Microfluidic Fabrication of Core-Shell Microcapsules carrying Human Pluripotent Stem Cell Spheroids

Summary

This article describes encapsulation of human pluripotent stem cells (hPSCs) using a co-axial flow focusing device. We demonstrate that this microfluidic encapsulation technology enables efficient formation of hPSC spheroids.

Abstract

Three-dimensional (3D) or spheroid cultures of human pluripotent stem cells (hPSCs) offer the benefits of improved differentiation outcomes and scalability. In this paper, we describe a strategy for the robust and reproducible formation of hPSC spheroids where a co-axial flow focusing device is utilized to entrap hPSCs inside core-shell microcapsules. The core solution contained single cell suspension of hPSCs and was made viscous by the incorporation of high molecular weight poly(ethylene glycol) (PEG) and density gradient media. The shell stream comprised of PEG-4 arm-maleimide or PEG-4-Mal and flowed alongside the core stream toward two consecutive oil junctions. Droplet formation occurred at the first oil junction with shell solution wrapping itself around the core. Chemical crosslinking of the shell occurred at the second oil junction by introducing a di-thiol crosslinker (1,4-dithiothreitol or DTT) to these droplets. The crosslinker reacts with maleimide functional groups via click chemistry, resulting in the formation of a hydrogel shell around the microcapsules. Our encapsulation technology produced 400 µm diameter capsules at a rate of 10 capsules per second. The resultant capsules had a hydrogel shell and an aqueous core that allowed single cells to rapidly assemble into aggregates and form spheroids. The process of encapsulation did not adversely affect the viability of hPSCs, with >95% viability observed 3 days post-encapsulation. For comparison, hPSCs encapsulated in solid gel microparticles (without an aqueous core) did not form spheroids and had <50% viability 3 days after encapsulation. Spheroid formation of hPSCs inside core-shell microcapsules occurred within 48 h after encapsulation, with the spheroid diameter being a function of cell inoculation density. Overall, the microfluidic encapsulation technology described in this protocol was well-suited for hPSCs encapsulation and spheroid formation.

Introduction

There is considerable interest in 3D cultures of human pluripotent stem cells (hPSCs) due to the improved pluripotency and differentiation potential afforded by this culture format^1,2,3. hPSCs are typically formed into spheroids or other 3D culture formats by means of bioreactors, microwells, hydrogels, and polymeric scaffolds^4,5,6. Encapsulation offers another means for organizing single hPSCs into spheroids. Once encapsulated hPSC spheroids may be handled with ease and transferred into microtiter plates for differentiation, disease modeling, or drug testing experiments. Encasing hPSCs in a hydrogel layer also protects cells against shear damage and allows to culture spheroids in a bioreactor at high rates of stirring⁷.

Our methodology for stem cell encapsulation evolved over time. First, we focused on solid hydrogel microparticles and demonstrated successful encapsulation and cultivation of mouse embryonic stem cells (mESCs)⁸. However, it was noted that human embryonic stem cells (hESCs) had low viability when encapsulated in such hydrogel microparticles, presumably due to the greater need for these cells to re-establish cell-cell contacts after the encapsulation. We reasoned that heterogeneous microcapsule, possessing an aqueous core, may be better suited for encapsulation of cells that rely on rapid re-establishment of cell-cell contacts. The concept of co-axial flow focusing microfluidic device for making aqueous core/hydrogel shell microcapsules was adapted from He et al.⁹, but instead of alginate employed in the original approach, a PEG-based hydrogel was incorporated into the shell. We first demonstrated successful encapsulation and spheroid formation of primary hepatocyte in core-shell microcapsules¹⁰ and most recently described encapsulation of hES and iPS cells⁷. As outlined in Figure 1A, capsules are fabricated in a flow focusing device where the shell and core flow streams transition from side-to-side to co-axial flow before ejection into the oil phase. The core flow contains cells and additives that increase the viscosity of the solution (non-reactive PEG MW 35kD and iodixanol - commercial name OptiPrep) while the shell stream contains reactive molecules (PEG-4-Mal). Continuous co-axial flow stream is discretized into droplets that retain core-shell architecture. The core-shell structure is made permanent by exposure to di-thiol crosslinker (DTT), which reacts with PEG-4-Mal via click chemistry and results in formation of a thin (~10 µm) hydrogel skin or shell. After the emulsion is broken and capsules are transferred into an aqueous phase, molecules of PEG diffuse from the core and are replaced by water molecules. This results in aqueous core and hydrogel shell microcapsules.

Provided below are step-by-step instructions on how to make microfluidic devices, how to prepare cells, and how to carry out encapsulation of hPSCs.

Protocol

1. Device fabrication

1. Make the designs for the microencapsulation device and dissociation device using CAD software^10,11.
2. Spin-coat the three layers of SU-8 photoresist sequentially on a silicon wafer (Figure 2A) to achieve structures with the desired heights: 60, 100, and 150 µm.
   NOTE: The process for the top and bottom molds is identical.
   1. Spin coat a clean 10 cm silicon wafer with SU-8 2025 negative photoresist at 1,100 rpm to create the first 60 µm layer. After a soft bake at 65 °C for 3 min and 95 °C for 10 min on a hot plate, expose the mold using a maskless aligner by uploading the design file of the core channel pattern to the µPG 101 PC. Then, proceed with the post-exposure bake at 65 °C for 3 min and at 95 °C for 10 min.
   2. Spin coat the second SU-8 2025 layer (40 µm) at 1,500 rpm and expose by uploading the appropriate CAD file for the shell channel pattern.
      NOTE: Soft and post-exposure bakes were similar to the previous step.
   3. Spin coat the third SU-8 2025 layer at 1,400 rpm to achieve 50 µm height and repeat the above process but expose the structures for the oil phase.
   4. Develop the mold with all three layers in a single step by submersion in SU-8 developer until all the unexposed photoresist is removed.
   5. Hard bake the mold on a hot plate at 160 °C for 10 min to improve adhesion and seal minor cracks that could appear after the development.
   6. Expose the mold to chlorotrimethylsilane to avoid elastomer bonding in the next step and place it in 15 cm Petri dishes until use.
3. Prepare the dissociation device mold in the same manner, as described in Figure 1D and Figure 2B. Spin coat one layer of SU-8 photoresist on a silicon wafer, as described earlier in step 1.2.3, to achieve structures with the desired height: 50 µm. Conduct the soft and post-exposure bake, development, and hard bake similarly to the previous step.
   NOTE: An array of triangular-shaped posts covered the whole chamber, with spacing between posts decreasing as chamber width decreased toward the outlet. Triangle posts were 200 µm per side with a pitch ranging from 400 µm (at the inlet) to 30 µm (at the outlet).
4. Prepare the molds by soft lithography using polydimethylsiloxane (PDMS).
   1. Mix PDMS elastomer base and elastomer curing agent in a 10:1 w/w ratio in a planetary centrifuge. Pour the mixture onto both microencapsulation master molds and dissociation master mold to create a 3-4 mm layer.
      NOTE: A mixture of 50 g of elastomer base with 5 g of curing agent is sufficient to cover a master mold with 3 mm thickness.
   2. Place the Petri dishes containing the molds in a vacuum desiccator for 15 min to de-gas the uncured PDMS.
   3. Move the Petri dishes to an oven and bake at 80 °C for a minimum of 60 min.
   4. Remove the master molds from the oven and allow them to cool down. Using a precision knife, carefully cut the PDMS following the shape of the wafer and peel out the PDMS pieces from the master mold.
   5. Cut out the PDMS slabs by trimming the edges of each device with a scalpel, then punch out inlet/outlet fluidic ports in the dissociation device and only in the top microfluidic device using stainless steel needles. Cover the devices with magic tape to avoid contamination.
      NOTE: The needle gauge is 14 G and 15 G for inlet and outlet ports, respectively.
   6. For bonding, treat the patterned sides of the top and bottom PDMS pieces with O₂ plasma on a plasma etcher for 2 min.
   7. Align both PDMS parts under a stereoscope after adding a thin separating layer of distilled water directly in the microchannels (2 µL).
   8. Place the aligned PDMS device in the oven at 80 °C overnight to complete the bonding and restore the PDMS to its original hydrophobic state. Store the devices until further use.
      NOTE: This results in a coaxial flow-focusing device with three different heights of 120 µm for core, 200 µm for shell, and 300 µm for oil channels.
   9. In order to use the device right after the plasma bonding, carefully but firmly inject 30 µL of hydrophobic coating solution into the fluidic channels to achieve hydrophobic coating. Then, immediately purge air into the channels until no residues of the hydrophobic coating solution are observed in the device.
   10. Bond the dissociation device by first treating the patterned side of the device and a cleaned slide glass with O₂ plasma for 2 min, and then assemble them for further curing in the oven at 80 °C overnight.
       ​NOTE: Devices can be stored until further use.

2. Preparation of solutions

1. Stock solutions. First, prepare stock solutions (concentrated solutions) that will be diluted to lower concentrations for actual use.
   NOTE: Stock solutions are used to save preparation time, conserve materials, reduce storage space, and improve accuracy when preparing a working solution in lower concentrations.
   1. Prepare 30 mL of 2x core solution (16% PEG and 34% density gradient media): mix 4.8 g of 35 kDa PEG, 10.2 mL of density gradient media, and 19.8 mL of DMEM/F12 media. Filter this core solution using a 0.22 μm syringe filter.
   2. Prepare 50 mL of mineral oil with 3% surfactant: mix 48.5 mL of mineral oil and 1.5 mL of surfactant. Keep in a sterile condition after filtration through a 0.22 µm syringe filter.
   3. Prepare 50 mL of mineral oil with 0.5% surfactant: mix 49.75 mL of mineral oil and 0.25 mL of surfactant. Keep in a sterile condition.
   4. Prepare 1 M Dithiotheritol (DTT): dissolve 1.5425 g of DTT in 10 mL distilled water. Keep in a sterile condition.
   5. Prepare 1 M Triethanolamine (TEA): add 66.4 µL of TEA in 433.6 µL of distilled water. Keep in a sterile condition.
   6. Prepare 1% Pluronic F127 (PF127): dissolve 100 mg of PF127 in 10 mL of distilled water. Keep in a sterile condition.
2. Working solutions
   1. Prepare a crosslinker emulsion by mixing 4.5 mL of mineral oil with 3% surfactant and 300 µL of 1 M DTT (1:15 ratio). Vortex the solution for 2 min and sonicate for 45-60 min in an ultrasonic bath at 20 °C. Load this solution to a 5 mL syringe with a 27 G needle.
      NOTE: Emulsion is generated by sonicating oil/water mixture.
   2. Prepare shielding oil solution by loading the mineral oil with 0.5% surfactant to a 5 mL syringe with a 27 G needle.
   3. Prepare shell (8% w/v PEG-4-Mal and 15 mM TEA) solution by adding 32 mg of PEG-4-Mal in 400 µL of 1x DPBS to form 8% w/v solution, and vortex the solution for 2 min. Then, add 6 µL of 1 M TEA (final concentration 15 mM TEA). Finally, centrifuge at 13,000 x g for 5 min through a spin-filter and keep it in the dark on the rocker for 30 min. Then, load this solution to a 1 mL syringe with a 27 G needle.
      NOTE: Leave the PEG-4-Mal container to sit at room temperature for 10 min before opening the lid, and blow N₂ gas to replace the O₂ with N₂ before closing the lid. Vortex TEA before adding to the solution.
3. Prepare the cell suspension in core solution
   1. Treat the hPSCs with trypsin for 5 to 10 min at 37 °C. Then, collect them from plates. Quench the trypsin with the medium after cell detachment, and then transfer the cells to a 15 mL conical tube.
   2. Centrifuge the bulk cell suspension (400 x g, 5 min). Carefully aspirate the supernatant and then resuspend the cell pellet using a minimal volume of growth medium. Count the cells using an automated cell counter.
      NOTE: Typical cell aliquots contain 12-20 x 10⁶ cells and are enough to make 400 µL of the core solution.
   3. Take 12-20 x 10⁶ cells from the bulk cell suspension and centrifuge the cell/media suspension (400 x g, 5 min).
   4. Carefully aspirate media from the cell pellet. Then, add 200 µL media and 200 µL of 2x PEG solution (final concentration 30-50 x 10⁶ cell/mL) and mix gently.
      NOTE: Low cell concentrations (less than 20 x 10⁶ cells/mL) resulted in many empty capsules.
   5. Add 30 µL of 1% PF127 to the solution.
   6. Insert a micro stirrer bar (2 mm x 7 mm) into a 1 mL syringe, and then load the cell containing core solution to the syringe with a 27 G needle. Keep the solution cold with ice during the whole encapsulation process.

3. Experimental setup

1. Place bonded PDMS droplet device, four pieces of 20 cm long and one piece of 5 cm long inlet micro tubes (0.38 mm I.D. x 1.1 mm O.D.), one piece of 10 cm outlet tube (0.5 mm I.D. x 1.5 mm O.D.), and six pieces of 0.5 cm fitting tubes (1 mm I.D. x 1.8 mm O.D.) beneath a germicidal light source (typically built into biological safety cabinets) and sterilize for 30 min.
2. Use forceps to fit the tubing into the fluidic inlet ports and the dissociation ports.
3. Use the three pieces of 20 cm long inlet microtubes for the shell, oil, crosslinker emulsion inlets, and one piece for the inlet of the dissociation device. Then, insert the opposite end of the tubes to the needle of the syringe with the corresponding solution. Meanwhile, connect the core inlet of the microfluidic device and the outlet of the dissociation device with one 5 cm microtube (Figure 1C).
   NOTE: The inlet microtubes should be tightly secured within the fitting tubes, which were inserted in the last step.
4. Insert one outlet tube into the fluidic outlet port and place the opposite end into a collection reservoir.
5. Place the device on a microscope stage and attach the tubing to avoid moving. Align and focus the microscope on the device nozzle for flow inspection.
6. Place each syringe on different syringe pumps and secure properly (Figure 1B). Program each pump according to manufacturer's protocols to the following flow rates: core (3-5 µL/min), shell (3-5 µL/min), shielding oil (20-80 µL/min), and crosslinking oil (40-60 µL/min). Start the flow in all pumps.
7. Wait for each fluid to enter the device and fill up the channels while pushing out the remaining air.
   NOTE: If there is a large amount of air in the inlet tubing, temporarily increase each flow rate until the air is completely removed. Be mindful that excessive flow rate could lead to PDMS-to-PDMS bond failure.
8. When the capsule formation is stabilized (Figure 3), place the opposite end of the collection tube to a new conical tube with 5 mL of mTeSR media.
   NOTE: The media contains 10 μM ROCK inhibitor, 100 U/mL penicillin, and 100 μg/mL streptomycin.
9. After a sufficient number of capsules are collected, incubate at 37 °C with 5% CO₂ for 10 min. Capsules residing in the oil phase will be at the top of the tube (see Figure 4A). Gently tapping on the tube causes capsules to sediment to the bottom. After this, most of the oil and media may be aspirated.
10. Collect the capsules from the bottom of the conical tube, place them on a cell strainer (100 μm pore size), and wash with copious amounts of media. Then, collect microcapsules using 2 mL media in a 6-well culture plate by running the media through the filter as it is inverted on top of the well-plate (see Figure 4A).

4. hPSC culture and analysis in microcapsules

1. Basic culture
   1. Incubate the stem cell capsules in a 6-well plate culture dish at 37 °C with 5% CO₂.
   2. Change the media every other day by collecting the capsules on a cell strainer filter, washing them with excess media, and resuspending them to a new well in 6-well plates with 2 mL media as was done in step 3.10.
   3. Culture the capsules for at least 10 days.
2. Perform the live/dead assay to determine viability of encapsulated stem cells.
   1. Thaw live/dead assay solutions (ethidium homodimer-1 and calcein AM).
   2. Add 4 µL of the 2 μM ethidium homodimer-1 and 1 µL of the 4 μM calcein AM solutions to 2 mL of sterile DPBS. Vortex to ensure complete mixing.
   3. Collect approximately 100 microcapsules on a cell strainer and rinse them with sterile DPBS to allow diffusion of medium out from the capsules.
   4. Collect them again to a 12 well culture plate by using 1 mL of the solution prepared in step 4.2.2. Incubate at 37 °C for 20 min.
   5. Visualize the cells under a fluorescence microscope.
      NOTE: Cell viability is quantified by calculating the percentage of live cells, which are visualized as green, among the total number of cells.
3. Spheroid size characterization.
   1. When desired, place the well plate with microcapsules under the microscope and measure the diameter of spheroids shown on the related software with proper scale bars.
   2. Measure and analyze the spheroid size.

Results

By following the above-mentioned protocol, the reader will be able to fabricate microfluidic devices and produce cell-carrying microcapsules. Figure 3A shows examples of optimal and suboptimal microcapsules fabricated using microfluidic droplet generation. Different formulations of PEG-4-Mal resulted in capsules of varying morphologies - wrinkled capsules were associated with poor gelation, low mechanical integrity, and did not withstand cultivation in a stirred bioreactor. Smooth capsules o...

Discussion

The encapsulation process described here results in reproducible formation of hPSC spheroids. The microcapsule format makes it easy to dispense spheroids into wells of a microtiter plate for experiments aimed at improving/optimizing differentiation protocols or testing therapies. Encapsulated stem cell spheroids may also be used in suspensions cultures where hydrogel shell protects cells against shear-induced damage⁷.

There are several critical steps within the protocol...

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
0.22 µm Syringe Filters	Genesee Scientific	25-244
1 ml syringe luer-lock tip	BD	309628
1x DPBS	Corning	23220003
4-arm PEG maleimide, 10kDa	Laysan Inc.	164-68
5 ml syringe luer-lock tip	BD	309646
6-WELL NON-TREATED PLATE	USA Scientific	CC7672-7506
Aquapel Applicator Pack	Aquapel Glass Treatment	47100
CAD software	Autodesk	AutoCAD v2020
CELL STRAINER 100 µm pore size	cardinal	335583
Chlorotrimethylsilane	Aldrich	386529-100mL
Countess II FL Automated Cell Counter	Life technology	A27974
Digital hot plate	Dataplate
Digital vortex mixer	Fisher Scientific	215370
Distilled water	Gibco	15230-162
Dithiotheritol (DTT)	Sigma	D0632-10G
DMEM/F12 media	gibco	11320-033
Falcon 15 mL Conical Centrifuge Tubes	Fisher scientific	14-959-53A
Fisherbrand accuSpin Micro 17 Microcentrifuge	live	13-100-675
HERACELL VIOS 160i CO2 Incubator	Thermo Scientific	50144906
Inverted Fluorescence Motorized Microscope	Olympus	Olympus IX83
Laurell Spin Coaters	Laurell Technologies	WS-650MZ-23NPPB
Live/Dead mammalian staining kit	Fisher	L3224
Magic tape	Staples	483535
Micro Medical Tubing (0.015" I.D. x 0.043" O.D.)	Scientific Commodities, Inc	BB31695-PE/2
Micro stir bar	Daigger Scientific	EF3288E
MilliporeSigma Filter Forceps	Fisher scientific	XX6200006P
Mineral oil	Sigma	M8410-1L
mTeSR 1 Basal Medium	STEMCELL TECHNOLOGY	85850
Needles-Stainless Steel  14 Gauge	CML supply	901-14-025
Needles-Stainless Steel  15 Gauge	CML supply	901-15-050
OptiPrep	STEMCELL TECHNOLOGY	7820
Oven	Thermo Scientific	HERA THERM Oven
Penicillin:Streptomycin (10,000 U/mL Penicillin G, 10mg/mL Streptomycin)	Gemini	400-109
Petri Dish 150X20 Sterile Vent	Sarstedt, Inc.	82.1184.500
Plasma Cleaning System	Yield Engineering System, Inc.	YES-G500
Pluronic F-127	Sigma	P2443-250G
Poly(ethylene glycol) 35kDa	Sigma	94646-250G-F
PrecisionGlide Needle 27G	BD	305109
Rock inhibitor Y-27632 dihydrocloride	SELLECK CHEM	S1049-10mg
Silicon wafer 100mm	University Wafer	452
Slide glass (75mm ´ 25mm)	CardinalHealth	M6146
Span 80	Sigma	S6760-250ML
SpeedMixer	Thinky	ARE-310
Spin-X Centrifuge Tube Filter (0.22 µm)	Costar	8160
SU-8 2025	Kayaku Advanced Materials	Y111069 0500L1GL
SU-8 developer	Kayaku Advanced Materials	Y020100 4000L1PE
Surgical Design Royaltek Stainless Steel Surgical Scalpel Blades	fisher scientific	22-079-684
SYLGARD TM 184 Silicone Elastomer Kit (PDMS)	Dow Corning	2065622
Syringe pump	New Era Pump System, Inc	NE-4000
Triethanolamine	Sigma-aldrich	T58300-25G
TrypLE Express	Gibco	12604-013
Tygon Tubing (0.02" I.D. x 0.06" O.D.)	Cole-Parmer	06419-01
Tygon Tubing (0.04" I.D. x 0.07" O.D.)	Cole-Parmer	06419-04
Ultrasonic cleaner FS20D	Fisher Scientific	CPN-962-152R
Vacuum desiccator	Bel-Art	F42025-0000
Zeiss Stemi DV4 Stereo Microscope 8x-32x	ZEISS	435421-0000-000
μPG 101 laser writer	Heidelberg Instruments	HI 1128