Apr 21, 2023

Public workspaceDifferentiation of human Dopamine Neurons (DaNs) from induced pluripotent stem cells (iPSCs) V.1

DOI
dx.doi.org/10.17504/protocols.io.q26g7y1jqgwz/v1
  • 1Oxford Parkinson’s Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK;
  • 2Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, South Park Road, Oxford OX1 3QU, United Kingdom;
  • 3Kavli Institute for Neuroscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Park Road, Oxford OX1 3QU, United Kingdom;
  • 4Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA;
  • 5Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA;
  • 6Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford, OX1 3QU, UK;
  • 7University of Oxford
Cláudia C. Mendes
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DOI: dx.doi.org/10.17504/protocols.io.q26g7y1jqgwz/v1
Protocol Citation: Ana Belen Malpartida, Maria Claudia Caiazza, Richard Wade-Martins, Brent Ryan, Kaitlyn ML Cramb 2023. Differentiation of human Dopamine Neurons (DaNs) from induced pluripotent stem cells (iPSCs). protocols.io https://dx.doi.org/10.17504/protocols.io.q26g7y1jqgwz/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: February 21, 2023
Last Modified: April 21, 2023
Protocol Integer ID: 77411
Keywords: iPSCs, differentiation, human dopamine neurons
Funders Acknowledgement:
Aligning Science Across Parkinson’s (ASAP)
Grant ID: ASAP-020370
Abstract
This protocol employs a floor plate-based differentiation method to produce human midbrain dopaminergic neurons from induced pluripotent stem cells. Based on Kriks, S. et al., 2011 with adaptations from Fedele, S. et al., 2017, this protocol incorporates expansion of floor plate progenitors which can be frozen and thawed with limited cell death. By the end of the protocol, tyrosine hydroxylase positive neurons are produced with high efficiency that fire action potentials and produce and release dopamine upon stimulus.
Materials
Reagents:

Preparing KO DMEM KSR base media:
  1. Remove 90mL of KO DMEM (total 500 mL) and save for spinning tubes.
  2. Add to KO DMEM:
  • 75 mL of KSR (15%)
  • 10μM Β-mercaptoethanol
  • 1:100 L-glutamine
  • 1x NEAA

Preparing NNB base media:
  1. Add to 500 mL Neurobasal (without Vitamin A) media:
  • 1:200 N2 (2.5 mL in 500 mL)
  • 1:100 B27 (5 mL in 500 mL)
  • 1:100 L-glutamine (5 mL in 500 mL)

Preparing NB base media (use within 3 weeks):
  1. Add to 500 mL Neurobasal (without vitamin A) media:
  • 1:50 B27 (10 mL in 500 mL)
  • 1:100 L-glutamine (5 mL in 500 mL)

Preparing Final Maturation Media: 1. Add to NB base media:
  • 1:5000 BDNF
  • 1:5000 GDNF
  • 1:10 000 TGFβ3
  • 1:10 000 DAPT
  • 1:1000 Ascorbic Acid
  • 1:200 dCAMP
  • Optional: 1:100 anti-anti

Preparing MitoC media: 1. Add to NB base media:
  • 1:1000 Mitomycin C
Before start
All growth-factor containing medias should be prepared fresh the day of the feedings. All medias throughout the entirety of the protocol should be filtered using a 0.22μm filter prior to their use to prevent risk of contamination. Rock inhibitor should be included at any steps containing a split or replating of cells, and its use should typically be followed by a full feed containing media with no rock inhibitor.
These cells are particularly temperature sensitive, so media should always be at least at room temperature before use but preferentially briefly warmed to 37⁰C
Cells should be checked daily at least until final replating day. The most success will come from gauging best practices from experience based on how cells look under a brightfield microscope at each stage.
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 KO DMEM 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
2.2.1. Add 49 μL of Phosphate Buffered Saline (PBS) to one Eppendorf per cell line for cell dilution.
2.2.2. Add 1 μL of Solution 18 to a separate Eppendorf for counting.
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 (automatically using cell counter)
2.4.1. Dilute cells by adding 1 μL of cell suspension to 49 μL of previously prepared PBS in an Eppendorf.
2.4.2. Mix thoroughly.
2.4.3. Take 19 μL of diluted cell mixture and add to Eppendorf containing 1 μL of Solution 18.
2.4.4. Mix thoroughly and count cells.
2.4.5. Calculate and plate cells based on the following optimal density for Day -1 plating: 1.425 million cells / well of 6-well plate (150 000/ cm2).
Note
Cells may also be replated 2 days before starting the protocol, for which the following optimal density should be used for calculations:

Day -2 plating: 1.19 million cells/ well of a 6 well plate (125 000/cm2)

2.4.6. Transfer cells to a 6-well plate after aspirating the Matrigel, and top up with mTesR media to have 2 mL media total.
Differentiation of iPSCs into Dopamine Neurons (DaNs)
Differentiation of iPSCs into Dopamine Neurons (DaNs)
Before starting, check the confluency. The iPSCs should be at least >80% confluent to start, otherwise feed the cells and wait another day. If in doubt, more confluent is better.

Thaw growth factors at room temperature and make every media fresh daily and filter immediately before use.

Days 0 through 20 of the protocol contain no antibiotics and therefore, it is extra pertinent to use the most aseptic technique.

If at any point Day 1 through Day 10 the cells peel, they can be replated by collecting the media and, if any cells remain adhered, using Accutase as described in step 4.3.
Day prior to preparing differentiation medias
3.1.1. Thaw supplements (KSR, B27 and N2) (ideally in fridge overnight).
3.1.2. Prepare KO DMEM KSR base media and NNB base media (see Materials).
Note
Full media changes are 4 mL / well of a 6 well plate.
Half media changes are 2mL / well of a 6 well plate.

Day 0: Full media change
1. Add to KO DMEM KSR base media:
1:10 000 LDN
1:1000 SB
Day 1 : Full media change
1. Add to KO DMEM KSR base media:
1:10 000 LDN
1:1000 SB
1:1000 SHH
1:5000 FGF8a
1:5000 Puro
Day 2: Half media change
1. Add to KO DMEM KSR base media:
1:10 000 LDN
1:1000 SB
1:1000 SHH
1:5000 FGF8a
1:5000 Puro
Day 3: Full media change
1. Add to KO DMEM KSR base media:
1:10 000 LDN
1:1000 SB
1:1000 SHH
1:5000 FGF8a
1:5000 Puro
Day 4: Half media change
1. Add to KO DMEM KSR base media:
1:10 000 LDN
1:1000 SB
1:1000 SHH
1:5000 FGF8a
1:5000 Puro
1:3333 CHIR
Day 5 : Full media change
75% KO DMEM KSR base media
25% NNB base media
1:10 000 LDN
1:1000 SHH
1:5000 FGF8a
1:5000 Puro
1:3333 CHIR
Day 6: Half media change
75% KO DMEM KSR base media
25% NNB base media
1:10 000 LDN
1:1000 SHH
1:5000 FGF8a
1:5000 Puro
1:3333 CHIR
Day 7: Full media change
50% KO DMEM KSR base media
50% NNB base media
1:10 000 LDN
1:3333 CHIR
Day 8: Half media change
50% KO DMEM KSR base media
50% NNB base media
1:10 000 LDN
1:3333 CHIR
Day 9: Full media change
25% KO DMEM KSR base media
75% NNB base media
1:10 000 LDN
1:3333 CHIR
Day 10: Full media change (D10 media)
25% KO DMEM KSR base media
75% NNB base media
1:10 000 LDN
1:3333 CHIR
Expansion of NPCs
Expansion of NPCs
This section is optional. If not desired, continue on to Section: Patterning NPCs into dopaminergic neurons Day 11 to 22+.

Expansion allows for the freezing and thawing of progenitors midway through the protocol, as well as evidence suggests the final neurons may be more mature (Fedele. S. et al., 2017). It consists of maintaining progenitors cells on Day 10 media (D10; step 3.12) for 1 to 21 days with splits throughout. Therefore, time points are labelled (D10+exp), for instance, cells in Day 10 media for 4 days are labelled D10+4exp .
Day 10: Preparation on day prior to first expansion split
Geltrex 6-well plates as described in step 1.
Day 10+1: Preparation on the day of the first expansion split.
4.2.1. Pre-warm spinning falcons containing 9mL of KO DMEM base media.
4.2.2. Prepare D10 media (step 3.12) + ROCKi (1:1000).
4.2.3. Allow an aliquot of desired volume (1mL per well of a 6-well plate) to reach room temperature.
Note
If cells have recently peeled and been replated, or are not very confluent, it is fine to maintain cells in D10 media with daily media changes and wait until cells reach confluency before splitting.

Day 10+1: Splitting Day 10 NPCs
Some lines may survive 1:2, but it is advisable to split cells 2:3, as there will be quite some cell death and the cells need to be fairly confluent to maintain viability and cell identity. If split too harshly, they may differentiate into other cell types.

4.3.1. Aspirate media and wash each well with 1mL of PBS.
4.3.2. Immediately aspirate PBS and add 1mL of Accutase.
4.3.3. Incubate at 37⁰C for 5 minutes.
4.3.4. Gently collect cells using a 1000 μL pipette and place in pre-warmed spinning falcon.
4.3.5. Spin cells for 5 minutes at 350g.
4.3.6. While cells are spinning, aspirate Geltrex and replace with 3mL of pre-warmed D10 media (step 3.12)+ ROCKi (1:1000).
4.3.7. Aspirate media from pelleted cells, re-suspend pellet in 1mL of D10 media (step 3.12) + ROCKi and add dropwise to well of 6-well plate.
4.3.8. Gently swirl to distribute cells evenly around dish.
Day 10+2: Maintaining NPCs in Day 10 Expansion Media 4.2.1. Day following expansion split, full feed cells with D10 media (step 3.12).
4.2.2. Subsequently feed neurons daily with D10 media (also named as D10 expansion media), alternating between half and full feeds.
4.2.3. Passage cells when confluent, generally success is found with a 1:2 split on Day 10+8, Day 10+15 and Day 10+20.
Note
Cells may be frozen down during the expansion stage of the protocol, but it is recommended to do so at the later stages for improved success rates.

Freezing Day 10+expNPCs
4.5.1. Passage cells as described in step 4.3.
4.5.2. Resuspend pellet in freezing media containing 90% D10 media (step 3.12) and 10% DMSO.
4.5.3. Store in liquid nitrogen.
Note
Wells of cells can be frozen and thawed at a ratio of 1 well: 1 well, particularly at the later stages of the expansion. More caution should be taken if freezing at the earlier stages of the expansion step as they can be more vulnerable (freeze/thawing at a ratio of 1.3:1 for example).

To plan accordingly for experiments, 1 well of 6 well plate will give roughly 5-10 million cells/ well, but can vary greatly for each line and differentiation.

The last split of expansion is typically seen as the last opportunity to freeze cells as freezing neurons during the patterning stage or later is not recommended due to low viability.

Patterning NPCs into Dopaminergic Neurons (DaNs)
Patterning NPCs into Dopaminergic Neurons (DaNs)
Day 11: Full media change
1. Add to NB base media:
1:3333 CHIR
1:5000 BDNF
1:5000 GDNF
1:10 000 TGFβ3
1:10 000 DAPT
1:1000 Ascorbic Acid
1:200 dCAMP
Day 12: Half media change
1. Add to NB base media:
1:3333 CHIR
1:5000 BDNF
1:5000 GDNF
1:10 000 TGFβ3
1:10 000 DAPT
1:1000 Ascorbic Acid
1:200 dCAMP
Note
While plenty of cell death is present throughout this protocol, it might be especially apparent the first few days of the patterning stage.

Day 13 - Day 19: Daily media changes
Alternate half and full feeds with Final Maturation Media (see Materials).
Final replating of Dopamine Neurons (DaNs)
Final replating of Dopamine Neurons (DaNs)
Replate the dopamine neurons into final desired dish on Day 20±1 of the protocol (this has been tested to be equally successful on Day 19 and 21). Replating neurons at later stages of their maturation is not recommended and will decrease viability.
One to two days prior to final replating: Dish coating
Choice of coating will affect cell distribution and likelihood of peeling. Geltrex and PLO/Biolaminin are both suitable for replating the neurons. PLO/Biolaminin is thought to reduce peeling and provide a more distributed layer of neurons advantageous for imaging.

If using Geltrex:
1 day prior to Day 20 replating:
  • Coat dishes with Geltrex prepared in neurobasal media

If using PLO/Biolaminin:
2 days prior to Day 20 replating:
  • Coat plates with undiluted PLO

1 day prior to Day 20 replating:
  • Wash 3x with PBS without letting plates dry.
  • Dilute Biolaminin 1:10 in cold, sterile PBS.
  • Aspirate and add Biolaminin at same volume as PLO.
Replating of Day 20 Dopamine Neurons
Note
Before starting:
  • Prepare and pre-warm spinning falcons containing 9mL of neurobasal media.
  • Prepare, filter and pre-warm Final Maturation Media (see Materials) with ROCKi (1:1000) and optional anti-anti (1:100).
  • Warm Accutase to room temperature.

On Day 20 and onwards, cells may be kept in anti-anti if desired without significant effects to their morphology or activity, but notably, extensive testing has not been taken to see its effects on maturing dopamine neurons

If replating many lines, media may be aliquoted and kept in the fridge throughout the day and pre-warmed immediately before use.

8.2.1. Wash cells 1x with 1mL PBS and replace with 1 mL Accutase, incubate at 37⁰C for 5 minutes.
8.2.2. Gently collect cells into a pre-warmed spinning falcon.
8.2.3. Spin at 350g for 5 minutes.
8.2.4. Resuspend pellet in 1 mL of pre-warmed Final Maturation Media (see Materials) and count cells using Solution 18.
8.2.5. Replate at final desired concentrations (Table 1).
ABCD
Plate Type Surface Area (cm2) Useful for Ideal density
12 well3.8Protein & RNA collections1 x106/ well
24 well 1.9Protein & RNA collections5 x 105/ well
24 well + 10 mm coverslip0.78Electrophysiology1 x 105/ well
96 well half area0.15Imaging 3-5 x 104/ well
Table 1: Recommended densities for various types of experiments.

Remove non-neuronal proliferating cell types (Mitomycin C treatment)
Remove non-neuronal proliferating cell types (Mitomycin C treatment)
It is normal to produce a small number of non-neuronal cells throughout this protocol, but ideally these should be at a minimum. We try to reduce the amount remaining in our culture following the final replating of post-mitotic dopamine neurons (previous section) by treating the cells with Mitomycin C on Day 22.
Day 22: Prepare medias
9.1.1. Prepare MitoC media (see Materials), Neurobasal (wash media) and Final Maturation Media (see Materials).
9.1.2. Pre-warm and filter all three medias.
Day 22: Mitomycin C treatment
9.2.1. Aspirate Final Maturation Media from DaNs.
9.2.2. Add pre-warmed and filtered MitoC media from step 9.1.1.
9.2.3. Incubate at 37⁰C for 1 hour.
9.2.4. Aspirate Mitomycin C and wash 1x with pre-warmed Neurobasal media.
9.2.5. Aspirate Neurobasal media and replace with Final Maturation Media.
Maintaining and maturing Dopaminergic Neurons (DaNs) in culture
Maintaining and maturing Dopaminergic Neurons (DaNs) in culture
Dopaminergic neurons can be kept in culture for multiple months before obvious demise. The length of survival will depend on feeding schedule, density and various other factors.
Day 24 - Day 25: Full media change
First feed immediately following Mitomycin C treatment should be a full feed with Final Maturation Media (see Materials).
Day 25+: Biweekly Half media changes
10.2.1. From Day 25 onwards, half feed neurons with Final Maturation Media (see Materials) two to three times a week.
10.2.2. Monitor cells regularly using a brightfield microscope for cell health and contamination.
Note
The optimal time point at which to perform experiments varies depending on type of experiment. Measuring synaptic function is recommended post-Day 70, while organelle biology can be assessed as early as Day 35.