We thank T. Shatova for helpful discussion on experimental design and data analysis. The assistance and expertise of G. Paradis, the personnel of the flow cytometry core at the Koch Institute, and the staff of the Microsystems Technology Laboratory at Massachusetts Institute of Technology are gratefully acknowledged. This work was supported by National Institutes of Health Grants RC1 EB011187-02, DE013023, DE016516, EB000351, and partially by National Cancer Institute Cancer Center Support (Core) Grants P30-CA14051 and MPP-09Call-Langer-60.

1. Storage
<ol>
	<li>Store the reservoirs, holders, O-rings and microfluidic devices in 70% ethanol. Use a container (e.g. jar or beaker) that has a lid to prevent evaporation and contamination by dust or outside particles. Place the devices in one container (1), reservoirs and O-rings in a second container (2), and holders in the third (3).</li>
</ol>
Note: The use of 70% ethanol for storage is to maintain sterility. If the only components of the solution are ethanol and water (i.e. no denaturing agents), all system components should be fully compatible and will not degrade over time.
<ol start="2">
	<li>Change ethanol solution in containers (2) and (3) before each use to prevent cross-contamination across experiments and minimize the presence of unwanted particles that can cause clogging.</li>
</ol>
2. Experiment Preparation
<ol>
	<li>Place containers (2) and (3) in an ultrasound bath for 5-10 min&#160;before each use. This helps remove any contaminating particles from previous experiments.</li>
	<li>Clean workspace in biosafety cabinet with 70% ethanol solution.</li>
	<li>Spray all materials (3 containers, and tweezers) with a 70% ethanol solution before placing them inside the biosafety cabinet.</li>
</ol>
3. Assembly
<ol>
	<li>Set down 2-3 low-lint wipes in the work area.</li>
	<li>Remove plastic reservoirs from their container with tweezers and set them on the wipes to facilitate evaporation of ethanol solution from inner surfaces. Gently tap the reservoirs on the surface or blow air through them to facilitate removal of the ethanol solution.</li>
	<li>Insert O-rings into their appropriate slot on the reservoirs.</li>
	<li>Remove the holder and chips from respective containers and allow ethanol to evaporate (~1-2 min).</li>
	<li>Use tweezers to place the desired chip face-up (i.e. access holes up) in the holder. Raise the holder with the chip to eyelevel to make sure the chip is lying flat in the holder and adjust if necessary with the tweezers. IMPORTANT: If the device does not fit properly in its holder, there is a risk that it will break during the subsequent steps.</li>
	<li>Next, gently place the reservoirs on the holder and align them with the clips. Be careful that O-rings do not fall out of their slots during this process.</li>
	<li>Gently press down on the reservoirs until they click into place. Ensure that both sides of the reservoirs are secure and that the chip appears to be in the correct position.</li>
</ol>
4. Cell Preparation
<ol>
	<li>For adherent cells (primary or established lines): Plate cells 1-2 days prior to the experiment such that they are no more than 80% confluent on the day of the experiment.</li>
	<li>Place cells in suspension (in PBS or relevant media) and aim for an operating concentration of 1.0 x 106 cells/ml&#160;to 1.0 x 107 cells/ml. NOTE: We have not observed significant changes in delivery performance due to cell concentration.</li>
	<li>Mix cells and the desired delivery material in a separate tube to obtain the desired material concentration for the experiment. IMPORTANT: Because the described delivery method relies on diffusion to facilitate delivery, a higher material concentration will yield higher delivery. If possible, it is recommended to use a 1 &#181;M solution of the desired material for initial trials. This concentration can then be titrated down in future experiments as needed. The lowest reported concentration used with this device is 10 nM21.</li>
</ol>
5. Operation
<ol>
	<li>Pipette mixture of cells and delivery material into a reservoir (current design has a max 150 &#181;l capacity). NOTE: Most device designs are fully reversible therefore direction of flow through the channels does not matter. Samples may be loaded into either of the two reservoirs.</li>
	<li>Attach pressure tubing to the filled reservoir and tighten the nut to ensure proper sealing (finger tight is often sufficient).</li>
	<li>Adjust pressure to the desired level on the regulator. This controls the speed at which cells travel through the device. Note that cell flow does not start until button is pressed.</li>
</ol>
NOTE: In previous work, nitrogen or compressed air have worked equally well as the carrier gas.
<ol start="4">
	<li>Raise device to eye level and orient it so that the liquid in the reservoir is easily visible. NOTE: Track the liquid column to shut off the system before the reservoir is emptied.</li>
	<li>Press the button to pressurize the reservoir and begin cell flow.</li>
	<li>When the liquid level is approximately 2 mm from the bottom of the reservoir, quickly turn the regulator to 0 psi to stop flow. IMPORTANT: If one fails to stop the flow before the reservoir is emptied, one risks ejecting the sample from the collection reservoir. Also note that if the fluid column is not moving at an appreciable pace, or has slowed substantially relative to its initial flow rate (e.g. 3x slower), the mounted device is probably clogged and needs to be exchanged. Operating a clogged device can lead to higher cell death.</li>
	<li>Collect the treated cells from the appropriate reservoir and place them in the desired collection tube/plate. IMPORTANT: Do not dilute the collected cells in any buffers at this stage as the porated cells will continue to uptake material for up to 10 min20. After this window has passed, dilute the cells in the desired media/buffer.</li>
	<li>To collect more treated cells or try alternative experimental conditions, repeat steps 5.1 - 5.7 as needed. Recall that the chips are reversible, therefore samples can be mounted in either reservoir. Be sure to exchange chips as needed if they clog. Discard clogged devices.</li>
</ol>
6. Disassembly
<ol>
	<li>Gently disconnect the reservoirs from the main holder by pushing aside the clip arms.</li>
	<li>Place each part in the appropriate storage container (detailed in section 1).</li>
	<li>Place used chips in a separate container for disposal.</li>
</ol>

<ol>
	<li>Schaffert, D., Wagner, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gene+therapy+progress+and+prospects:+synthetic+polymer-based+systems.">Gene therapy progress and prospects: synthetic polymer-based systems.</a> Gene. Ther. 15, 1131-1138 (2008).</li><li>Whitehead, K. A., Langer, R., Anderson, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Knocking+down+barriers:+advances+in+siRNA+delivery.">Knocking down barriers: advances in siRNA delivery.</a> Nat. Rev. Drug Discov. 8, 129-138 (2009).</li><li>Leader, B., Baca, Q. J., Golan, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+therapeutics:+a+summary+and+pharmacological+classification.">Protein therapeutics: a summary and pharmacological classification.</a> Nat. Rev. Drug Discov. 7, 21-39 (2008).</li><li>Kim, D., 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=Generation+of+Human+Induced+Pluripotent+Stem+Cells+by+Direct+Delivery+of+Reprogramming+Proteins.">Generation of Human Induced Pluripotent Stem Cells by Direct Delivery of Reprogramming Proteins.</a> Cell Stem Cell. 4, 472-476 (2009).</li><li>Dhar, S., Daniel, W. L., Giljohann, D. A., Mirkin, C. A., Lippard, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polyvalent+Oligonucleotide+Gold+Nanoparticle+Conjugates+as+Delivery+Vehicles+for+Platinum(IV)+Warheads.">Polyvalent Oligonucleotide Gold Nanoparticle Conjugates as Delivery Vehicles for Platinum(IV) Warheads.</a> J. Am. Chem. Soc. 131, 14652-14653 (2009).</li><li>Jiang, Z. -. X., Zhang, Z. -. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+PTPs+with+small+molecule+inhibitors+in+cancer+treatment.">Targeting PTPs with small molecule inhibitors in cancer treatment.</a> Cancer and Metastasis Reviews. 27, 263-272 (2008).</li><li>Derfus, A. M., Chan, W. C. W., Bhatia, S. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intracellular+Delivery+of+Quantum+Dots+for+Live+Cell+Labeling+and+Organelle+Tracking.">Intracellular Delivery of Quantum Dots for Live Cell Labeling and Organelle Tracking.</a> Adv. Mater. 16, 961-966 (2004).</li><li>Michalet, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantum+Dots+for+Live+Cells+in+Vivo+Imaging,+and+Diagnostics.">Quantum Dots for Live Cells in Vivo Imaging, and Diagnostics.</a> Science. 307, 538-544 (2005).</li><li>Dahan, M., 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=Diffusion+Dynamics+of+Glycine+Receptors+Revealed+by+Single-Quantum+Dot+Tracking.">Diffusion Dynamics of Glycine Receptors Revealed by Single-Quantum Dot Tracking.</a> Science. 302, 442-445 (2003).</li><li>Slowing, I. I., Trewyn, B. G., Lin, V. S. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mesoporous+Silica+Nanoparticles+for+Intracellular+Delivery+of+Membrane-Impermeable+Proteins.">Mesoporous Silica Nanoparticles for Intracellular Delivery of Membrane-Impermeable Proteins.</a> J. Am. Chem. Soc. 129, 8845-8849 (2007).</li><li>Pack, D. W., Hoffman, A. S., Pun, S., Stayton, P. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+development+of+polymers+for+gene+delivery.">Design and development of polymers for gene delivery.</a> Nat. Rev. Drug Discov. 4, 581-593 (2005).</li><li>Joseph, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cationic+lipids+used+in+gene+transfer.">Cationic lipids used in gene transfer.</a> Advanced Drug Delivery Reviews. 27 (97), 17-28 (1997).</li><li>Verma, 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=Surface-structure-regulated+cell-membrane+penetration+by+monolayer-protected+nanoparticles.">Surface-structure-regulated cell-membrane penetration by monolayer-protected nanoparticles.</a> Nat. Mater. 7, 588-595 (2008).</li><li>Yan, M., 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=A+novel+intracellular+protein+delivery+platform+based+on+single-protein+nanocapsules.">A novel intracellular protein delivery platform based on single-protein nanocapsules.</a> Nat. Nano. 5, 48-53 (2010).</li><li>Shi Kam, N. W., Jessop, T. C., Wender, P. A., Dai, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nanotube+Molecular+Transporters:+Internalization+of+Carbon+Nanotube-Protein+Conjugates+into+Mammalian+Cells.">Nanotube Molecular Transporters: Internalization of Carbon Nanotube-Protein Conjugates into Mammalian Cells.</a> J. Am. Chem. Soc. 126, 6850-6851 (2004).</li><li>Varkouhi, A. K., Scholte, M., Storm, G., Haisma, H. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endosomal+escape+pathways+for+delivery+of+biologicals.">Endosomal escape pathways for delivery of biologicals.</a> Journal of Controlled Release. 151, 220-228 (2011).</li><li>li, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electroporation+Gene+Therapy:+New+Developments+In+Vivo+and+In+Vitro.">Electroporation Gene Therapy: New Developments In Vivo and In Vitro.</a> Current Gene Therapy. 4, 309-316 (2004).</li><li>Fox, M., 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=Electroporation+of+cells+in+microfluidic+devices:+a+review.">Electroporation of cells in microfluidic devices: a review.</a> Anal. Bioanal. Chem. 385, 474-485 (2006).</li><li>Miller, D. 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The authors Armon Sharei, Robert Langer, and Klavs F. Jensen are shareholders of SQZ Biotechnologies Company that produces the microfluidic devices used in this article.

Certain aspects of the described experimental procedure (i.e. factors other than chip design and operating speed) may need to be optimized depending on the cell type and delivery material the system is applied to. The discussion that follows addresses some of the most common factors to consider when designing experiments.
To improve the delivery signal for fluorescently labeled compounds, one needs to address sources of background fluorescence. Surface binding and endocytosis, for exa...

Delivery of macromolecules to the cell cytoplasm is a critical step in therapeutic and research applications. Nanoparticle mediated delivery, for example, has shown potential in gene therapy1,2, while protein delivery is a promising means of affecting cellular function in both clinical3 and laboratory4 settings. Other materials, such as small molecule drugs, quantum dots, or gold nanoparticles, are of interest in applications ranging from cancer therapeutics5,6 to intracellular labeling7,8, and single molecule tracking9.
The cell membrane is largely impermeable to macromolecules. Many existing techniques use polymeric nanoparticles10,11, liposomes12, or chemical modifications13 to facilitate membrane disruption or endocytotic delivery. In these methods, the delivery efficiency and cell viability are often dependent on the structure of the target molecule and the cell type. These methods can be efficient at the delivery of structurally uniform materials, such as nucleic acids, but are often ill-suited for the delivery of more structurally diverse materials, such as proteins14,15 and nanomaterials7. Moreover, the endosome disruption mechanism that most of these methods rely on is often inefficient, hence leaving much material trapped in vesicle structures16. Finally, methods that are often developed for use with established cell lines do not translate well to primary cells.
Membrane poration methods, such as electroporation17,18 and sonoporation19, are an attractive alternative in some applications; however, they are known to cause low cell viability and can be limited by the charge of the target delivery material.
Rapid mechanical deformation of cells, a microfluidic approach to delivery, has recently demonstrated its advantages over current techniques in the context of cell reprogramming20 and nanomaterial delivery21. This method relies on mechanical disruption o the cell membrane to facilitate cytosolic delivery of materials present in the surrounding buffer. The system has demonstrated enabling potential in previously challenging cell types (e.g. primary immune cells and stem cells) and materials (e.g. antibodies and carbon nanotubes). Herein, the general procedure to use these devices for intracellular delivery of target macromolecules is described. The procedure is generalizable to most cell types and delivery materials; however, it is recommended that one conduct a brief optimization of conditions, as detailed in our previously reported design guidelines20, for any previously unreported applications. To date, the system has been used successfully for the delivery of RNA, DNA, gold nanoparticles, quantum dots, carbon nanotubes, proteins, and dextran polymers20,21.

<table border="0" cellpadding="0" cellspacing="0" width="777">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:375px;">Device Holder &#38; Plastic reservoir</td>
			<td style="width:136px;">SQZ Biotechnologies</td>
			<td style="width:149px;">Holder</td>
			<td style="width:117px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">LSRFortessa Analyzer</td>
			<td>Becton Dickinson</td>
			<td>N/A</td>
			<td>Flow cytometry machine used at the Koch Institute Core Facilities</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Microfluidic device</td>
			<td>SQZ Biotechnologies</td>
			<td>Cell Squeeze</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">O-Rings</td>
			<td>McMaster</td>
			<td>9452K311</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Pressure system to operate device</td>
			<td>SQZ Biotechnologies</td>
			<td>Pressure System</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Tweezers</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Ultrasound bath</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

cell squeezing as a robust, microfluidic intracellular delivery platform

Rapid mechanical deformation of cells has emerged as a promising, vector-free method for intracellular delivery of macromolecules and nanomaterials. This technology has shown potential in addressing previously challenging applications; including, delivery to primary immune cells, cell reprogramming, carbon nanotube, and quantum dot delivery. This vector-free microfluidic platform relies on mechanical disruption of the cell membrane to facilitate cytosolic delivery of the target material. Herein, we describe the detailed method of use for these microfluidic devices including, device assembly, cell preparation, and system operation. This delivery approach requires a brief optimization of device type and operating conditions for previously unreported applications. The provided instructions are generalizable to most cell types and delivery materials as this system does not require specialized buffers or chemical modification/conjugation steps. This work also provides recommendations on how to improve device performance and trouble-shoot potential issues related to clogging, low delivery efficiencies, and cell viability.

Figure 1 contains a descriptive schematic of the microfluidic delivery system. Figures 2a-b illustrate typical results from treating HeLa cells with different device designs in the presence of fluorescently conjugated 3 kDa dextran20. If the procedure is followed correctly, system performance will be sensitive to device type and operating speed. Therefore, one should optimize these conditions for a given application before proceeding to more complex experiments. In the range o...

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Cell Squeezing as a Robust, Microfluidic Intracellular Delivery Platform

Rapid mechanical deformation of cells has emerged as a promising, vector-free method for intracellular delivery of macromolecules and nanomaterials. This protocol provides detailed steps on how to use the system for a broad range of applications.

Rapid mechanical deformation of cells has emerged as a promising, vector-free method for intracellular delivery of macromolecules and nanomaterials. This ...

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12.7K Views.  Massachusetts Institute of Technology. Rapid mechanical deformation of cells has emerged as a promising, vector-free method for intracellular delivery of macromolecules and nanomaterials. This protocol provides detailed steps on how to use the system for a broad range of applications.

Video: Cell Squeezing as a Robust, Microfluidic Intracellular Delivery Platform

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 ...

High-throughput Protein Expression Generator Using a Microfluidic Platform

Rapidly increasing fields, such as systems biology, require the development and implementation of new technologies, enabling high-throughput and high-fidelity measurements of large systems. Microfluidics promises to fulfill many of these requirements, such as performing high-throughput screening experiments on-chip, encompassing biochemical, biophysical, and cell-based assays1. Since the early days of microfluidics devices, this field has drastically evolved, leading to the development of microfluidic large-scale integration2,3. This technology allows for the integration of thousands of micromechanical valves on a single device with a postage-sized footprint (Figure 1). We have developed a high-throughput microfluidic platform for generating in vitro expression of protein arrays (Figure 2) named PING (Protein Interaction Network Generator). These arrays can serve as a template for many experiments such as protein-protein 4, protein-RNA5 or protein-DNA6 interactions.
The device consist of thousands of reaction chambers, which are individually programmed using a microarrayer. Aligning of these printed microarrays to microfluidics devices programs each chamber with a single spot eliminating potential contamination or cross-reactivity Moreover, generating microarrays using standard microarray spotting techniques is also very modular, allowing for the arraying of proteins7, DNA8, small molecules, and even colloidal suspensions. The potential impact of microfluidics on biological sciences is significant. A number of microfluidics based assays have already provided novel insights into the structure and function of biological systems, and the field of microfluidics will continue to impact biology.

We present a microfluidic approach for the expression of protein arrays. The device consists of thousands of reaction chambers controlled by micro-mechanical valves. The microfluidic device is mated to a microarray-printed gene library. These genes are then transcribed and translated on-chip, resulting in a protein array ready for experimental use.

Rapidly increasing fields, such as systems biology, require the development and implementation of new technologies, enabling high-throughput and ...

The Multi-organ Chip - A Microfluidic Platform for Long-term Multi-tissue Coculture

The ever growing amount of new substances released onto the market and the limited predictability of current in vitro test systems has led to a high need for new solutions for substance testing. Many drugs that have been removed from the market due to drug-induced liver injury released their toxic potential only after several doses of chronic testing in humans. However, a controlled microenvironment is pivotal for long-term multiple dosing experiments,&#160;as even minor alterations in extracellular conditions may greatly influence the cell physiology. We focused within our research program on the generation of a microengineered bioreactor, which can be dynamically perfused by an on-chip pump and combines at least two culture spaces for multi-organ applications. This circulatory system mimics the in vivo conditions of primary cell cultures better and assures a steadier,&#160;more quantifiable extracellular relay of signals to the cells. 
For demonstration purposes, human liver equivalents, generated by aggregating differentiated HepaRG cells with human hepatic stellate cells in hanging drop plates, were cocultured with human skin punch biopsies for up to 28 days inside the microbioreactor. The use of cell culture inserts enables the skin to be cultured at an air-liquid interface, allowing topical substance exposure. The microbioreactor system is capable of supporting these cocultures at near physiologic fluid flow and volume-to-liquid ratios, ensuring stable and organotypic culture conditions. The possibility of long-term cultures enables the repeated exposure to substances. Furthermore, a vascularization of the microfluidic channel circuit using human dermal microvascular endothelial cells yields a physiologically more relevant vascular model.

Here, we present a protocol to coculture primary cells, tissue models and punch biopsies in a microfluidic multi-organ chip for up to 28 days. Human dermal microvascular endothelial cells, liver aggregates and skin biopsies were successfully combined in a common media circulation.

The ever growing amount of new substances released onto the market and the limited predictability of current in vitro test systems has led to a high need ...

A Microfluidic Platform for High-throughput Single-cell Isolation and Culture

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet high-throughput, method to perform single-cell culture experiments. Here, we report a microfluidic chip-based strategy for high-efficiency single-cell isolation (~77%) and demonstrate its capability of performing long-term single-cell culture (up to 7 d) and cellular heterogeneity analysis using clonogenic assay. These applications were demonstrated with KT98 mouse neural stem cells, and A549 and MDA-MB-435 human cancer cells. High single-cell isolation efficiency and long-term culture capability are achieved by using different sizes of microwells on the top and bottom of the microfluidic channel. The small microwell array is designed for precisely isolating single-cells, and the large microwell array is used for single-cell clonal culture in the microfluidic chip. This microfluidic platform constitutes an attractive approach for single-cell culture applications, due to its flexibility of adjustable cell culture spaces for different culture strategies, without decreasing isolation efficiency.

Here, we present a protocol for isolating and culturing single cells with a microfluidic platform, which utilizes a new microwell design concept to allow for high-efficiency single cell isolation and long-term clonal culture.

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet ...

Microfluidic Platform with Multiplexed Electronic Detection for Spatial Tracking of Particles

Microfluidic processing of biological samples typically involves differential manipulations of suspended particles under various force fields in order to spatially fractionate the sample based on a biological property of interest. For the resultant spatial distribution to be used as the assay readout, microfluidic devices are often subjected to microscopic analysis requiring complex instrumentation with higher cost and reduced portability. To address this limitation, we have developed an integrated electronic sensing technology for multiplexed detection of particles at different locations on a microfluidic chip. Our technology, called Microfluidic CODES, combines Resistive Pulse Sensing with Code Division Multiple Access to compress 2D spatial information into a 1D electrical signal. In this paper, we present a practical demonstration of the Microfluidic CODES technology to detect and size cultured cancer cells distributed over multiple microfluidic channels. As validated by the high-speed microscopy, our technology can accurately analyze dense cell populations all electronically without the need for an external instrument. As such, the Microfluidic CODES can potentially enable low-cost integrated lab-on-a-chip devices that are well suited for the point-of-care testing of biological samples.

We demonstrate a microfluidic platform with an integrated surface electrode network that combines resistive pulse sensing (RPS) with code division multiple access (CDMA), to multiplex detection and sizing of particles in multiple microfluidic channels.

Microfluidic processing of biological samples typically involves differential manipulations of suspended particles under various force fields in order to ...

A Microfluidic Platform for Longitudinal Imaging in Caenorhabditis elegans

In the last decade, microfluidic techniques have been applied to study small animals, including the nematode Caenorhabditis elegans, and have proved useful as a convenient live imaging platform providing capabilities for precise control of experimental conditions in real time. In this article, we demonstrate live imaging of individual worms employing WormSpa, a previously-published custom microfluidic device. In the device, multiple worms are individually confined to separate chambers, allowing multiplexed longitudinal surveillance of various biological processes. To illustrate the capability, we performed proof-of-principle experiments in which worms were infected in the device with pathogenic bacteria, and the dynamics of expression of immune response genes and egg laying were monitored continuously in individual animals. The simple design and operation of this device make it suitable for users with no previous experience with microfluidic-based experiments. We propose that this approach will be useful for many researchers interested in longitudinal observations of biological processes under well-defined conditions.

A Microfluidic Platform for Longitudinal Imaging in Caenorhabditis elegans

In this article, we demonstrate live imaging of individual worms employing a custom microfluidic device. In the device, multiple worms are individually confined to separate chambers, allowing multiplexed longitudinal surveillance of various biological processes.

In the last decade, microfluidic techniques have been applied to study small animals, including the nematode Caenorhabditis elegans, and have proved ...

Recombinant Collagen I Peptide Microcarriers for Cell Expansion and Their Potential Use As Cell Delivery System in a Bioreactor Model

Tissue engineering is a promising field, focused on developing solutions for the increasing demand on tissues and organs regarding transplantation purposes. The process to generate such tissues is complex, and includes an appropriate combination of specific cell types, scaffolds, and physical or biochemical stimuli to guide cell growth and differentiation. Microcarriers represent an appealing tool to expand cells in a three-dimensional (3D) microenvironment, since they provide higher surface-to volume ratios and mimic more closely the in vivo situation compared to traditional two-dimensional methods. The vascular system, supplying oxygen and nutrients to the cells and ensuring waste removal, constitutes an important building block when generating engineered tissues. In fact, most constructs fail after being implanted due to lacking vascular support. In this study, we present a protocol for endothelial cell expansion on recombinant collagen-based microcarriers under dynamic conditions in spinner flask and bioreactors, and we explain how to determine in this setting cell viability and functionality. In addition, we propose a method for cell delivery for vascularization purposes without additional detachment steps necessary. Furthermore, we provide a strategy to evaluate the cell vascularization potential in a perfusion bioreactor on a decellularized&#160;biological matrix. We believe that the use of the presented methods could lead to the development of new cell-based therapies for a large range of tissue engineering applications in the clinical practice.

We propose a cell expansion protocol on macroporous microcarriers and their use as delivery system in a perfusion bioreactor to seed a decellularized tissue matrix. We also include different techniques to determine cell proliferation and viability of cells cultured on microcarriers. Furthermore, we demonstrate functionality of cells after bioreactor cultures.

Tissue engineering is a promising field, focused on developing solutions for the increasing demand on tissues and organs regarding transplantation ...

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of cellular heterogeneity in biological systems. However, single-cell sequencing of large populations has been hampered by limitations in processing genomes for sequencing. In this paper, we describe a method for single-cell genome sequencing (SiC-seq) which uses droplet microfluidics to isolate, amplify, and barcode the genomes of single cells. Cell encapsulation in microgels allows the compartmentalized purification and tagmentation of DNA, while a microfluidic merger efficiently pairs each genome with a unique single-cell oligonucleotide barcode, allowing &gt;50,000 single cells to be sequenced per run. The sequencing data is demultiplexed by barcode, generating groups of reads originating from single cells. As a high-throughput and low-bias method of single-cell sequencing, SiC-seq will enable a broader range of genomic studies targeted at diverse cell populations.

Single-cell sequencing reveals genotypic heterogeneity in biological systems, but current technologies lack the throughput necessary for the deep profiling of community composition and function. Here, we describe a microfluidic workflow for sequencing &gt;50,000 single-cell genomes from diverse cell populations.

Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of ...

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

The limitations of cell-based synthetic biology are becoming increasingly apparent as researchers aim to develop larger and more complex synthetic genetic regulatory circuits. The analysis of synthetic genetic regulatory networks in vivo is time consuming and suffers from a lack of environmental control, with exogenous synthetic components interacting with host processes resulting in undesired behavior. To overcome these issues, cell-free characterization of novel circuitry is becoming more prevalent. In vitro transcription and translation (IVTT) mixtures allow the regulation of the experimental environment and can be optimized for each unique system. The protocols presented here detail the fabrication of a multilayer microfluidic device that can be utilized to sustain IVTT reactions for prolonged durations. In contrast to batch reactions, where resources are depleted over time and (by-) products accumulate, the use of microfluidic devices allows the replenishment of resources as well as the removal of reaction products. In this manner, the cellular environment is emulated by maintaining an out-of-equilibrium environment in which the dynamic behavior of gene circuits can be investigated over extended periods of time. To fully exploit the multilayer microfluidic device, hardware and software have been integrated to automate the IVTT reactions. By combining IVTT reactions with the microfluidic platform presented here, it becomes possible to comprehensively analyze complex network behaviors, furthering our understanding of the mechanisms that regulate cellular processes.

The fabrication process of a PDMS-based, multilayer, microfluidic device that allows in vitro transcription and translation (IVTT) reactions to be performed over prolonged periods is described. Furthermore, a comprehensive overview of the hardware and software required to automate and maintain these reactions for prolonged durations is provided.

The limitations of cell-based synthetic biology are becoming increasingly apparent as researchers aim to develop larger and more complex synthetic genetic ...

A Microfluidic Platform for Stimulating Chondrocytes with Dynamic Compression

Mechanical stimuli are known to modulate biological functions of cells and tissues. Recent studies have suggested that compressive stress alters growth plate cartilage architecture and results in growth modulation of long bones of children. To determine the role of compressive stress in bone growth, we created a microfluidic device actuated by pneumatic pressure, to dynamically (or statically) compress growth plate chondrocytes embedded in alginate hydrogel cylinders. In this article, we describe detailed methods for fabricating and characterizing this device. The advantages of our protocol are: 1) Five different magnitudes of compressive stress can be generated on five technical replicates in a single platform, 2) It is easy to visualize cell morphology via a conventional light microscope, 3) Cells can be rapidly isolated from the device after compression to facilitate downstream assays, and 4) The platform can be applied to study mechanobiology of any cell type that can grow in hydrogels.

This article provides detailed methods for fabricating and characterizing a pneumatically actuating microfluidic device for chondrocyte compression.

Mechanical stimuli are known to modulate biological functions of cells and tissues. Recent studies have suggested that compressive stress alters growth ...