Real Time Visualization of Somatic Reprogramming

Stable and Efficient Genetic Modification of Cells in the Adult Mouse V-SVZ for the Analysis of Neural Stem Cell Autonomous and Non-autonomous Effects

Relatively quiescent somatic stem cells support life-long cell renewal in most adult tissues. Neural stem cells in the adult mammalian brain are restricted to two specific neurogenic niches: the subgranular zone of the dentate gyrus in the hippocampus and the ventricular-subventricular zone (V-SVZ; also called subependymal zone or SEZ) in the walls of the lateral ventricles. The development of in vivo gene transfer strategies for adult stem cell populations (i.e. those of the mammalian brain) resulting in long-term expression of desired transgenes in the stem cells and their derived progeny is a crucial tool in current biomedical and biotechnological research. Here, a direct in vivo method is presented for the stable genetic modification of adult mouse V-SVZ cells that takes advantage of the cell cycle-independent infection by LVs and the highly specialized cytoarchitecture of the V-SVZ niche. Specifically, the current protocol involves the injection of empty LVs (control) or LVs encoding specific transgene expression cassettes into either the V-SVZ itself, for the in vivo targeting of all types of cells in the niche, or into the lateral ventricle lumen, for the targeting of ependymal cells only. Expression cassettes are then integrated into the genome of the transduced cells and fluorescent proteins, also encoded by the LVs, allow the detection of the transduced cells for the analysis of cell autonomous and non-autonomous, niche-dependent effects in the labeled cells and their progeny.

Here we describe a procedure based on the use of lentiviral particles for the long-term genetic modification of neural stem cells and/or their adjacent ependymal cells in the adult ventricular-subventricular neurogenic niche which allows the separate analysis of cell autonomous and non-autonomous, niche-dependent effects on neural stem cells.

Relatively quiescent somatic stem cells support life-long cell renewal in most adult tissues. Neural stem cells in the adult mammalian brain are ...

Evaluation of Injury-induced Senescence and In Vivo Reprogramming in the Skeletal Muscle

Cellular senescence is a stress response that is characterized by a stable cellular growth arrest, which is important for many physiological and pathological processes, such as cancer and ageing. Recently, senescence has also been implicated in tissue repair and regeneration. Therefore, it has become increasingly critical to identify senescent cells in vivo. Senescence-associated &#946;-galactosidase (SA-&#946;-Gal) assay is the most widely used assay to detect senescent cells both in culture and in vivo. This assay is based on the increased lysosomal contents in the senescent cells, which allows the histochemical detection of lysosomal &#946;-galactosidase activity at suboptimum pH (6 or 5.5). In comparison with other assays, such as flow cytometry, this allows the identification of senescent cells in their resident environment, which offers valuable information such as the location relating to the tissue architecture, the morphology, and the possibility of coupling with other markers via immunohistochemistry&#160;(IHC). The major limitation of the SA-&#946;-Gal assay is the requirement of fresh or frozen samples.
Here, we present a detailed protocol to understand how cellular senescence promotes cellular plasticity and tissue regeneration in vivo. We use SA-&#946;-Gal to detect senescent cells in the skeletal muscle upon injury, which is a well-established system to study tissue regeneration. Moreover, we use&#160;IHC to detect Nanog, a marker of pluripotent stem cells, in a transgenic mouse model. This protocol enables us to examine and quantify cellular senescence in the context of induced cellular plasticity and in vivo reprogramming.

Evaluation of Injury-induced Senescence and In Vivo Reprogramming in the Skeletal Muscle

Here we present a detailed protocol to detect both senescent and pluripotent stem cells in the skeletal muscle upon injury while inducing in vivo reprogramming. This method is suitable for evaluating the role of cellular senescence during tissue regeneration and reprogramming in vivo.

Cellular senescence is a stress response that is characterized by a stable cellular growth arrest, which is important for many physiological and ...

Multi-Photon Time Lapse Imaging to Visualize Development in Real-time: Visualization of Migrating Neural Crest Cells in Zebrafish Embryos

Congenital eye and craniofacial anomalies reflect disruptions in the neural crest, a transient population of migratory stem cells that give rise to numerous cell types throughout the body. Understanding the biology of the neural crest has been limited, reflecting a lack of genetically tractable models that can be studied in vivo and in real-time. Zebrafish is a particularly important developmental model for studying migratory cell populations, such as the neural crest. To examine neural crest migration into the developing eye, a combination of the advanced optical techniques of laser scanning microscopy with long wavelength multi-photon fluorescence excitation was implemented to capture high-resolution, three-dimensional, real-time videos of the developing eye in transgenic zebrafish embryos, namely Tg(sox10:EGFP) and Tg(foxd3:GFP), as sox10 and foxd3 have been shown in numerous animal models to regulate early neural crest differentiation and likely represent markers for neural crest cells. Multi-photon time-lapse imaging was used to discern the behavior and migratory patterns of two neural crest cell populations contributing to early eye development. This protocol provides information for generating time-lapse videos during zebrafish neural crest migration, as an example, and can be further applied to visualize the early development of many structures in the zebrafish and other model organisms.

A combination of the advanced optical techniques of laser scanning microscopy with long wavelength multi-photon fluorescence excitation was implemented to capture high-resolution, three-dimensional, real-time imaging of neural crest migration in Tg(sox10:EGFP) and Tg(foxd3:GFP) zebrafish embryos.

Congenital eye and craniofacial anomalies reflect disruptions in the neural crest, a transient population of migratory stem cells that give rise to ...

Real-time Measurement of Epithelial Barrier Permeability in Human Intestinal Organoids

Advances in 3D culture of intestinal tissues obtained through biopsy or generated from pluripotent stem cells via directed differentiation, have resulted in sophisticated in vitro models of the intestinal mucosa. Leveraging these emerging model systems will require adaptation of tools and techniques developed for 2D culture systems and animals. Here, we describe a technique for measuring epithelial barrier permeability in human intestinal organoids in real-time. This is accomplished by microinjection of fluorescently-labeled dextran and imaging on an inverted microscope fitted with epifluorescent filters. Real-time measurement of the barrier permeability in intestinal organoids facilitates the generation of high-resolution temporal data in human intestinal epithelial tissue, although this technique can also be applied to fixed timepoint imaging approaches. This protocol is readily adaptable for the measurement of epithelial barrier permeability following exposure to pharmacologic agents, bacterial products or toxins, or live microorganisms. With minor modifications, this protocol can also serve as a general primer on microinjection of intestinal organoids and users may choose to supplement this protocol with additional or alternative downstream applications following microinjection.

This protocol describes the measurement of epithelial barrier permeability in real-time following pharmacologic treatment in human intestinal organoids using fluorescent microscopy and live cell microscopy.

Advances in 3D culture of intestinal tissues obtained through biopsy or generated from pluripotent stem cells via directed differentiation, have resulted ...

Kinetic Analysis of Vasculogenesis Quantifies Dynamics of Vasculogenesis and Angiogenesis In Vitro

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of vasculogenesis has become a central readout of endothelial progenitor cell functionality, and therefore, several attempts have been made to improve both in vitro and in vivo vasculogenesis models. However, standard methods are limited in scope, with static measurements failing to capture many aspects of this highly dynamic process. Therefore, the goal of developing this novel protocol was to assess the kinetics of in vitro vasculogenesis in order to quantitate rates of network formation and stabilization, as well as provide insight into potential mechanisms underlying vascular dysfunction. Application of this protocol is demonstrated using fetal endothelial colony forming cells (ECFCs) exposed to maternal diabetes mellitus. Fetal ECFCs were derived from umbilical cord blood following birth, cultured, and plated in slides containing basement membrane matrix, where they underwent vasculogenesis. Images of the entire slide wells were acquired using time-lapse phase contrast microscopy over 15 hours. Images were analyzed for derivation of quantitative data using an analysis software called Kinetic Analysis of Vasculogenesis (KAV). KAV uses image segmentation followed by skeletonization to analyze network components from stacks of multi-time point phase contrast images to derive ten parameters (9 measured, 1 calculated) of network structure including: closed networks, network areas, nodes, branches, total branch length, average branch length, triple-branched nodes, quad-branched nodes, network structures, and the branch to node ratio. Application of this protocol identified altered rates of vasculogenesis in ECFCs obtained from pregnancies complicated by diabetes mellitus. However, this technique has broad implications beyond the scope reported here. Implementation of this approach will enhance mechanistic assessment and improve functional readouts of vasculogenesis and other biologically important branching processes in numerous cell types or disease states.

Kinetic Analysis of Vasculogenesis Quantifies Dynamics of Vasculogenesis and Angiogenesis In Vitro

Here, we present a protocol for time-lapse imaging and analysis of vasculogenesis in vitro using phase contrast microscopy coupled with the open source software, Kinetic Analysis of Vasculogenesis. This protocol can be applied to quantitatively assess the vasculogenic potential of numerous cell types or experimental conditions that model vascular disease.

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of ...

Direct Lineage Reprogramming of Adult Mouse Fibroblast to Erythroid Progenitors

Erythroid cell commitment and differentiation proceed through activation of a lineage-restricted transcriptional network orchestrated by a group of cell fate determining and maturing factors. We previously set out to define the minimal set of factors necessary for instructing red blood cell development using direct lineage reprogramming of fibroblasts into induced erythroid progenitors/precursors (iEPs). We showed that overexpression of Gata1, Tal1, Lmo2, and c-Myc (GTLM) can rapidly convert murine and human fibroblasts directly to iEPs that resemble bona fide erythroid cells in terms of morphology, phenotype, and gene expression. We intend that iEPs will provide an invaluable tool to study erythropoiesis and cell fate regulation. Here we describe the stepwise process of converting murine tail tip fibroblasts into iEPs via transcription factor-driven direct lineage reprogramming (DLR). In this example, we perform the reprogramming in fibroblasts from erythroid lineage-tracing mice that express the yellow fluorescent protein (YFP) under the control of the erythropoietin receptor gene (EpoR) promoter, enabling visualization of erythroid cell fate induction upon reprogramming. Following this protocol, fibroblasts can be reprogrammed into iEPs within five to eight days. 
While improvements can still be made to the process, we show that GTLM-mediated reprogramming is a rapid and direct process, yielding cells with properties of bona fide erythroid progenitor and precursor cells.

Here we present our protocol for producing induced erythroid progenitors (iEPs) from mouse adult fibroblasts using transcription factor-driven direct lineage reprogramming (DLR).

Erythroid cell commitment and differentiation proceed through activation of a lineage-restricted transcriptional network orchestrated by a group of cell ...

RNA-based Reprogramming of Human Primary Fibroblasts into Induced Pluripotent Stem Cells

Induced pluripotent stem cells (iPSCs) have proven to be a valuable tool to study human development and disease. Further advancing iPSCs as a regenerative therapeutic requires a safe, robust, and expedient reprogramming protocol. Here, we present a clinically relevant, step-by-step protocol for the extremely high-efficiency reprogramming of human dermal fibroblasts into iPSCs using a non-integrating approach. The core of the protocol consists of expressing pluripotency factors (SOX2, KLF4, cMYC, LIN28A, NANOG, OCT4-MyoD fusion) from in vitro transcribed messenger RNAs synthesized with modified nucleotides (modified mRNAs). The reprogramming modified mRNAs are transfected into primary fibroblasts every 48 h together with mature embryonic stem cell-specific microRNA-367/302 mimics for two weeks. The resulting iPSC colonies can then be isolated and directly expanded in feeder-free conditions. To maximize efficiency and consistency of our reprogramming protocol across fibroblast samples, we have optimized various parameters including the RNA transfection regimen, timing of transfections, culture conditions, and seeding densities. Importantly, our method generates high-quality iPSCs from most fibroblast sources, including difficult-to-reprogram diseased, aged, and/or senescent samples.

Here we describe a clinically relevant, high-efficiency, feeder-free method to reprogram human primary fibroblasts into induced pluripotent stem cells using modified mRNAs encoding reprogramming factors and mature microRNA-367/302 mimics. Also included are methods to assess reprogramming efficiency, expand clonal iPSC colonies, and confirm expression of the pluripotency marker TRA-1-60.

Induced pluripotent stem cells (iPSCs) have proven to be a valuable tool to study human development and disease. Further advancing iPSCs as a regenerative ...

Hemogenic Reprogramming of Human Fibroblasts by Enforced Expression of Transcription Factors

The cellular and molecular mechanisms underlying specification of human hematopoietic stem cells (HSCs) remain elusive. Strategies to recapitulate human HSC emergence in vitro are required to overcome limitations in studying this complex developmental process. Here, we describe a protocol to generate hematopoietic stem and progenitor-like cells from human dermal fibroblasts employing a direct cell reprogramming approach. These cells transit through a hemogenic intermediate cell-type, resembling the endothelial-to-hematopoietic transition (EHT) characteristic of HSC specification. Fibroblasts were reprogrammed to hemogenic cells via transduction with GATA2, GFI1B and FOS transcription factors. This combination of three factors induced morphological changes, expression of hemogenic and hematopoietic markers and dynamic EHT transcriptional programs. Reprogrammed cells generate hematopoietic progeny and repopulate immunodeficient mice for three months. This protocol can be adapted towards the mechanistic dissection of the human EHT process as exemplified here by defining GATA2 targets during the early phases of reprogramming. Thus, human hemogenic reprogramming provides a simple and tractable approach to identify novel markers and regulators of human HSC emergence. In the future, faithful induction of hemogenic fate in fibroblasts may lead to the generation of patient-specific HSCs for transplantation.

This protocol demonstrates the induction of a hemogenic program in human dermal fibroblasts by enforced expression of the transcription factors GATA2, GFI1B and FOS to generate hematopoietic stem and progenitor cells.

The cellular and molecular mechanisms underlying specification of human hematopoietic stem cells (HSCs) remain elusive. Strategies to recapitulate human ...

A Layered Mounting Method for Extended Time-Lapse Confocal Microscopy of Whole Zebrafish Embryos

Dynamics of development can be followed by confocal time-lapse microscopy of live transgenic zebrafish embryos expressing fluorescence in specific tissues or cells. A difficulty with imaging whole embryo development is that zebrafish embryos grow substantially in length. When mounted as regularly done in 0.3-1% low melt agarose, the agarose imposes growth restriction, leading to distortions in the soft embryo body. Yet, to perform confocal time-lapse microscopy, the embryo must be immobilized. This article describes a layered mounting method for zebrafish embryos that restrict the motility of the embryos while allowing for the unrestricted growth. The mounting is performed in layers of agarose at different concentrations. To demonstrate the usability of this method, whole embryo vascular, neuronal and muscle development was imaged in transgenic fish for 55 consecutive hours. This mounting method can be used for easy, low-cost imaging of whole zebrafish embryos using inverted microscopes without requirements of molds or special equipment.

This article describes a method to mount fragile zebrafish embryos for extended time-lapse confocal microscopy. This low-cost method is easy to perform using regular glass-bottom microscopy dishes for imaging on any inverted microscope. The mounting is performed in layers of agarose at different concentrations.

Dynamics of development can be followed by confocal time-lapse microscopy of live transgenic zebrafish embryos expressing fluorescence in specific tissues ...

Real-time Bioluminescence Imaging of Notch Signaling Dynamics during Murine Neurogenesis

Notch signaling regulates the maintenance of neural stem/progenitor cells by cell-cell interactions. The components of Notch signaling exhibit dynamic expression. Notch signaling effector Hes1 and the Notch ligand Delta-like1 (Dll1) are expressed in an oscillatory manner in neural stem/progenitor cells. Because the period of the oscillatory expression of these genes is very short (2 h), it is difficult to monitor their cyclic expression. To examine such rapid changes in the gene expression or protein dynamics, fast response reporters are required. Because of its fast maturation kinetics and high sensitivity, the bioluminescence reporter luciferase is suitable to monitor rapid gene expression changes in living cells. We used a destabilized luciferase reporter for monitoring the promoter activity and a luciferase-fused reporter for visualization of protein dynamics at single cell resolution. These bioluminescence reporters show rapid turnover and generate very weak signals; therefore, we have developed a highly sensitive bioluminescence imaging system to detect such faint signals. These methods enable us to monitor various gene expression dynamics in living cells and tissues, which are important information to help understand the actual cellular states.

Neural stem/progenitor cells exhibit various expression dynamics of Notch signaling components that lead to different outcomes of cellular events. Such dynamic expression can be revealed by real-time monitoring, not by static analysis, using a highly sensitive bioluminescence imaging system that enables visualization of rapid changes in gene expressions.

Notch signaling regulates the maintenance of neural stem/progenitor cells by cell-cell interactions. The components of Notch signaling exhibit dynamic ...