Jul 19, 2023

Public workspaceDifferentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs) V.1

 Forked from Differentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs) and their coculture with rat astrocytes
DOI
dx.doi.org/10.17504/protocols.io.bp2l69qr5lqe/v1
  • Quyen Do1,2,3,
  • Bryan Ng1,2,
  • Richard Wade-Martins1,2,3
  • 1Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford OX1 3QU, United Kingdom;
  • 2Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford OX1 3QU, United Kingdom;
  • 3Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
Cláudia C. Mendes
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DOI: dx.doi.org/10.17504/protocols.io.bp2l69qr5lqe/v1
Protocol Citation: Quyen Do, Bryan Ng, Richard Wade-Martins 2023. Differentiation of human cortical neurons (CNs) from induced pluripotent stem cells (iPSCs). protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l69qr5lqe/v1Version created by Cláudia C. Mendes
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: July 19, 2023
Last Modified: July 19, 2023
Protocol Integer ID: 85235
Keywords: Cortical neurons, iPSC
Funders Acknowledgement:
Aligning Science Across Parkinson’s (ASAP)
Grant ID: Grant ID: ASAP-020370
Abstract
This protocol described the production of human cortical neurons from induced pluripotent stem cells. The differentiation protocol of cortical neurons is adapted and modified from Shi, Y. et al., 2012 (pharmacologically directed) and Zhang, Y. et al., 2013 (transcription factor directed), as previously described by Hedegaard et.al., 2020. These neurons exhibited molecular and functional hallmarks of cortical neurons.
Materials
Reagents:

Preparing Neural Induction Medium (NIM):
1. Add to NMM base medium:
  • 100 nM LDN193189 (1:10000)
  • 10 mM SB431542 (1:1000)

Preparing Neural maintenance base medium (NMM):
  • 1:1 mixture of N2 and B27 containing media.

Preparing N2 base medium:
  • DMEM/F12 GlutaMAX
  • 1X N2
  • 5 mg/ml insulin
  • 100 mM non-essential amino acids
  • 100 mM B-mercaptoethanol
  • 1 mM sodium pyruvate
  • P/S (50 U or mg per ml)

Preparing B27 base medium (use within 3 weeks):
  • Neurobasal
  • 1X B27 plus with Vitamin A
  • 2 mM L-glutamine

Preparing Ngn2 base medium (use within 1 week):
  • Neurobasal
  • 1X B27 with vitamin A
  • 1X Glutamax
  • P/S (50 U or mg per ml) (1:200)
  • 1 mg/ml Doxycycline (1:1000)
  • 10 ng/ml BDNF
  • 10 ng/ml NT-3 (1:1000)
  • 200 ng/ml Laminin (1:5000)
  • 200 mM Ascorbic acid (1:1000)

Preparing Neural Freezing Medium (made fresh):
  • NMM
  • 10% DMSO
  • 20 ng/ml FGF2
Safety warnings
Part of this procotol involves working with lentiviruses during which stage extra precaution should be exercised. All materials in contact with lentiviruses must be decontaminated with chemgene in allocated space after use prior to further autoclaving.
Before start
Sterile working techniques are an absolute must to ensure cell viability and vitality. This includes but not limited to filtering of all media to be used with 0.22μm filter, sterilisation of gloves, stripettes, falcons or any materials to be in contact with cells or cell media.

All growth factors should be added fresh on the day of intended use, or within 48 hours. Prior to use media must be warmed preferentially to 37ºC, or room temperature at the very least, as these cells are temperature-sensitive.
Differentiation of iPSCs into Neuronal Progenitor Cells (NPCs)
Differentiation of iPSCs into Neuronal Progenitor Cells (NPCs)
Day -2: Preparing plates for replating
Two days before intending on starting the differentiation (Day -2), add 1 mL/well in a 6-well plate of Geltrex one day prior to replating the iPSCs to begin the differentiation.
Note
Geltrex should be prepared in DMEM/F12 basal medium based on manufacturer’s dilution instructions and should be kept cold at all times.

Cells are typically replated the day before beginning the differentiation.

Day -1: Replating iPSCs for differentiation
Replating iPSCs for differentiation is identical to described in Protocol: Expansion and maintenance of human induced pluripotent stem cells (iPSCs), however, includes a cell counting step.
Prepare for splitting
Follow steps described in steps 6 and 7 of Protocol: Expansion and maintenance of human induced pluripotent stem cells (iPSCs).
Prepare for cell counting
Prepare 99 μl of Phosphate Buffered Saline (PBS) into one Eppendorf per cell line for cell dilution.
Replate iPSCs
As described in step 7 of Protocol: Expansion and maintenance of human induced pluripotent stem cells (iPSCs), pausing when cell pellet is suspended in 1 mL of mTesR media (i.e. mTesR plus their accompanying Supplement and 1% Penicilline/Streptomycin) + ROCKi (1:1000) to count cells.
Count cells (manually using a haemocytometer)
2.4.1. Dilute cells by adding 1 μL of cell suspension to 99 μL of previously prepared PBS in an Eppendorf.
2.4.2. Mix thoroughly.
2.4.3. Take 10 μL of diluted cell mixture and add to a haemocytometer.
2.4.4. Using a microscope, focus on the grid lines of the hemocytometer with a 10X objective.
2.4.5. Manually count cells from all 4 all 4 sets of 16 corners of the haemocytometer using a tally counter.
2.4.6. Average cell count from each of the sets of 16 corner squares and multiply by 10,000 (104).
2.4.7. Multiply by 100 to correct for the dilution in step 2.4.1.
2.4.8. Calculate and plate cells based on the following optimal density for Day -1 plating: 1.5 millions cells per 6 well .

Note
Cell lines of different proliferative rates could be seeded at slightly different cell number to allow for similar starting date of differentiation.

2.4.9. Replate about 1.5 to 2 million cells per 6-well suspended in mTesR media+ ROCKi (1:1000) and swirl plate gently in a figure 8 motion.
2.4.10. Add more mTesR media + ROCKi (1:1000) to make up the total volume of 3 mL per well of a 6-well plate.
Differentiation of NPCs into Cortical Neurons (CNs)
Differentiation of NPCs into Cortical Neurons (CNs)
Day 0: Differentiation starts when cells reach 90-100% confluency
Prepare Neural Induction Medium (NIM; see Materials).
Wash cells once with PBS, and add 2 mL of NIM media to each well.
Day 1 – Day 12: Daily feed with NIM
Replace medium every day and monitor morphological changes.


Note
Dense areas might appear brown after some time in NIM. Cells might peel to a certain extent from the edge of the wells.

Day 11: Prepare plates for Day 12 passaging
Coat new plates with 15 ug/mL fibronectin and incubate at 37°C overnight.
Day 12: Splitting cells


Prepare Neural Maintenance Medium (NMM)(see Materials).
Add 10 mL of NMM to a 15ml falcon (spinning tube) for each line to be passaged and pre-warmed to 37°C.


Note
Bigger falcon with larger NMM could be used if working with greater number of cells.

Add 10% medium volume of pre-warmed Dispase (10 mg/mL, sterilized, in PBS) directly into the well that still has medium in it.
Incubate at 37°C for 10 min at least.

Note
Some wells take longer (up to 30 min) for Dispase to lift the cell sheet. Check regularly.

In the well, break the cell sheet a couple of times with P1000 and keep the big clumps of cells as intact as possible.
Transfer the cells into 10 mL of NIM in 15-mL falcon tubes. Let the cells settle by gravity.
Remove the supernatant carefully without removing the cells at the bottom.
Add another 10 mL of NIM in 15-mL falcon tubes and repeat steps 6.6 and 6.7.
Split the cells 1:2 into 15 mg/mL fibronectin-coated plates with NIM and ROCKi (1:1000).
Allow cells to attach overnight.

Note
Colonies only attach on fibronectin-coating at this stage (can also pre-coat with 50 mg/mL poly-L-ornithine on Day 10 prior to fibronectin to enhance adhesion).

Day 13 : Full media change
1. Add to NMM base medium:
20 ng/ml FGF2

Note
If clumps of cells do not attached on Day 13, change medium, but keep the clumps in the plate as much as possible. They should attach after another 2 days.

Day 15 : Full media change
1. Add to NMM base media:
20 ng/ml FGF2

Note
Neural rosette structures should be obvious between Day 12 – 17.

Day 16 : Prepare plates for splitting
Wells are coated with fibronectin or 100 mg/mL poly-L-ornithine overnight followed by 10 mg/mL laminin for at least 2 hours (up to 24 hours).
Day 17 : Splitting of NPCs

Note
Culture should be relatively dense at Day 17 and so longer incubation with Disease might be necessary.

Cells could be split in 1:2 or 1:3.

Multiple wells of the same lines can be pooled into one tube and wash using more of NMM.

Repeat the splitting and washing steps as described in step 6.
Seed the cells on Poly-L-ornithine/Laminin/fibronectin-coated plates previously prepared in step 9 and feed with media as described in step 8.
Day 18 : Full media change
NMM base media

Day 20 – Day 26 : Full media change
Change NMM media every 2 days.
Day 26 : Freezing
Cells can be frozen at 5-10 million cells/vial.
Add 1 mL of Accutase per well to be frozen.
Spin the cells down at 300 g for 5 mins.
Resuspend the cells slightly into clumps in Cryostore 10 or self-made freezing medium (see Materials).
Lentivirus packaging
Lentivirus packaging
This section describes the third-generation lentiviral packaging of plasmids to be used for transduction of NPCs.

Plasmids to be packaged into lentiviruses:
1. FUdeltaGW-rtTA (rtTA; Addgene #19780)
2. pTet-O-Ngn2- puro (Ngn2; Addgene #52047)
3. pLV-TetO-hNGN2-eGFP-Puro (Ngn2-GFP; Addgene #79823)
Prepare HEK293T cells
14.1.1. Prepare DMEM/F12 medium supplemented with 10% FBS, 2 mM L-glutamine, and 50 U/mL Penicillin-Streptomycin.
14.1.2. Passage cells by single-cell passaging with TrypLE and seed at approximately 150,000 cells/cm2, and at least 24 hours before plasmid transfection.
Note
Seeding density can vary depending on the desirable day for transfection at which point cells should be at 80-90% confluence.
Day of transfection
14.2.1 Pre-warm Optimem to room temperature.

14.2.2 Prepare Lipofectamine mix (Tube 1):
14.2.2.1. Add Lipo 3K to Optimem.
14.2.2.2. Flick to mix.
14.2.2.3. Incubate for 5-20 min.

14.2.3. Prepare DNA mix (Tube 2):
14.2.3.1. Prepare master mix of packaging vectors + P3000 in Optimem.
14.2.3.2. Add transgene-expressing lentiviral vector (e.g. pLEX).
14.2.3.3. Mix by briefly vortexing.

14.2.4. Add DNA mix (Tube 2) to Lipofectamine mix (Tube 1), mix by flicking tube 8 times
14.2.5. Wait ~ 20 minutes
14.2.6. Add DNA/Lipofectamine mixture to cells dropwise, and swirl plate immediately to evenly mix with fresh cell media without penicillin/streptomycin.
ABCDEFGHIJK
Tube 1 Tube 2
Dish Cell # (x 106) Media Optimem Lipo 3K Optimem P3000 psPAX2 pMD2G pAdVantage Lenti vector
1 x 6 well2.5 3 mL150 uL1.9 uL150 uL5 uL1.6 ug0.6 ug0.2 ug2.4 ug
1 x 10 cm1518 mL900 uL11 uL900 uL30 uL10 ug3.4 ug1.4 ug14.6 ug
1 x 15 cm4536 mL2.4 mL30 uL2.4 mL 80 uL26.3 ug9 ug3.6 ug39 ug
List and quantity of reagents and plasmids to be used for lentiviral packaging in step 14.2.
Day of transfection +1
Replace media with 3 mL of DMEM/FCS medium + 6uL ViralBoost (Alstem).

Note
From this stage onwards, all materials that are in contact with the cells or cell media contain viruses/viral particles and hence, would be treated with chemgene prior to autoclaving.

Day of transfection +2 : Collecting cell media
Collect all cell media containing live viruses.

Note
Be careful to not disturb and collect unnecessary cell materials.

If no ViralBoost is used, smaller volumes of media can be collected (e.g.10ml for 10cm dish) daily and pool after 3 days (keep collections at 4°C until pooled).

Concentrating viruses
This step was adopted from manufacturer’s guideline for the TAKARA Lenti-X concentrator kit.

14.5.1. Lentivirus-containing supernatants are centrifuged briefly at 500g for 10 mins or filtered through a 0.45 μm filter.

Note
If filtering, use only cellulose acetate or polyethersulfone (PES) (low protein binding) filters.

Do not use nitrocellulose filters. Nitrocellulose binds surface proteins on the lentiviral envelope and destroys the virus.

14.5.2. Transfer clarified supernatant to a sterile container and combine 1 volume of Lenti-X Concentrator with 3 volumes of clarified supernatant.
14.5.3. Mix by gentle inversion. Larger volumes may be accommodated through the use of larger (i.e., 250 mL or 500 mL) centrifuge tubes.
14.5.4. Incubate mixture at 4°C overnight.
14.5.5. Centrifuge sample at 1,500g for 45 minutes at 4°C.
14.5.6. Carefully remove supernatant without disturbing the pellet. Residual supernatant can be removed with either a pipette tip or by brief centrifugation at 1,500g.
14.5.7. Gently resuspend the pellet in 1/100th of the original volume using complete DMEM.

Note
The pellet can be somewhat sticky at first, but will go into suspension quickly.

14.5.8. Immediately titrate sample into single-use aliquots and stored at -70°C.
Differentiation of NPCs into cortical neurons
Differentiation of NPCs into cortical neurons
The second part of the differentiation protocol beyond Day 26 was adapted and modified from Zhang, Y. et al., 2013. The protocol employs doxycycline-inducible overexpression system of Ngn2 to direct excitatory cortical neuronal identity.
Prepare plates for replating
Add 100 μg/mL of Poly-L-ornithinne onto plastic wells and incubate at 37⁰C overnight.
Prepare media for thawing and replating
15.2.1. Pre-warm spinning falcons containing 9 ml of Neurobasal.
15.2.2. Prepare Day 25 media (i.e. NMM) + ROCKi (1:1000) + 20 ng/mL FGF2.
Thawing and replating of Day 26 NPCs
15.3.1. Thaw cryovial containing Day 26 NPCs in water bath until only a small component remains frozen.
15.3.2. Carefully transfer contents of cryovial to pre-warmed spinning tubes.
15.3.3. Centrifuge at 350g for 5 min.
15.3.4. While spinning, aspirate Matrigel and replace with Day 25 media (i.e. NMM) + ROCKi (1:1000) + 20 ng/ml FGF2.
15.3.5. Aspirate media from cell pellet in spinning falcon and replace with Day 25 media (NMM) + ROCKi (1:1000) + 20 ng/ml FGF2, slowly and gently resuspending the pellet.
15.3.6. Transfer an appropriate amount of cell suspension into previously prepared wells and swirl plate gently in a figure 8 motion.
Transduction of Day 26 NPCs
15.4.1. Add Ngn2 and rTA lentiviruses directly into the well with cell media immediately after depositing the cell suspension.
15.4.2. Replace medium with fresh NMM 8 hours later.

Note
Transducing cell while in suspension often results in the best transduction efficiency.

The exact amount of lentiviruses to be added needs to be titrated.

Too high viral load might negatively affect cell health; too low viral load results in low yield of cortical neurons.


Day 28 – Doxycycline induction
The NMM media is replaced with freshly-made Ngn2 medium (see Materials) to induce doxycycline-dependent expression of Ngn2 in successfully transduced neurons.
Day 30 – Antibiotic selection
Full media change with freshly-made Ngn2 medium (see Materials) supplemented with 1 μg/mL puromycin to select for successfully transduced neurons.
Co-culture of iPS-cortical neurons with rat astrocytes
Co-culture of iPS-cortical neurons with rat astrocytes
Resulting iPS-cortical neurons are co-cultured with commercially available rat astrocytes as previously described in Hedegaard et.al., 2020. This coculture approach enhances both cortical intrinsic capacity to fire action potential and network-dependent synaptic activities.
Rat Astrocyte Expansion
16.1.1. Thaw and replate primary rat astrocytes onto uncoated T75 flasks according to manufacture's protocol, which is similar to steps 15.2 and 15.3. The only difference is the medium - use Astrocyte Maintenance Medium (AMM) (see Materials) for rat astrocytes.
16.1.2. Astrocytes are allowed to expand for 2 to 3 weeks till confluence.
16.1.3. Full media change twice a week.
Splitting of Rat Astrocytes
16.2.1. Astrocytes are split into 6 x uncoated T75 flasks.
16.2.2 Adherent astrocytes are washed with PBS once.
16.2.3. Add 10mL of Accutase per T75 flask and incubate the dish at 37°C for approximately 10-20 mins.
16.2.4. Check regularly for cell lifting.
16.2.5. Carefully transfer all of the dish content into a pre-warmed falcon.
16.2.6. Centrifuge at 350g for 5 mins.
16.2.7. While spinning, add fresh AMM to the new T75 flasks.
16.2.8. Aspirate media from cell pellet in spinning falcon and replace with AMM, slowly and gently resuspending the pellet.
16.2.9. Transfer an equal amount of cell suspension into previously prepared T75 flasks and swirl plate gently in a figure 8 motion.
16.2.10. Expand again for another 2 to 3 weeks till confluence.
Freezing of rat astrocytes
16.3.1. Lift confluent astrocytes using Accutase and centrifuge at 350g for 5 mins.
16.3.2. Remove the supernatant and resuspend cell pellet in AMM.
16.3.3. Freeze the cells at 2-5 million cells/vial in 90% v/v AMM + 10% v/v DMSO as P3 astrocytes.
Co-culturing of cortical neurons with rat astrocytes
16.4.1. P3 rat astrocytes are thawed and plated onto intended plates at 20,000 cells/cm2 following step 16.1.

Note
20,000 cells/cm2 astrocytes are plated 3 days prior to plating of cortical neurons (P3 rat astrocyte).

P3 rat astrocyte can continue to expand and hence, astrocyte plating density can be adjusted slightly depending on how early/late astrocyte plating is relative to that of cortical neurons.

16.4.2. Day 30 Cortical Neurons (step 15.6.) are lifted with Accutase and replated on top of the adherent astrocyte monolayer at the density of 100,000 cells/cm2.
16.4.3. Upon centrifugation, cell pellet is resuspended in Ngn2 medium.
16.4.4.2 On Day 32, half media change is performed with fresh Ngn2 medium + 100 nM AraC.
16.4.3. From now on, half media change is done twice per week.