Direct neuronal reprogramming generates neurons that maintain the age of the starting somatic cell. Here, we describe a single vector-based method to generate induced neurons from dermal fibroblasts obtained from adult human donors.
Induced neurons (iNs), the product of somatic cells directly converted to neurons, are a way to obtain patient-derived neurons from tissue that is easily accessible. Through this route, mature neurons can be obtained in a matter of a few weeks. Here, we describe a straightforward and rapid one-step protocol to obtain iNs from dermal fibroblasts obtained through biopsy samples from adult human donors. We explain each step of the process, including the maintenance of the dermal fibroblasts, the freezing procedure to build a stock of the cell line, seeding of the cells for reprogramming, as well as the culture conditions during the conversion process. In addition, we describe the preparation of glass coverslips for electrophysiological recordings, long-term coating conditions, and fluorescence activated cell sorting (FACS). We also illustrate examples of the results to be expected. The protocol described here is easy to perform and can be applied to human fibroblasts derived from human skin biopsies from patients with various different diagnoses and ages. This protocol generates a sufficient amount of iNs which can be used for a wide array of biomedical applications, including disease modeling, drug screening, and target validation.
Development of efficacious treatments for neurological disorders have been hampered by the limited access to living human brain cells to perform mechanistic studies and functional assays. About a decade ago, this situation radically changed with the development of induced pluripotent stem cell (iPSCs) technology1,2. This, combined with a better understanding of the neural differentiation mechanisms occurring during normal human development, has allowed for the generation of defined and diverse neuronal subtypes from patient and disease specific material. With such material, it is now possible to study intracellular mechanisms underlying neurological diseases and the potential of different compounds to alleviate those pathological features3.
While iPSCs have been revolutionary to the field of neuroscience, one major drawback of these cells is that their ageing signature is erased during the reprogramming process in such a way that the rejuvenated neuron does not retain the vulnerability associated with aging4,5,6. This particular feature of the neurons that are produced may end up being critical for recapitulating many aspects of the intracellular pathogenic cascade, particularly in the case of diseases for which old age is an important risk factor.
Direct neural reprogramming is a technology where a somatic cell is directly converted into an iN without going through a pluripotent intermediate stage. This allows for rapid generation of human neurons in vitro that can be both patient and disease specific. One remarkable characteristic of direct reprogramming is that the starting age of the donor cell is maintained, and with that, its vulnerability to ageing processes such as increased production of oxidative stress4,7. As a result, iNs from patients with neurological diseases associated with ageing, such as Alzheimer's and Parkinson's disease, are well suited for a broad range of biomedical applications including disease modeling, drug screening assays, and toxicology studies.
The main caveat that has prevented iNs from patients with neurodegenerative disorders being widely used is that they are not easy to reprogram, and this becomes even more difficult with expansion of the fibroblasts. As a result, generation of iN cells in quantities required for these types of applications has not been achieved until only recently8. We have now developed a simple method to reprogram fibroblasts from donors of any age in a very efficient manner. This method combines the forced expression of the neuronal transcription factors Ascl1 and Brn2 with a knockdown of the repressor protein RE1-silencing transcription factor (REST) using a single vector. Here, we describe the different steps leading to the generation of iNs converted from skin fibroblasts biopsied from elderly donors.
Adult dermal fibroblasts were obtained from the Parkinson's Disease Research and Huntington's disease clinics at the John van Geest Centre for Brain Repair (Cambridge, UK) and used under local ethical approval (REC 09/H0311/88). For details on the skin biopsy sampling procedure, see reference8.
1. Preparation of Skin Fibroblasts for Reprogramming
2. Freezing of Skin Fibroblasts
3. Plating for Reprogramming (Day −1)
NOTE: It is recommended to use a gelatin coating for short term experiments (up to 30 days); alternatively, for long term experiments it is recommended to start on a poly-L-ornithine, fibronectin and laminin (PFL) coating.
4. Viral Transduction (Day 0)
NOTE: Working with lentiviral particles requires category 2 equipment and the use of an agent to neutralize the virus. Wearing double pairs of gloves is also strongly recommended.
5. Maintenance of the Converting Cells
NOTE: Once conversion begins cells are susceptible to lifting; take care to tip the plate up and use a 1,000 µL pipette when removing media to avoid cells detaching.
Stock Concentration | Working Concentration | |
Fibroblast medium | ||
Basal medium | N/A | N/A |
Penicillin/Streptomycin | 10,000 U/mL | 100 mg/mL |
FBS | N/A | 10% |
Freezing medium | ||
Fibroblast medium | N/A | 45% |
FBS | N/A | 45% |
DMSO | N/A | 10% |
Early neuronal conversion medium (ENM) | ||
Neural differentiation medium | N/A | N/A |
Penicillin/Streptomycin | 10,000 U/mL | 100 mg/mL |
CHIR99021 | 10 mM | 2 µM |
SB-431542 | 20 mM | 10 µM |
Noggin | 100 µg/mL | 0.5 µg/mL |
LDN-1931189 | 10 mM | 0.5 µM |
VPA | 1 M | 1 mM |
LM-22A4 | 20 mM | 2 µM |
GDNF | 20 µg/mL | 2 ng/mL |
NT3 | 10 µg/mL | 10 ng/µL |
db-cAMP | 50 mM | 0.5 mM |
Late neuronal conversion medium (LNM) | ||
Neural differentiation medium | N/A | N/A |
Penicillin/Streptomycin | 10,000 U/mL | 100 mg/mL |
LM-22A4 | 20 mM | 2 µM |
GDNF | 20 µg/mL | 2 ng/mL |
NT3 | 10 µg/mL | 10 ng/µL |
db-cAMP | 50 mM | 0.5 mM |
FACS Buffer | ||
HBSS 1x [-calcium, -magnesium, – phenol red] | N/A | N/A |
BSA | N/A | 1% |
DNAase | N/A | 0.05% |
Table 1: Composition of the different media used. Full description of the composition for all media needed in this protocol including fibroblast medium, freezing medium, early neuronal conversion medium, late neuronal conversion medium, and FACS buffer.
6. Glass Coverslips for Electrophysiological Recordings
NOTE: It is recommended to wear a lab coat, goggles, double gloves, and complete all of the work in a fume hood. This protocol is adapted from 10.
7. PFL Coating for Long Term Culture
8. FACS
NOTE: To re-plate the cells after FACS sorting prepare a PFL-coated plate 48 h in advance. Cells can be sorted using a neural cell adhesion molecule (NCAM) antibody from day 20 onwards following transduction.
A clear change in cell morphology should be visible from day 5 onwards (Figure 1B). Some cell death is to be expected after viral transduction, although not overtly. From each well in a 24-well plate a total cell yield of 20,000-40,000 cells should be expected by day 25, of which about half should have become neurons. It is important to note that the yield and purity can vary across cell line, as well as with disease state and virus batches.
Cells will express most standard neuronal markers including MAP2 and TAU (Figure 1C) at day 25 in addition to exhibiting a mature neuronal morphology. It is possible to get a pure iN population by doing FACS based on the marker NCAM (see references8,11). Cells can thereafter be either re-plated onto PFL triple coating (see reference10) or directly frozen for biomolecular analyses.
If the cells are not sorted, immunofluorescence labeling with either MAP2 or TAU should be performed to identify the successfully converted cells and co-labeled with the protein of interest.
Figure 1: Evolution of the iN conversion over time. (A) Timeline of the experiment and map of the construct packaged in a lentivirus used to reprogram the adult human dermal fibroblasts. Each black arrow represents a medium change. (B) Representative phase contrast images depicting the changes in morphology of cells during the conversion process between day 0 to day 22 (as indicated on the upper right corner of each panel). Images were taken on a phase contrast microscope using the 10X objective. (C) Immunofluorescence image of a TAU and MAP2 double staining at day 35 post-transduction. Cells were fixed in 4% paraformaldehyde and permeabilized with 0.1% Triton in DPBS for 10 min. Cells were blocked for 30 min in a 5% serum solution in DPBS. The antibodies were diluted in blocking solution and applied overnight at 4 °C. Fluorophore-conjugated secondary antibodies were diluted in blocking solution and applied for 2 h. Cells were counterstained with DAPI for 15 min followed by 3 washes with DPBS. Images were taken on an inverted fluorescence microscope using the 20X objective. Scale bars = 100 µm (B, C). Abbreviations: ENM: early neuronal medium; LNM: late neuronal medium. Please click here to view a larger version of this figure.
This one-step/one vector reprogramming method provides an efficient way to obtain iNs from human adult fibroblasts. Human adult fibroblasts are normally much more difficult to covert than fetal fibroblasts, with limited studies previously reporting efficiencies of approximately 5-10%12,13. However, with this new protocol it is possible to achieve a neuronal yield (measured as MAP2+ cells) of approximately 50%8. Additionally, our protocol can be used on dermal fibroblasts that have been passaged multiple times without losing efficiency of conversion. Thus far we have used cells passaged up to 14 times without detecting any decrease in conversion efficiency. Also, there is no difference in reprogramming efficiency in our hands with fibroblasts from donors of age between 52 and 87. For more details on the age and disease of other cell lines tested with this construct see reference8. Other studies have also reported no difference in conversion efficiency using a lentiviral-based and small molecule-enhanced protocol with donors between 0 and 89 years4. Furthermore, consistent applicability with miRNA-based neuronal reprogramming has been reported in fibroblasts of all ages, with donors between 0 and 86 years7. Through this route, mature neurons can be obtained in approximately 12–15 weeks in vitro or approximately 8 weeks following transplantation in vivo8. This is advantageous because it gives access to both disease and patient specific human iNs from tissue that is easily accessible. Although this protocol is efficient, it will not produce a 100% neuronal yield, and as such a purification step using FACS for instance is required.
The most critical step within this protocol is viral transduction (protocol section 4). It is crucial that the virus titer is precise, in addition to having plated an accurate number of aHDFs for conversion. The recommended titer for use with this protocol is between 4 x 108 and 4 x 109. Using a titer of anything below 1 x 108 would not be recommended as adding large volumes of virus will be toxic to the cells. Moreover, as the fibroblasts begin to covert to iNs they will become more fragile and susceptible to lifting. It is essential to be gentle when changing the media as not to disturb the cells too much. This can be done by removing the fluid slowly with a 1,000 µL pipette. Finally, when plating for reprogramming (protocol section 3) it is important to ensure a healthy fibroblast population before beginning an experiment; this is indicated by a cell viability of above 90% with trypan blue staining. The aHDFs should always be passaged before reaching 95% confluency.
If there is noticeable cell death before viral transduction, do not begin conversion: double check that the cell viability is above 90% and that there were no problems with coating of the plate. It is expected to have a small amount of cell death following viral transduction, however, this should not be significant. In this case, confirm accurate seeding of 50,000 aHDFs/well and check the virus titer. If there is noticeable inconsistency between wells during conversion, first check that every well contains an equal amount of media and overt evaporation is not occurring at the edges (if necessary extra media can be added to the edge wells). Alternatively, check step 4.4, and ensure appropriate mixing for a homogenous suspension when transducing. It is crucial to add the lentivirus to the medium first, before adding this into the wells. Directly adding lentivirus into the wells will increase well to well variability and is also likely to be toxic to the cells. Lastly, always check that the medium is warmed to 37 °C before adding to cells.
This protocol includes optional sections for coating conditions for long term culture of iNs and FACS sorting to increase neuronal purity. For experiments wishing to investigate functional characterization of iNs, a protocol for preparation of glass coverslips for electrophysiology has also been included. The conversion protocol here is set up for use with a 24-well plate; if desired this can be modified to a 6-, 12-, 48-, 96-well plate or flasks. In this case, please adjust all volumes to the surface area of the plate or flask utilized.
This protocol uses the forced expression of Ascl1 and Brn2 in combination with a REST knockdown all packaged in one single vector8 to generate iNs of a pan-neuronal phenotype. The generation of any glial subtypes with this method, however, has not been assessed. This method would thus need to be modified for use with other reprogramming factors to obtain subtype specific neurons. Direct reprogramming has previously shown the possibility to generate motor neurons, sensory neurons, photoreceptors, striatal medium spiny neurons, and dopaminergic neurons10,14. This will be beneficial when investigating neurological diseases in which specific neuronal subtype are preferentially affected, for example Parkinson's disease and dopaminergic neurons.
Until very recently, direct neural reprogramming technology did not allow for the production of iNs in a standardized and efficient manner — to a level that is required for toxicology and drug screening assays on a large scale. This new method is very efficient and can be used on fibroblasts that have been passaged many times, such that it now removes these restrictions and opens up for a vast array of studies, not only in a human neural system, but also in a system that can be patient specific. The simplicity of this approach renders the iN technology accessible for any groups wanting to perform similar studies in-house and can be easily used not only for large scale biomedical applications, such as drug screening and toxicology assays, but also to support data derived from animal models and human post mortem tissue samples.
The authors have nothing to disclose.
We thank Marie Persson Vejgården for technical assistance. The research leading to these results has received funding from the New York Stem Cell Foundation, the European Research Council under the European Union's Seventh Framework Programme: FP/2007-2013 Neuro Stem Cell Repair (no. 602278) and ERC Grant Agreement no. 30971, the Swedish Research Council (grant agreement 521-2012-5624, 2016-00873 and 70862601/ Bagadilico), Swedish Parkinson Foundation (Parkinsonfonden), and the Strategic Research Area at Lund University Multipark (multidisciplinary research in Parkinson's disease). Janelle Drouin-Ouellet is supported by a Canadian Institutes of Health Research (CIHR) fellowship (#358492), and Roger Barker is supported by an NIHR Biomedical Research Centre grant to the University of Cambridge/Addenbrooke's Hospital. Malin Parmar is a New York Stem Cell Foundation Robertson Investigator. Shelby Shrigley is funded by the European Union Horizon 2020 Programme (H2020-MSCA-ITN-2015) under the Marie Skłodowska-Curie Innovative Training Network and Grant Agreement No. 676408.
Cell Lines | |||
Adult human dermal fibroblasts | [C2 passage #7] Donor was a 67 year old male. Cells obtained from the Parkinson’s Disease Research and Huntington’s disease clinics at the John van Geest Centre for Brain Repair (Cambridge, UK). | ||
Reagents for Fibroblast Culture, Transduction and Conversion | |||
Dulbecco's phosphate-buffered saline (DPBS) [-CaCl2, -MgCl2] | Gibco | 14190094 | |
Trypsin-EDTA [0.5%] | Gibco | 15400-054 | Dilute to 0.05% in DPBS. |
Virkon (agent used to neutralize virus) | Viroderm | 7511 | Dilute to 1% solution with warm water. |
Milli-Q Water | Millipore | ||
Basal medium – Dulbecco’s Modified Eagle Medium (DMEM) + GlutaMax | Gibco | 61965059 | |
Penicillin/Streptomycin [10,000 U/mL] | Gibco | 15140-122 | |
Fetal Bovine Serum (FBS) | Gibco | 10270-106 | |
CryoMACS® dimethyl sulfoxide (DMSO) 10 | Miltenyi | 170-076-303 | |
Neural differentiation medium – NDiff 227 | Takara-Clontech | Y40002 | |
LM-22A4 | Tocris | 4607 | Dilute 10 mg in 1450 µL DMSO. Stock concentration: 20 mM. |
Glial cell line-derived neurotrophic factor (GDNF) [recombinant human] | R&D systems | 212-GD-010 | Dilute 10 ug in 500 µL 0,1% BSA in DPBS. Stock concentration: 20 µg/mL. |
NT3 [recombinant human] | R&D systems | 267-N3-025 | Dilute 25 µg in 2,5 mL 0,1% BSA in DPBS. Stock concentration: 10 µg/mL. |
db-cAMP | Sigma Aldrich | D0627 | Dilute 1 g in 40,7 mL Milli-Q water. Filter and make 500 µL aliquots or stock tubes of 10 mL. Stock concentration: 50 mM. |
CHIR99021 | Axon | 1386 | Dilute 2 µg in 429,8 µL DMSO. Stock concentration: 10 mM. |
SB-431542 | Axon | 1661 | Dilute 5 mg in 595 µL DMSO. Stock concentration: 20 mM. |
Noggin [recombinant human] | Miltenyi | 130-103-456 | Dilute 100 µg in 100 µL of Milli-Q water + 900 µL 0,1% BSA in DPBS. Stock concentration: 100 µg/mL. |
LDN-193189 | Axon | 1509 | Dilute 2 mg in 360 µL DMSO. Stock concentration: 10 mM. |
Valproic acid sodium salt (VPA) | Merck Millipore | 676380 | Dilute 5 g in Milli-Q water to acheive a stock concentration of 1 M. CAUTION: Avoid ingestion, contact with skin, and breathing dust formation. |
Reagents for Coatings | |||
Gelatin | Sigma Aldrich | G2500 | Dilute to 0.1% in Milli-Q water. |
Poly-L-ornithine | Sigma Aldrich | P3655 | Dissolve in Milli-Q water. Use at 15µg/mL. |
Fibronectin | ThermoFisher Scientific | 33010-018 | 2 mL of Milli-Q water + 70 µL 0,25 M NaOH. Use at 5 µg/mL. |
Laminin | ThermoFisher Scientific | 23017-015 | Store at -80°C. Thaw on ice, keep cool and aliquot 30 µL. Use at 5 µg/mL. |
Reagents for Fluorescence Activated Cell Sorting | |||
Cell dissociation agent – Accutase (Stem Pro) | ThermoFisher Scientific | A1110501 | |
Hanks' Balanced Salt Solution (HBSS) 1X [-calcium, -magnesium, – phenol red] | ThermoFisher Scientific | 14175-046 | |
Bovine Serum Albumin (BSA) | Sigma Aldrich | A2153 | Use at 1% concentration for Anti-Human CD56 (NCAM). |
DNAase | Sigma Aldrich | DN-25 | Use at 0.05% concentration. |
Anti-Human CD56 (NCAM) Antibody [Mouse] | BD Pharmingen | 555518 | Use at 1 : 50. |
Propidium iodide | Sigma Aldrich | P4170 | Dilute to 1mg/mL in PBS and keep sterile. Use at 1:1000 to achieve a concentration of 10µg/mL. |
Reagents for Glass Coverslips | |||
Autoclaved deionized water | |||
Alconox detergent | Sigma Aldrich | Z273228 | |
Ethanol 95% | |||
Nitric Acid | Sigma Aldrich | 438073-M | CAUTION: Concentrated nitric acid is highly corrosive, and its vapours are potentially harmful. |
Concentrated hydrochloric acid (HCI) | CAUTION: Concentrated hydrochloric acid is highly corrosive, and its vapours are potentially harmful. | ||
Reagents for Immunocytochemistry | |||
Paraformaldehyde (PFA) | Merck Millipore | 1040051000 | Use at a concentration of 4%. CAUTION: PFA is a potent fixative. Avoid ingestion and contact with skin |
Triton X-100 | Fisher Scientific | 10254640 | Use at a concentration of 0.1%. |
Serum [Donkey] | Merck Millipore | S30-100ML | |
Anti-MAP2 Antibody [Chicken] | Abcam | ab5392 | Use at a concentration of 1 : 5,000. |
Tau HT7 Monoclonal Antibody [Mouse] | ThermoFisher Scientific | MN1000 | Use at a concentration of 1 : 500. |
Cy3 Anti-Chicken Antibody [Donkey] | Jackson ImmunoResearch | 703-165-155 | Use at a concentration of 1 : 400. |
Alexa Fluor488 Anti-Mouse Antibody [Donkey] | Jackson ImmunoResearch | 715-545-150 | Use at a concentration of 1 : 400. |
4′,6-Diamidine-2′-phenylindole dihydrochloride (DAPI) | Sigma Aldrich | D9542 | Reconstitute the powder in Milli-Q water to 1 mg/mL. Aliquot and store at -20°C, light sensitive. Use at a concentration of 1 : 500. |
Equipment | |||
T75 flask [Nunclon Delta Surface] | ThermoFisher Scientific | 156499 | |
24-well plate [Nunc] | ThermoFisher Scientific | 142485 | |
1.5 mL polypropylene tube | Sigma Aldrich | Z336769 | |
15 mL falcon tube | Sarstedt | 62.554.502 | |
50 mL falcon tube | Sarstedt | 62.547.254 | |
CryoPure tube 1.6 mL | Sarstedt | 72.380 | |
Pippette controller | For pipetting volumes 1-25 mL. | ||
Sterile serological pipettes: 5, 10 and 25 mL | Sarstedt | 86.1253.001, 86.1254.001, 86.1685.001 | |
Adjustable volume pipettors: 5, 20, 200, and 1,000 µL | |||
Sterile pipette tips | For pipetting volumes of 0.5 – 1,000 µL. | ||
Glass coverslips | NeuVitro | GG-12-1.5-oz | #1.5 thickness, 12mm diameter, 0.5oz, CE certified, fit 24 well plates. |
Glass dish | Approximately 150mm diameter. | ||
Glass beaker | Make sure to have an appropriate size beaker for the sonicator bath available. Water from the sonicator bath should not overflow into the glass beaker. | ||
Parafilm M | VWR | ||
ThawSTAR Automated Cell Thawing System | BioCision | BCS-601 | |
Countess II Automated Cell Counter | ThermoFisher Scientific | AMQAX1000 | |
Cell counting chambers [50 slides] and trypan blue [0.4%] | ThermoFisher Scientific | C10228 | For use with Countess II Automated Cell Counter. |
CoolCell Cell LX Controlled-rate Freezing Container | Biocision | BCS-405 | |
Laminar flow hood | |||
Humidified 5% CO2 37 °C incubator | |||
Centrifuge | Suitable for 1,5, 15 and 50 mL tubes. | ||
Orbital shaker | |||
Sonicator – Bransonic Model B200 cleaner | Sigma Aldrich | Z305359 | Frequency = 50-60Hz, Amplitude = 30 Watts |
FACS Aria III cell sorter | BD Pharmingen | ||
Phase contrast microscope | Olympus | CKX31 | |
Inverted fluorescence microscope | Leica | DMI6000 B |