We would like to acknowledge funding from CIRM grant RB5-07409. J.M.M. would like to thank FuiBoon Kai, Dhruv Thakar, and Roger Oria for various discussions that guided the generation and troubleshooting of this method. J.M.M. also thanks the UCSF Discovery Fellowship for the ongoing support of his work.

<ol>
	<li>Tabar, V., Studer, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pluripotent+stem+cells+in+regenerative+medicine:+Challenges+and+recent+progress.">Pluripotent stem cells in regenerative medicine: Challenges and recent progress.</a> Nature Reviews Genetics. 15, 82-92 (2014).</li><li>Avior, Y., Sagi, I., Benvenisty, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pluripotent+stem+cells+in+disease+modelling+and+drug+discovery.">Pluripotent stem cells in disease modelling and drug discovery.</a> Nature Reviews Molecular Cell Biology. 17, 170-182 (2016).</li><li>Trounson, A., DeWitt, N. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pluripotent+stem+cells+progressing+to+the+clinic.">Pluripotent stem cells progressing to the clinic.</a> Nature Reviews Molecular Cell Biology. 17, 194-200 (2016).</li><li>Li, Y., Li, L., Chen, Z. N., Gao, G., Yao, R., Sun, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering-derived+approaches+for+iPSC+preparation,+expansion,+differentiation+and+applications.">Engineering-derived approaches for iPSC preparation, expansion, differentiation and applications.</a> Biofabrication. 9 (3), 032001 (2017).</li><li>Stevens, K. R., Murry, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+Pluripotent+Stem+Cell-Derived+Engineered+Tissues:+Clinical+Considerations.">Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations.</a> Cell Stem Cell. 22 (3), 294-297 (2018).</li><li>Itskovitz-Eldor, J., 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=Differentiation+of+human+embryonic+stem+cells+into+embryoid+bodies+comprising+the+three+embryonic+germ+layers.">Differentiation of human embryonic stem cells into embryoid bodies comprising the three embryonic germ layers.</a> Molecular Medicine. 6 (2), 88-95 (2000).</li><li>Lakins, J. N., Chin, A. R., Weaver, V. M., Mace, K., Braun, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exploring+the+link+between+human+embryonic+stem+cell+organization+and+fate+using+tension-calibrated+extracellular+matrix+functionalized+polyacrylamide+gels.">Exploring the link between human embryonic stem cell organization and fate using tension-calibrated extracellular matrix functionalized polyacrylamide gels.</a> Progenitor Cells. Methods in Molecular Biology (Methods and Protocols). 916, 317-350 (2012).</li><li>Warmflash, A., Sorre, B., Etoc, F., Siggia, E. D., Brivanlou, A. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+method+to+recapitulate+early+embryonic+spatial+patterning+in+human+embryonic+stem+cells.">A method to recapitulate early embryonic spatial patterning in human embryonic stem cells.</a> Nature Methods. 11 (8), 847-854 (2014).</li><li>Przybyla, L., Lakins, J. N., Sunyer, R., Trepat, X., Weaver, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monitoring+developmental+force+distributions+in+reconstituted+embryonic+epithelia.">Monitoring developmental force distributions in reconstituted embryonic epithelia.</a> Methods. 94, 101-113 (2016).</li><li>Przybyla, L., Lakins, J. N., Weaver, V. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+Mechanics+Orchestrate+Wnt-Dependent+Human+Embryonic+Stem+Cell+Differentiation.">Tissue Mechanics Orchestrate Wnt-Dependent Human Embryonic Stem Cell Differentiation.</a> Cell Stem Cell. 19 (4), 462-475 (2016).</li><li>Shahbazi, M. N., 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=Self-organization+of+the+human+embryo+in+the+absence+of+maternal+tissues.">Self-organization of the human embryo in the absence of maternal tissues.</a> Nature Cell Biology. 18, 700-708 (2016).</li><li>Shao, Y., Taniguchi, K., Townshend, R. F., Miki, T., Gumucio, D. L., Fu, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+pluripotent+stem+cell-based+model+for+post-implantation+human+amniotic+sac+development.">A pluripotent stem cell-based model for post-implantation human amniotic sac development.</a> Nature Communications. 8 (208), 1-15 (2017).</li><li>Simunovic, M., Brivanlou, A. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Embryoids,+organoids+and+gastruloids:+new+approaches+to+understanding+embryogenesis.">Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis.</a> Development. 144, 976-985 (2017).</li><li>Thomson, J. A., 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=Embryonic+stem+cell+lines+derived+from+human+blastocysts.">Embryonic stem cell lines derived from human blastocysts.</a> Science. 282 (5391), 1145-1147 (1998).</li><li>Shahbazi, M. N., Zernicka-Goetz, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Deconstructing+and+reconstructing+the+mouse+and+human+early+embryo.">Deconstructing and reconstructing the mouse and human early embryo.</a> Nature Cell Biology. 20, 878-887 (2018).</li><li>Li, Q., 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=Extracellular+matrix+scaffolding+guides+lumen+elongation+by+inducing+anisotropic+intercellular+mechanical+tension.">Extracellular matrix scaffolding guides lumen elongation by inducing anisotropic intercellular mechanical tension.</a> Nature Cell Biology. 18 (3), 311-318 (2016).</li></ol>

The authors have nothing to disclose.

To simplify a long and detailed protocol, this method consists of three critical stages: 1) generating patterns of ECM ligand on glass coverslips, 2) transferring the patterns to polyacrylamide hydrogels during polymerization of the gel, and 3) seeding hESCs on the patterned hydrogel. There are critical steps that must be considered at each of these three stages. In order to generate high-fidelity patterns on the glass coverslips, the stencil must be firmly pressed onto the coverslip to prevent leaking of the ligand solu...

Human embryonic stem cells (hESCs) hold great promise for use in regenerative medicine and tissue engineering applications. The pluripotent nature of these cells gives them the ability to differentiate into any adult cell type. While great strides have been made in directing the fate of hESCs to particular cell types, it has remained very difficult to generate whole tissues or organs de novo1,2,3,4,5. This is due, in large part, to a limited understanding of the mechanisms that drive the formation of these tissues during human development. In order to fill this gap in knowledge, a number of methods have emerged in recent years to model the early embryo and subsequent stages of development with embryonic stem cells6,7,8,9,10,11,12,13.
Shortly after the derivation of the first hESC lines14, it was demonstrated that embryoid bodies formed from hESCs were capable of spontaneously producing cells of the three primary germ layers6. However, due to the inherent lack of control over the size and morphology of embryoid bodies, the organization of germ layers varied significantly and failed to match the organization of the early embryo. More recently, Warmflash et al. developed a method to confine colonies of hESCs on glass substrates via micropatterning, providing control and consistency over the size and geometry of the colonies8. In the presence of BMP4, an important morphogen in early development, these confined colonies were capable of self-organizing reproducible patterns of specification to fates representing the primary germ layers. Although this provided a useful model for studying the mechanisms by which primary germ layers are established, the patterns of fate specification did not precisely match the organization and morphogenesis observed during embryogenesis15. A more faithful recapitulation of early embryonic development was achieved by embedding hESCs in a three-dimensional extracellular matrix (ECM) of matrigel11, providing the strongest evidence to date for the ability of hESCs to self-organize and model the early stages of embryogenesis ex vivo. However, this method yields inconsistent results and is thus incompatible with a number of assays that could be used to reveal the underlying mechanisms of self-organization and fate specification.
Given these existing methods and their respective limitations, we sought to develop a method for reproducibly culturing hESC colonies of defined geometries in conditions that model the extracellular environment of the early embryo. To achieve this, we used polyacrylamide hydrogels of tunable elasticity to control the mechanical properties of the substrate. Using atomic force microscopy on gastrulation-stage chicken embryos, we found that the elasticity of the epiblast ranged from hundreds of pascals to a few kilopascals. Thus, we focused on generating polyacrylamide hydrogels with elasticity in this range to serve as the substrate for hESC colonies. We modified our previous methods for culturing hESCs on polyacrylamide hydrogels7,9 to provide robust control over the geometry of the colonies. We achieved this by first patterning ECM ligands, namely matrigel, onto glass coverslips through microfabricated stencils, as previously reported16. We then designed a novel technique to transfer the patterned ligand to the surface of polyacrylamide hydrogels during polymerization. The method we describe here involves using photolithography to fabricate a silicon wafer with the desired geometric patterns, creating stamps of theses geometric features with polydimethylsiloxane (PDMS), and using these stamps to generate the stencils that ultimately allow patterning of ligand onto the surface of glass coverslips and transfer to polyacrylamide.
In addition to recapitulating the mechanical environment of the early embryo, confining hESC colonies on polyacrylamide enables the measurement of cell-generated forces with traction force microscopy (TFM), as reported in our previous method9. In brief, fluorescent beads can be embedded in the polyacrylamide and used as fiducial markers. Cell-generated forces are calculated by imaging the displacement of these beads after seeding hESCs onto the patterned substrate. Furthermore, the resulting traction force maps can be combined with traditional assays, such as immunostaining, to examine how the distribution of cell-generated forces in confined hESC colonies may regulate or modulate downstream signaling. We expect these methods will reveal that mechanical forces play a critical role in the patterning of cell fate specification during early embryonic development that is currently overlooked.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.05% Trypsin</td>
			<td>Gibco</td>
			<td>25300054</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mm glass petri dish</td>
			<td>Fisher Scientific</td>
			<td>08-747B</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mm plastic petri dish</td>
			<td>Fisher Scientific</td>
			<td>FB0875712</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL conical-bottom tubes</td>
			<td>Corning</td>
			<td>352095</td>
			<td></td>
		</tr>
		<tr>
			<td>150 mm plastic petri dish</td>
			<td>Fisher Scientific</td>
			<td>FB0875714</td>
			<td></td>
		</tr>
		<tr>
			<td>18 mm diameter #1 coverslips</td>
			<td>Thermo Scientific</td>
			<td>18CIR-1</td>
			<td></td>
		</tr>
		<tr>
			<td>2% bisacrylamide</td>
			<td>Bio-Rad</td>
			<td>161-0142</td>
			<td></td>
		</tr>
		<tr>
			<td>3-aminopropyltrimethoxysilane</td>
			<td>ACROS Organics</td>
			<td>313251000</td>
			<td></td>
		</tr>
		<tr>
			<td>40% acrylamide</td>
			<td>Bio-Rad</td>
			<td>161-0140</td>
			<td></td>
		</tr>
		<tr>
			<td>Aluminum foil</td>
			<td>Fisher Scientific</td>
			<td>01-213-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Basic fibroblast growth factor</td>
			<td>Sigma-Aldrich</td>
			<td>F0291</td>
			<td></td>
		</tr>
		<tr>
			<td>Bleach</td>
			<td>Clorox</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge with swing-buckets</td>
			<td>Eppendorf</td>
			<td>22623508</td>
			<td>Model: 5804 R</td>
		</tr>
		<tr>
			<td>Collagen</td>
			<td>Corning</td>
			<td>354236</td>
			<td></td>
		</tr>
		<tr>
			<td>Dessicator</td>
			<td>Fisher Scientific</td>
			<td>08-642-7</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Fisher Scientific</td>
			<td>AC615095000</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>Gibco</td>
			<td>16000044</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescent microspheres</td>
			<td>Thermo Scientific</td>
			<td>F8821</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps (for coverslips)</td>
			<td>Fisher Scientific</td>
			<td>16-100-122</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps (for wafers)</td>
			<td>Fisher Scientific</td>
			<td>17-467-328</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel holders</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Gel holders are custom 3D-printed, CAD drawing available on request</td>
		</tr>
		<tr>
			<td>Glutaraldehyde</td>
			<td>Fisher Scientific</td>
			<td>50-261-94</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Thermo Scientific</td>
			<td>J16926A1</td>
			<td></td>
		</tr>
		<tr>
			<td>Hot plate</td>
			<td>Fisher Scientific</td>
			<td>HP88854100</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid</td>
			<td>Fisher Scientific</td>
			<td>A144S-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropyl alcohol</td>
			<td>Fisher Scientific</td>
			<td>A416-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Kimwipes (delicate task wipes)</td>
			<td>Kimberly-Clark Professional</td>
			<td>34120</td>
			<td></td>
		</tr>
		<tr>
			<td>Knockout serum replacement</td>
			<td>Gibco</td>
			<td>10828028</td>
			<td></td>
		</tr>
		<tr>
			<td>Knockout-DMEM</td>
			<td>Gibco</td>
			<td>10829018</td>
			<td></td>
		</tr>
		<tr>
			<td>Mask aligner (for photolithography)</td>
			<td>Karl Suss America, Inc.</td>
			<td>Karl Suss MJB3 Mask Aligner</td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel</td>
			<td>Corning</td>
			<td>354277</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope for traction force</td>
			<td>Nikon</td>
			<td>N/A</td>
			<td>Model: Eclipse TE200 U</td>
		</tr>
		<tr>
			<td>Motorized positioning stage</td>
			<td>Prior Scientific</td>
			<td>N/A</td>
			<td>Model: HLD117</td>
		</tr>
		<tr>
			<td>Nitrogen gas</td>
			<td>Airgas</td>
			<td>NI 250</td>
			<td></td>
		</tr>
		<tr>
			<td>Norland optical adhesive 74 (UV-curable polymer)</td>
			<td>Norland Products</td>
			<td>NOA 74</td>
			<td></td>
		</tr>
		<tr>
			<td>Oven</td>
			<td>Thermo Scientific</td>
			<td>PR305225G</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm (laboratory film)</td>
			<td>Fisher Scientific</td>
			<td>13-374-12</td>
			<td></td>
		</tr>
		<tr>
			<td>PDMS (Sylgard 184)</td>
			<td>Fisher Scientific</td>
			<td>NC9285739</td>
			<td></td>
		</tr>
		<tr>
			<td>Photomask</td>
			<td>CAD/Art Services, Inc.</td>
			<td>N/A</td>
			<td>Photomasks are custom made. CAD drawing for our designs available upon request</td>
		</tr>
		<tr>
			<td>Plasma cleaner</td>
			<td>Fisher Scientific</td>
			<td>NC9332171</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic for gasket</td>
			<td>Marian Chicago</td>
			<td>HT6135</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic for spacer</td>
			<td>TAP Plastics</td>
			<td>N/A</td>
			<td>Polycarbonate sheet, .01 inch thickness</td>
		</tr>
		<tr>
			<td>Potassium chloride (for making PBS)</td>
			<td>Fisher Scientific</td>
			<td>P217-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic (for making PBS)</td>
			<td>Fisher Scientific</td>
			<td>P285-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Pottassium persulfate</td>
			<td>ACROS Organics</td>
			<td>424185000</td>
			<td></td>
		</tr>
		<tr>
			<td>Scalpel</td>
			<td>Fisher Scientific</td>
			<td>14-840-00</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicon wafer</td>
			<td>Electron Microscopy Sciences</td>
			<td>71893-06</td>
			<td>Type P, 3 inch, silicon wafers</td>
		</tr>
		<tr>
			<td>Sodium chloride (for making PBS)</td>
			<td>Fisher Scientific</td>
			<td>S271-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydroxide</td>
			<td>Fisher Scientific</td>
			<td>S318-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium phosphate dibasic dihydrate (for making PBS)</td>
			<td>Fisher Scientific</td>
			<td>S472-500</td>
			<td></td>
		</tr>
		<tr>
			<td>SU8-3050 Photoresist</td>
			<td>MicroChem</td>
			<td>SU8-3000</td>
			<td></td>
		</tr>
		<tr>
			<td>SU8-Developer</td>
			<td>MicroChem</td>
			<td>Y020100</td>
			<td></td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>Bio-Rad</td>
			<td>161-0800</td>
			<td></td>
		</tr>
		<tr>
			<td>UV-sterilization box</td>
			<td>Bio-Rad</td>
			<td>N/A</td>
			<td>Bio-Rad GS Gene Linker UV Chamber</td>
		</tr>
		<tr>
			<td>Y27632 (Rho kinase inhibitor)</td>
			<td>StemCell Technologies</td>
			<td>72304</td>
			<td></td>
		</tr>
	</tbody>
</table>

patterning the geometry of human embryonic stem cell colonies on compliant substrates to control tissue-level mechanics

Human embryonic stem cells demonstrate a unique ability to respond to morphogens in vitro by self-organizing patterns of cell fate specification that correspond to primary germ layer formation during embryogenesis. Thus, these cells represent a powerful tool with which to examine the mechanisms that drive early human development. We have developed a method to culture human embryonic stem cells in confined colonies on compliant substrates that provides control over both the geometry of the colonies and their mechanical environment in order to recapitulate the physical parameters that underlie embryogenesis. The key feature of this method is the ability to generate polyacrylamide hydrogels with defined patterns of extracellular matrix ligand at the surface to promote cell attachment. This is achieved by fabricating stencils with the desired geometric patterns, using these stencils to create patterns of extracellular matrix ligand on glass coverslips, and transferring these patterns to polyacrylamide hydrogels during polymerization. This method is also compatible with traction force microscopy, allowing the user to measure and map the distribution of cell-generated forces within the confined colonies. In combination with standard biochemical assays, these measurements can be used to examine the role mechanical cues play in fate specification and morphogenesis during early human development.

The main challenge to overcome in attempting to culture hESCs in colonies of controlled geometry on compliant substrates is to generate a homogenous pattern of ECM-ligand on the surface of the substrate. The strategy presented in this method involves first generating the desired pattern on the surface of a glass coverslip and then subsequently transferring that pattern to the surface of a polyacrylamide hydrogel during polymerization of the gel (Figure 1<stro...

Watch this Scientific Journal Video about Patterning the Geometry of Human Embryonic Stem Cell Colonies on Compliant Substrates to Control Tissue-Level Mechanics at JoVE.com

Patterning the Geometry of Human Embryonic Stem Cell Colonies on Compliant Substrates to Control Tissue-Level Mechanics

Extracellular matrix ligands can be patterned onto polyacrylamide hydrogels to enable the culture of human embryonic stem cells in confined colonies on compliant substrates. This method can be combined with traction force microscopy and biochemical assays to examine the interplay between tissue geometry, cell-generated forces, and fate specification.

Human embryonic stem cells demonstrate a unique ability to respond to morphogens in vitro by self-organizing patterns of cell fate specification that ...

patterning-geometry-human-embryonic-stem-cell-colonies-on-compliant

Research

JoVE Journal

Bioengineering

8.1K Views.  University of California San Francisco and University of California Berkeley. Extracellular matrix ligands can be patterned onto polyacrylamide hydrogels to enable the culture of human embryonic stem cells in confined colonies on compliant substrates. This method can be combined with traction force microscopy and biochemical assays to examine the interplay between tissue geometry, cell-generated forces, and fate specification.

Video: Patterning the Geometry of Human Embryonic Stem Cell Colonies on Compliant Substrates to Control Tissue-Level Mechanics

Alginate Microcapsule as a 3D Platform for Propagation and Differentiation of Human Embryonic Stem Cells (hESC) to Different Lineages

Human embryonic stem cells (hESC) are emerging as an attractive alternative source for cell replacement therapy since they can be expanded in culture indefinitely and differentiated to any cell types in the body. Various types of biomaterials have also been used in stem cell cultures to provide a microenvironment mimicking the stem cell niche1-3. The latter is important for promoting cell-to-cell interaction, cell proliferation, and differentiation into specific lineages as well as tissue organization by providing a three-dimensional (3D) environment4 such as encapsulation. The principle of cell encapsulation involves entrapment of living cells within the confines of semi-permeable membranes in 3D cultures2. These membranes allow for the exchange of nutrients, oxygen and stimuli across the membranes, whereas antibodies and immune cells from the host that are larger than the capsule pore size are excluded5. Here, we present an approach to culture and differentiate hESC DA neurons in a 3D microenvironment using alginate microcapsules. We have modified the culture conditions2 to enhance the viability of encapsulated hESC. We have previously shown that the addition of p160-Rho-associated coiled-coil kinase (ROCK) inhibitor, Y-27632 and human fetal fibroblast-conditioned serum replacement medium (hFF-CM) to the 3D platform significantly enhanced the viability of encapsulated hESC in which the cells expressed definitive endoderm marker genes1. We have now used this 3D platform for the propagation of hESC and efficient differentiation to DA neurons. Protein and gene expression analyses after the final stage of DA neuronal differentiation showed an increased expression of tyrosine hydroxylase (TH), a marker for DA neurons, &gt;100 folds after 2 weeks. We hypothesized that our 3D platform using alginate microcapsules may be useful to study the proliferation and directed differentiation of hESC to various lineages. This 3D system also allows the separation of feeder cells from hESC during the process of differentiation and also has potential for immune-isolation during transplantation in the future.

Alginate Microcapsule as a 3D Platform for Propagation and Differentiation of Human Embryonic Stem Cells hESC to Different Lineages

We have optimized a microencapsulation technique as an effective 3D platform for propagation and differentiation of embryonic stem cells to endoderm and dopaminergic (DA) neurons. It also provides an opportunity for immune-isolation of cells from the host during transplantation. This platform can be adapted for other cell types.

Human embryonic stem cells (hESC) are emerging as an attractive alternative source for cell replacement therapy since they can be expanded in culture ...

Visualization of Cortex Organization and Dynamics in Microorganisms, using Total Internal Reflection Fluorescence Microscopy

TIRF microscopy has emerged as a powerful imaging technology to study spatio-temporal dynamics of fluorescent molecules in vitro and in living cells1. The optical phenomenon of total internal reflection occurs when light passes from a medium with high refractive index into a medium with low refractive index at an angle larger than a characteristic critical angle (i.e. closer to being parallel with the boundary). Although all light is reflected back under such conditions, an evanescent wave is created that propagates across and along the boundary, which decays exponentially with distance, and only penetrates sample areas that are 100-200 nm near the interface2. In addition to providing superior axial resolution, the reduced excitation of out of focus fluorophores creates a very high signal to noise ratios and minimizes damaging effects of photobleaching2,3. Being a widefield technique, TIRF also allows faster image acquisition than most scanning based confocal setups.
At first glance, the low penetration depth of TIRF seems to be incompatible with imaging of bacterial and fungal cells, which are often surrounded by thick cell walls. On the contrary, we have found that the cell walls of yeast and bacterial cells actually improve the usability of TIRF and increase the range of observable structures4-8. Many cellular processes can therefore be directly accessed by TIRF in small, single-cell microorganisms, which often offer powerful genetic manipulation techniques. This allows us to perform in vivo biochemistry experiments, where kinetics of protein interactions and activities can be directly assessed in living cells.
We describe here the individual steps required to obtain high quality TIRF images for Saccharomyces cerevisiae or Bacillus subtilis cells. We point out various problems that can affect TIRF visualization of fluorescent probes in cells and illustrate the procedure with several application examples. Finally, we demonstrate how TIRF images can be further improved using established image restoration techniques.

Total Internal Reflection Fluorescence (TIRF) microscopy is a powerful approach to observe structures close to the cell surface at high contrast and temporal resolution. We demonstrate how TIRF can be employed to study protein dynamics at the cortex of cell wall-enclosed bacterial and fungal cells.

TIRF microscopy has emerged as  a powerful imaging technology to study spatio-temporal dynamics of fluorescent molecules  in vitro and in living cells1. ...

Development, Expansion, and In vivo Monitoring of Human NK Cells from Human Embryonic Stem Cells (hESCs) and Induced Pluripotent Stem Cells (iPSCs)

We present a method for deriving natural killer (NK) cells from undifferentiated hESCs and iPSCs using a feeder-free approach. This method gives rise to high levels of NK cells after 4 weeks culture and can undergo further 2-log expansion with artificial antigen presenting cells. hESC- and iPSC-derived NK cells developed in this system have a mature phenotype and function. The production of large numbers of genetically modifiable NK cells is applicable for both basic mechanistic as well as anti-tumor studies. Expression of firefly luciferase in hESC-derived NK cells allows a non-invasive approach to follow NK cell engraftment, distribution, and function. We also describe a dual-imaging scheme that allows separate monitoring of two different cell populations to more distinctly characterize their interactions in vivo. This method of derivation, expansion, and dual in vivo imaging provides a reliable approach for producing NK cells and their evaluation which is necessary to improve current NK cell adoptive therapies.

Development, Expansion, and In vivo Monitoring of Human NK Cells from Human Embryonic Stem Cells hESCs and Induced Pluripotent Stem Cells iPSCs

This protocol describes the development, expansion, and in vivo imaging of NK cells derived from hESCs and iPSCs.

We present a method for deriving natural killer (NK) cells from undifferentiated hESCs and iPSCs using a feeder-free approach. This method gives rise to ...

Cell Patterning on Photolithographically Defined 
Parylene-C: SiO2 Substrates

Cell patterning platforms support broad research goals, such as construction of predefined in vitro neuronal networks and the exploration of certain central aspects of cellular physiology. To easily combine cell patterning with Multi-Electrode Arrays (MEAs) and silicon-based &#8216;lab on a chip&#8217; technologies, a microfabrication-compatible protocol is required. We describe a method that utilizes deposition of the polymer parylene-C on SiO2&#160;wafers. Photolithography enables accurate and reliable patterning of parylene-C at micron-level resolution. Subsequent activation by immersion in fetal bovine serum (or another specific activation solution) results in a substrate in which cultured cells adhere to, or are repulsed by, parylene or SiO2 regions respectively. This technique has allowed patterning of a broad range of cell types (including primary murine hippocampal cells, HEK 293 cell line, human neuron-like teratocarcinoma cell line, primary murine cerebellar granule cells, and primary human glioma-derived stem-like cells). Interestingly, however, the platform is not universal; reflecting the importance of cell-specific adhesion molecules. This cell patterning process is cost effective, reliable, and importantly can be incorporated into standard microfabrication (chip manufacturing) protocols, paving the way for integration of microelectronic technology.

Cell Patterning on Photolithographically Defined 
Parylene-C: SiO2 Substrates

This protocol describes a microfabrication-compatible method for cell patterning on SiO2. A predefined parylene-C design is photolithographically printed on SiO2 wafers. Following incubation with serum (or other activation solution) cells adhere specifically to (and grow according to the conformity of) underlying parylene-C, whilst being repulsed by SiO2 regions.

Cell patterning platforms support broad research goals, such as construction of predefined in vitro neuronal networks and the exploration of certain ...

Using Adhesive Patterning to Construct 3D Paper Microfluidic Devices

We demonstrate the use of patterned aerosol adhesives to construct both planar and nonplanar 3D paper microfluidic devices. By spraying an aerosol adhesive through a metal stencil, the overall amount of adhesive used in assembling paper microfluidic devices can be significantly reduced. We show on a simple 4-layer planar paper microfluidic device that the optimal adhesive application technique and device construction style depends heavily on desired performance characteristics. By moderately increasing the overall area of a device, it is possible to dramatically decrease the wicking time and increase device success rates while also reducing the amount of adhesive required to keep the device together. Such adhesive application also causes the adhesive to form semi-permanent bonds instead of permanent bonds between paper layers, enabling single-use devices to be non-destructively disassembled after use. Nonplanar 3D origami devices also benefit from the semi-permanent bonds during folding, as it reduces the likelihood that unrelated faces may accidently stick together. Like planar devices, nonplanar structures see reduced wicking times with patterned adhesive application vs uniformly applied adhesive.

We demonstrate the use of patterned aerosol adhesives to construct 3D paper microfluidic devices. This method of adhesive application forms semi-permanent bonds between layers, enabling single-use devices to be non-destructively disassembled after use and to ease folding complex nonplanar structures.

We demonstrate the use of patterned aerosol adhesives to construct both planar and nonplanar 3D paper microfluidic devices. By spraying an aerosol ...

Evaluation of Keratinocyte Proliferation on Two- and Three-dimensional Type I Collagen Substrates

Type I collagen, useful as a substrate for cell culture, exists in two forms: the two-dimensional, non-fibrous form and three-dimensional, fibril form. Both forms can be prepared with the same type I collagen. In general, the non-fibrous form promotes cell adhesion and proliferation. The fibril form (gels) provides more physiological conditions in many types of cells; therefore, gel culture is useful for examining physiological behaviors of cells, such as drug efficacy.
Researchers can select the appropriate form according to the purpose of its use. For example, in the case of keratinocytes, on-gel culture has been used as a wound healing model. FEPE1L-8, a keratinocyte cell line cultured on the non-fibrous form of type I collagen, promote cell adhesion. Notably, keratinocyte proliferation is slower on the fibril form than the non-fibrous form. Protocols for the preparation of type I collagen for cell culture are simple and have wide applications depending on the experimental needs.

Here, we present a protocol for the preparation of two different forms of culture substrates utilizing type I collagen. Depending on how collagen is handled, collagen molecules either maintain two-dimensional, non-fibrous form or reassemble into three-dimensional, fibril form. Cell proliferation on type I collagen is drastically affected by fibril formation.

Type I collagen, useful as a substrate for cell culture, exists in two forms: the two-dimensional, non-fibrous form and three-dimensional, fibril form. ...

Single-Cell Optical Action Potential Measurement in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Conventional intracellular microelectrode techniques to quantify cardiomyocyte electrophysiology are extremely complex, labor intensive, and typically carried out in low throughput. Rapid and ongoing expansion of induced pluripotent stem cell (iPSC) technology presents a new standard in cardiovascular research and alternate methods are now necessary to increase throughput of electrophysiological data at a single cell level. VF2.1Cl is a recently derived voltage sensitive dye which provides a rapid single channel, high magnitude response to fluctuations in membrane potential. It possesses kinetics superior to those of other existing voltage indicators and makes available functional data equivalent to that of traditional microelectrode techniques. Here, we demonstrate simplified, non-invasive action potential characterization in externally paced human iPSC derived cardiomyocytes using a modular and highly affordable photometry system.

Here we describe optical acquisition and characterization of action potentials from induced pluripotent stem cell derived cardiomyocytes using a high-speed modular photometry system.

Conventional intracellular microelectrode techniques to quantify cardiomyocyte electrophysiology are extremely complex, labor intensive, and typically ...

A Culture Method to Maintain Quiescent Human Hematopoietic Stem Cells

Human hematopoietic stem cells (HSCs), like other mammalian HSCs, maintain lifelong hematopoiesis in the bone marrow. HSCs remain quiescent in vivo, unlike more differentiated progenitors, and enter the cell cycle rapidly after chemotherapy or irradiation to treat bone marrow injury or in vitro culture. By mimicking the bone marrow microenvironment in the presence of abundant fatty acids, cholesterol, low concentration of cytokines, and hypoxia, human HSCs maintain quiescence in vitro. Here, a detailed protocol for maintaining functional HSCs in the quiescent state in vitro is described. This method will enable studies of the behavior of human HSCs under physiological conditions.

This protocol enables the maintenance of quiescent human hematopoietic stem cells in vitro by mimicking the bone marrow microenvironment using abundant fatty acids, cholesterol, lower concentrations of cytokines, and hypoxia.

Human hematopoietic stem cells (HSCs), like other mammalian HSCs, maintain lifelong hematopoiesis in the bone marrow. HSCs remain quiescent in vivo, ...

Control of Cell Geometry through Infrared Laser Assisted Micropatterning

Micropatterning is an established technique in the cell biology community used to study connections between the morphology and function of cellular compartments while circumventing complications arising from natural cell-to-cell variations. To standardize cell shape, cells are either confined in 3D molds or controlled for adhesive geometry through adhesive islands. However, traditional micropatterning techniques based on photolithography and deep UV etching heavily depend on clean rooms or specialized equipment. Here we present an infrared laser assisted micropatterning technique (microphotopatterning) modified from Doyle et al. that can be conveniently set up with commercially available imaging systems. In this protocol, we use a Nikon A1R MP+ imaging system to generate micropatterns with micron precision through an infrared (IR) laser that ablates preset regions on poly-vinyl alcohol coated coverslips. We employ a custom script to enable automated pattern fabrication with high efficiency and accuracy in systems not equipped with a hardware autofocus. We show that this IR laser assisted micropatterning (microphotopatterning) protocol results in defined patterns to which cells attach exclusively and take on the desired shape. Furthermore, data from a large number of cells can be averaged due to the standardization of cell shape. Patterns generated with this protocol, combined with high resolution imaging and quantitative analysis, can be used for relatively high throughput screens to identify molecular players mediating the link between form and function.

The protocol presented here enables automated fabrication of micropatterns that standardizes cell shape to study cytoskeletal structures within mammalian cells. This user-friendly technique can be set up with commercially available imaging systems and does not require specialized equipment inaccessible to standard cell biology laboratories.

Micropatterning is an established technique in the cell biology community used to study connections between the morphology and function of cellular ...

Control of Cell Adhesion using Hydrogel Patterning Techniques for Applications in Traction Force Microscopy

Traction force microscopy (TFM) is the main method used in mechanobiology to measure cell forces. Commonly this is being used for cells adhering to flat soft substrates that deform under cell traction (2D-TFM). TFM relies on the use of linear elastic materials, such as polydimethylsiloxane (PDMS) or polyacrylamide (PA). For 2D-TFM on PA, the difficulty in achieving high throughput results mainly from the large variability of cell shapes and tractions, calling for standardization. We present a protocol to rapidly and efficiently fabricate micropatterned PA hydrogels for 2D-TFM studies. The micropatterns are first created by maskless photolithography using near-UV light where extracellular matrix proteins bind only to the micropatterned regions, while the rest of the surface remains non-adhesive for cells. The micropatterning of extracellular matrix proteins is due to the presence of active aldehyde groups, resulting in adhesive regions of different shapes to accommodate either single cells or groups of cells. For TFM measurements, we use PA hydrogels of different elasticity by varying the amounts of acrylamide and bis-acrylamide and tracking the displacement of embedded fluorescent beads to reconstruct cell traction fields with regularized Fourier Transform Traction Cytometry (FTTC).
To further achieve precise recording of cell forces, we describe the use of a controlled dose of patterned light to release cell tractions in defined regions for single cells or groups of cells. We call this method local UV illumination traction force microscopy (LUVI-TFM). With enzymatic treatment, all cells are detached from the sample simultaneously, whereas with LUVI-TFM traction forces of cells in different regions of the sample can be recorded in sequence. We demonstrate the applicability of this protocol (i) to study cell traction forces as a function of controlled adhesion to the substrate, and (ii) to achieve a greater number of experimental observations from the same sample.

Near-UV lithography and traction force microscopy are combined to measure cellular forces on micropatterned hydrogels. The targeted light-induced release of single cells enables a high number of measurements on the same sample.

Traction force microscopy (TFM) is the main method used in mechanobiology to measure cell forces. Commonly this is being used for cells adhering to flat ...