The authors thank Tom Yohannan for the editorial advice and M. Segura-Feliu for the technical assistance. This work was funded by the CERCA Programme and by the Commission for Universities and Research of the Department of Innovation, Universities, and Enterprise of the Generalitat de Catalunya (SGR2017-648). This work was funded by the Spanish Ministry of Research, Innovation and University (MEICO) through BFU2015-67777-R and and RTI2018-099773-B-100, the Spanish Prion Network (Prionet Spain AGL2017-90665-REDT), and the Institute Carlos III, CIBERNED (PRY-2018-2).

All animal experiments were performed under the guidelines and protocols of the Ethical Committee for Animal Experimentation (CEEA) of the University of Barcelona, and the protocol for the use of rodents in this study was reviewed and approved by the CEEA of the University of Barcelona (CEEA approval #276/16 and 141/15).&#160;
1. Purification of Rat Tail Collagen
<ol>
	<li>Collect adult Sprague-Dawley rat tails (8-9 weeks old) after sacrificing the animal following ethical guidelines and rinse in 95% ethanol. Place 2-4 tails on ice (4 &#176;C) and keep them covered with ice during the process. &#160;</li>
	<li>To obtain tail tendons, fix the tail at the most caudal vertebrae of the tail using a hemostat and compress the tail with a second hemostat positioned around 5-7 mm from the first. Break the tail by twisting it sharply with both hemostats. To do this, fold/unfold the vertebrae several times until it breaks.</li>
	<li>Pull the vertebrae slowly with the hemostat to detach the tendons from their sheath as it comes out. At this moment, cut tendons with small scissors. Keep these tendon pieces in a sterile 100 mm Petri dish on ice.</li>
	<li>Repeat the clamping and sliding for the rest of the tail&#160;until the tendons are totally extracted.</li>
	<li>Repeat steps 1.2-1.4 for all the obtained tails.</li>
	<li>Observe the tendons under a microscope. Discard blood vessels by cutting with small scissors and holding with straight fine forceps to improve the tendon&#8217;s purity and rinse the tendons 3 times with ultrapure water.</li>
	<li>Collect 3-4 g of wet tendons. Dissolve the tendons in 150 mL of 3% glacial acetic acid at 4 &#176;C in a 200-250 mL glass conical flask for 24-36 h, under gentle stirring.</li>
	<li>Centrifuge at 20,000 x g for 1 h. In parallel, prepare the dialysis tubing membrane by cutting a piece of around 10-15 cm in length and boil it in ultrapure water containing 1 mM ethylenediaminetetraacetic acid (EDTA) for 15 min. Thereafter, gently rinse the dialysis membrane thoroughly with ultrapure water.</li>
	<li>After centrifugation, collect the supernatant in the dialysis tubing membrane by decantation. The pellet contains acidic insoluble material (non-collagenous proteins) and the supernatant contains soluble collagen proteins.</li>
	<li>Dialyze the supernatant against 2 L of sterile 0.1x Minimum Essential Medium Eagle (MEM), pH 4.0 in a 2-5 L glass beaker. Dialyze for 3 days. Change 0.1x MEM solution at least twice a day checking the pH at every change before using. If pH has turned basic, modify it with a few drops of 0.1 M acetic acid until pH is 4.0.</li>
	<li>After dialysis, add antibiotics (1.5 mL of penicillin/streptomycin (Pen-Strep)) to the dialyzed collagen solution. Make 5 mL aliquots of the collagen stock solution and store at 4 &#176;C. 
	NOTE: From this point, all handling procedures must be performed under sterile conditions in a laminar flow hood.</li>
	<li>Proceed with the gelation test of the prepared collagen stock solution following the next steps.
	<ol>
		<li>Since the stock collagen is usually too concentrated, prepare 3 working dilutions (75%, 50%, and 25% collagen solution) by diluting the stock in 0.1x MEM, pH 4.0. The final volume recommended for each working dilution is 5 mL. In each condition, check the protein concentration using a protein colorimetric assay.</li>
		<li>Place several empty 1.5 mL conical centrifuge tubes (one for each working dilution), 10x MEM tubes, 7.5% sodium bicarbonate solution and different working dilutions of collagen on ice. Wait until these are cooled.</li>
		<li>Add 40-50 &#181;L of 10x MEM to a cold (4 &#176;C) centrifuge tube. Next, mix it gently with 7-8 &#956;L of sodium bicarbonate solution.</li>
		<li>Add 310-330 &#956;L of one of the different collagen dilutions to this tube and mix it gently with the pipette avoiding any bubble formation. Keep the collagen-MEM-sodium bicarbonate mixture on ice (4 &#176;C) for at least 5 min.</li>
		<li>Pipette 10-25 &#956;L of the mixture into a 35 mm Petri dish.</li>
		<li>Place the Petri dish in the CO2 incubator set at 37 &#176;C until the gelation of the hydrogel (&#177; 15-20 min) is observed.</li>
		<li>Repeat steps 1.12.3-1.12.6 for the remaining collagen dilutions in different Petri dishes.</li>
		<li>Select the collagen working dilution that renders the best results. 
		NOTE: The best gelled hydrogel should have a uniform translucent texture, grey color and should not be lumpy or stringy. In our experience, a dilution of 3:1 (Collagen: 0.1x MEM) generates the best experimental results.</li>
	</ol>
	</li>
</ol>
2. Preparation of Cell (COS1) Aggregates Genetically-modified to Secrete a Candidate Molecule in 3-D Collagen Hydrogels
<ol>
	<li>Plate 2 x 106&#160;COS1 cells into a 35 mm Petri dishes and incubate with complete culture medium composed of 100 mL of D-MEM containing 10% (vol/vol) heat-inactivated fetal bovine serum, 0.5% (wt/vol) glutamine and 1% (wt/vol) Pen/Strep in a cell culture&#160;incubator, in order to reach 70-80% confluency overnight. Prepare one Petri dish for each transfection procedure.</li>
	<li>The following day transfect COS1 cells with the DNA encoding the candidate molecule (Netrin-1 or Sema3E) using liposome-based transfection method following the manufacturer&#39;s instructions.
	<ol>
		<li>To do this, mix 250 &#181;L of serum-free medium and DNA (1-2 &#956;g per condition) to a 1.5 mL centrifuge tube (DNA tube) and mix. Incubate at room temperature (RT) for 5 min. Prepare a second tube (liposomal tube) by adding 240 &#181;L of the serum-free medium and 10 &#181;L of the liposomal transfection reagent. Incubate at RT for 5 min.</li>
		<li>After incubation, add the content of the DNA-tube to the liposomal tube and mix gently. Now incubate at RT for 15 min. Replace the medium on the cultured cells with 1.5 mL of the serum-free medium and add the DNA-liposomes mixture to the Petri dish slowly dropwise. Incubate for 3 h in the CO2 cell culture incubator.</li>
	</ol>
	</li>
	<li>After 3 h of transfection incubation, replace the medium with the complete culture medium and incubate overnight in the incubator.</li>
	<li>Next day, rinse the cells with 0.1 M Dulbecco&#8217;s phosphate buffered saline (D-PBS), treat cultures with Trypsin-EDTA (800 &#181;L per each dish for 5-15 min in the CO2 incubator) and collect detached cells with 15 mL of complete culture medium.</li>
	<li>Centrifuge the cells at 4 &#176;C at 130 x g for 5 min. After centrifugation, remove media and preserve the pellet containing COS1 cells on ice.</li>
	<li>Repeat steps 1.12.3-1.12.6 to prepare the collagen working mixture.</li>
	<li>Add 100-150 &#956;L of the collagen mixture to the pellet of the transfected cells and mix gently by pipetting up and down and spread 45-50 &#181;L of this mixture onto a Petri dish (35 mm diameter) to form a uniform band of collagen-cells of around 1-1.5 cm in length. Place the dish in the incubator at 37 &#176;C (5% CO2) until the gelation (&#177; 15-20 min) is observed.</li>
	<li>Prepare a second strip containing control cells (mock transfection) in a second culture dish and plate it in the incubator (&#177; 15-20 min) and when gelation is completed add 3-4 mL of warmed (37 &#176;C) COS1 complete culture medium to each dish containing the gelled collagen-cells strips and keep them in the CO2 cell culture incubator. Thereafter, cut the collagen-cells strips to generate small square pieces (400 to 500 &#181;m in length) using a fine scalpel or a tissue chopper.</li>
	<li>Transfer all the sections from the same transfection condition to a Petri dish containing 3-3.5 mL of neuronal culture media (NCM) and check under a dissection microscope the quality of the pieces. Again, keep them in the CO2 cell culture incubator. 
	NOTE: Neuronal culture medium consists of Neurobasal medium containing 1-5% (vol/vol) heat-inactivated horse serum, 2 mM glutamine, 0.5% (wt/vol) glucose, 1% (wt/vol) Pen-Strep solution and 0.044% (wt/vol) NaHCO3. Ensure that the pH is between 7.2-7.3.</li>
</ol>
3. Generation of Embryonic Explant for Culture
<ol>
	<li>Sterilize the surgical tools (scissors, scalpel blade handle, straight and curved forceps) by autoclaving following routine sterilization guidelines. In parallel prepare 500 mL of Hank&#8217;s balanced salt solution-glucose buffer and 4-5 Petri dishes (100 mm diameter) containing 10 mL of HBSS-G. Place these plates on ice (4 &#176;C).</li>
	<li>Sacrifice the pregnant female rat (embryonic day 16.5) outside the sterile area, following the approved ethical procedures. Cut the embryo horns with scissors from the abdominal cavity and place it into a large Petri dish containing cold HBSS-G.</li>
	<li>Place the dish in the laminar flow hood and extract the embryos with straight forceps. Place them into a new dish containing cold HBSS-G. Next, remove the skin of the embryo using small forceps and carefully dissect the brain using the curved and straight forceps. Place them into a dish containing cold HBSS-G.</li>
	<li>Under a dissecting microscope, cut the brain in half along the midline to separate both the hemispheres with the scalpel or fine scissors and remove the diencephalon, the meninges and blood vessels from the brain pieces with fine forceps.</li>
	<li>Repeat steps 3.3-3.4&#160;with the rest of the embryos. Do not delay the dissection for more than 2 h to preserve the tissue quality.</li>
	<li>Clean all parts of the tissue chopper with 100% ethanol (especially the polytetrafluoroethylene (PTFE) cutting plate and the razor blade). Keep the tissue chopper in the laminar flux hood under UV illumination for 15 min.</li>
	<li>Transfer each tissue piece (e.g., cortex with hippocampus) to the cutting plate of the tissue chopper. For hippocampus, place it perpendicular to the razor blade and obtain tissue sections of 450-500 &#181;m in thickness.</li>
	<li>Prepare several 35 mm Petri dishes with 3-4 mL of complete NCM and transfer tissue pieces from the tissue chopper plate to the Petri dishes. Many dishes may be needed as regions of interest are dissected.</li>
	<li>Finish the tissue dissection in the complete NCM using fine tungsten needles. Check the quality of the obtained slices under the dissecting microscope. Ensure that the layers are clearly identifiable in the darkfield optics&#160;and dissect the region of interest (e.g., CA region of the hippocampus) with tungsten needles. Discard damaged slices. Keep hippocampal explants in complete NCM medium in the CO2 incubator.</li>
</ol>
4. Preparation of 3-D Co-cultures in Collagen Hydrogels
<ol>
	<li>Place several sterile 4-well culture plates in the laminar flow hood and prepare a collagen working mixture as previously indicated in steps 1.12.2-1.12.6.</li>
	<li>Place 15-20 &#956;L of the hydrogel mixture into the bottom of a well to produce a circular collagen base. Repeat this step for the rest of the wells. Do not prepare more than five plates at the same time to avoid excessive liquid evaporation from the hydrogel base.</li>
	<li>Keep the dishes in the incubator until the complete gelation (&#177; 15-20 min) is observed and take the plates out of the incubator only when the gelation is completed. Check the quality of the gelled collagen.</li>
	<li>Transfer a small piece of COS1 cell aggregate with a pipette. Place it onto the hydrogel base and place a tissue piece on the same base with a pipette close to the piece of cells aggregate at one explant-size.</li>
	<li>Prepare a new working collagen mixture on ice as in steps 1.12.2-1.12.6.</li>
	<li>Gently pipette 15-20 &#956;L of this new mixture and cover the explant and cell aggregate. A sandwich-like hydrogel culture will be observed. At this moment, re-orientate the explant with a fine tungsten needle (do not touch the COS1 cell aggregate!), so it faces the cell aggregate at &#177; 500-600 &#956;m.</li>
	<li>Return the plate to the incubator until the gelation is observed (&#177; 10-15 min), and 0.5 mL of complete NCM supplemented with 2% B27 supplement and keep cultures for 36 to 48 h in the incubator (37 &#176;C, 5% CO2).</li>
</ol>
5. Fixation of Explant-cell Aggregate Co-cultures and Immunocytochemical Procedure
<ol>
	<li>After 36-48 h of incubation, remove the medium and rinse with 0.1 M phosphate buffered saline (PBS), pH 7.3. Thereafter, fix the cultures for 1 h with 4% paraformaldehyde in 0.1 M phosphate buffer (PB), pH 7.3, at 4 &#176;C.</li>
	<li>Remove the fixative and gently rinse the cultures 3-4 times (10-15 min each) in 0.1 M PB, pH 7.3.</li>
	<li>Detach the hydrogel sandwich from the bottom of the well with spatula or forceps. Transfer the collagen block with a fine paintbrush to a 6-well culture plate containing 0.1 M PBS with 0.5% non-ionic detergent.</li>
	<li>Incubate free-floating hydrogels in the blocking solution (10% serum, 0.5% non-ionic surfactant, and 0.2% gelatin in 0.1 M PBS) for 2-3 h at RT with gentle agitation.</li>
	<li>Rinse 3 times (10-15 min each) with 0.1 M PBS containing 0.5% non-ionic surfactant.</li>
	<li>Incubate with primary antibody diluted in PBS containing 5% serum, 0.5% non-ionic surfactant, 0.2% gelatin, and 0.02% sodium azide. Incubate with the primary antibody for 36-48 h at 4 &#176;C on a shaker. 
	NOTE: Usually an antibody against class III &#946;-tubulin (&#945;-TUJ-1) (diluted 1:2,000) is used to define axonal growth in 3-D hydrogel cultures.</li>
	<li>After incubation, rinse as in step 5.5.</li>
	<li>Incubate with secondary antibody for 4 h at RT (or 6-7 h at 4 &#176;C) on a shaker diluted in 5% serum, 0.5% non-ionic surfactant, and 0.2% gelatin. A horse anti-mouse biotinylated antibody (diluted 1:200) is used in this experiment.</li>
	<li>Rinse cultures as in 5.5.</li>
	<li>Incubate the cultures for 2 days at 4 &#176;C with avidin-biotin complex (ABC) solution 1:100 diluted in PBS containing 5% serum, 0.5% non-ionic surfactant, and 0.2% gelatin. Alternatively, use horseradish peroxidase (HRP)-tagged streptavidin (diluted 1:300-400) in the same buffer.</li>
	<li>Rinse cultures as described in 5.5.</li>
	<li>Rinse the cultures several times with 0.1 M Tris-HCl buffer, pH 7.6 for 1 h.</li>
	<li>Incubate the cultures with 0.03% of 3,3&#8242;-Diaminobenzidine tetrahydrochloride (DAB) solution in 0.1 M Tris-HCl, pH 7.6.</li>
	<li>Add 5-8 &#181;L of 1% H2O2 and wait 10-15 min. Monitor the development of DAB under a microscope using a 4-10x objective.</li>
	<li>Stop the reaction by removing DAB solution with 0.1 M Tris-HCl buffer, pH 7.6.</li>
	<li>Rinse the cultures in PBS for 30 min (several changes).</li>
	<li>Mount the hydrogels onto glass slides using aqueous-based mounting media.</li>
	<li>Analyze the length and distribution of the axons inside the hydrogel using Sholl analysis plug-in or with NeuriteJ plug-in for ImageJ software30.</li>
</ol>

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S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Immobilized+concentration+gradients+of+nerve+growth+factor+guide+neurite+outgrowth.">Immobilized concentration gradients of nerve growth factor guide neurite outgrowth.</a> Journal of Biomedical Materials Research Part A. 68 (2), 235-243 (2004).</li><li>Torres-Espin, A., Santos, D., Gonzalez-Perez, F., del Valle, J., Navarro, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neurite-J:+an+image-J+plug-in+for+axonal+growth+analysis+in+organotypic+cultures.">Neurite-J: an image-J plug-in for axonal growth analysis in organotypic cultures.</a> Journal of Neuroscience Methods. 236, 26-39 (2014).</li><li>Balestrini, J. L., 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=Comparative+biology+of+decellularized+lung+matrix:+Implications+of+species+mismatch+in+regenerative+medicine.">Comparative biology of decellularized lung matrix: Implications of species mismatch in regenerative medicine.</a> Biomaterials. 102, 220-230 (2016).</li><li>Qian, J., 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=Kinetic+Analysis+of+the+Digestion+of+Bovine+Type+I+Collagen+Telopeptides+with+Porcine+Pepsin.">Kinetic Analysis of the Digestion of Bovine Type I Collagen Telopeptides with Porcine Pepsin.</a> Journal of Food Science. 81 (1), 27-34 (2016).</li><li>Eyre, D. R., Weis, M., Hudson, D. M., Wu, J. J., Kim, L. <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+3-hydroxyproline+(3Hyp)-rich+motif+marks+the+triple-helical+C+terminus+of+tendon+type+I+collagen.">A novel 3-hydroxyproline (3Hyp)-rich motif marks the triple-helical C terminus of tendon type I collagen.</a> Journal of Biological Chemistry. 286 (10), 7732-7736 (2011).</li><li>Garnotel, R., 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=Human+blood+monocytes+interact+with+type+I+collagen+through+alpha+x+beta+2+integrin+(CD11c-CD18,+gp150-95).">Human blood monocytes interact with type I collagen through alpha x beta 2 integrin (CD11c-CD18, gp150-95).</a> Journal of Immunology. 164 (11), 5928-5934 (2000).</li><li>Montolio, 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+semaphorin+3A+inhibitor+blocks+axonal+chemorepulsion+and+enhances+axon+regeneration.">A semaphorin 3A inhibitor blocks axonal chemorepulsion and enhances axon regeneration.</a> Chemistry and Biology. 16 (7), 691-701 (2009).</li><li>Garcia-Gareta, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Collagen+gels+and+the+'Bornstein+legacy':+from+a+substrate+for+tissue+culture+to+cell+culture+systems+and+biomaterials+for+tissue+regeneration.">Collagen gels and the 'Bornstein legacy': from a substrate for tissue culture to cell culture systems and biomaterials for tissue regeneration.</a> Experimental Dermatology. 23 (7), 473-474 (2014).</li></ol>

The authors have nothing to disclose.

The growth of developing axons is mainly invasive and includes ECM degradation and remodeling. Using the procedure presented here, researchers can obtain a homogenous 3-D matrix formed by the natural type I collagen in which axons (or cells) can respond to a chemical gradient secreted by genetically-modified cells as they do in vivo. Different axonal responses to gradients of attractive or inhibitory cues (protein, lipids, etc.) can be easily compared to specific control (mock transfected cells). As advantages, we must m...

Neuronal axons, ending in axonal growth cones, migrate long distances through the extracellular matrix (ECM) of the embryo over specific pathways to reach their appropriate targets. The growth cone is the distal portion of the axon and it is specialized to sense the physical and molecular environment of the cell1,2. From a molecular point of view, growth cones are guided by at least four different molecular mechanisms: contact attraction, chemoattraction, contact repulsion, and chemorepulsion triggered by different axonal guidance cues3,4,5,6. Contact-mediated processes can be partially monitored in two-dimensional (2D) cultures on micro-patterned substrates (e.g., with stripes7,8 or spots9 containing the molecules). However, axons can navigate to their target in a non-diffusive manner by sensing several attractive and repulsive molecules from guidepost cells in the environment4,5,10. Here, we describe an easy method of 3-D culture to check whether a secreted molecule induces chemorepulsive or chemoattractive effects on developing axons.
The earliest studies aimed to determine the effects of axon guidance cues used explant cultures in three-dimensional (3-D) matrices to generate gradients simulating in vivo conditions11,12. This approach, together with in vivo experiments, allowed for the identification of four major families of guidance cues: Netrins, Slits, Semaphorins, and Ephrins4,5,6. These molecular cues and other factors13 are integrated by the growing axons, triggering the dynamics of adhesion complexes and transducing mechanical forces via the cytoskeleton14,15,16. To generate molecular gradients in 3-D cultures for axonal navigation, pioneering researchers used plasma clot substrates17, which was also used for organotypic slice preparations18. However, in 1958, a new protocol to generate 3-D collagen hydrogels was reported for studying with Maximow&#180;s devices19, a culture platform, used in several studies suitable for microscopic observations20. Another pioneer study reported collagen gel as a tool to embed human fibroblasts for studying the differentiation of fibroblasts into myofibroblasts in wound healing processes21. In parallel, Lumsden and Davies applied collagen from the bovine dermis to analyze the putative effect of nerve growth factor (NGF) on the guiding of sensory nerve fibers22. With the development of new culture platforms (e.g., multi-well plates) by different companies and laboratories, collagen cultures were adapted to these new devices6,23,24,25,26. In parallel, an extract of ECM material derived from the Engelbreth-Holm-Swarm tumor cell line was made commercially available to expand these studies27.
Recently, several protocols have been developed to generate molecular gradients with putative roles in axon guidance using 3-D hydrogels (e.g., collagen, fibrin, etc.)28. Alternatively, the candidate molecule can be immobilized at different concentration in a porous matrix (e.g., NGF29) or generated by culturing in a small region of the 3-D hydrogel cell aggregates secreting the molecule to generate a radial gradient4,23,24,25,26. The last possibility will be explained in this protocol.
The procedure presented here is an easy, fast and highly reproducible method based on the analysis of axonal growth in 3-D hydrogel cultures of the embryonic mouse brain. In comparison with other methods, the protocol is well suited for non-trained researchers and can be fully developed after a short training (1-2 weeks). In this protocol, we first isolate collagen from adult rat tails to further generate 3-D matrices in which genetically-modified cell aggregates are cultured in front of the embryonic neuronal tissue. These cell aggregates form radial chemical gradients of a candidate molecule which elicits a response for the growing axons. Finally, the evaluation of the effects of the molecule on growing axons can easily be performed using a phase contrast microscopy or, alternatively, immunocytochemical methods.

<table><tbody><tr><td>&lt;strong&gt;Material&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>3,3&amp;prime;-Diaminobenzidine tetrahydrochloride 10 mg tablets (DAB)</td><td>Sigma</td><td>D5905</td><td></td></tr><tr><td>Adult Sprague-Dawley rats (8 to 9 weeks old)&amp;nbsp;</td><td>Criffa-Credo, Lyon, France</td><td></td><td></td></tr><tr><td>Avidin-biotin-peroxidase complex (ABC)</td><td>Vector Labs</td><td>PK-4000</td><td></td></tr><tr><td>B27 serum-free supplement 50x&amp;nbsp;</td><td>Invitrogen</td><td>17504-044</td><td></td></tr><tr><td>Bicinchoninic acid (BCA) protein assay kit</td><td>Pierce</td><td>23225</td><td></td></tr><tr><td>cDNA plasmid vectors</td><td></td><td></td><td></td></tr><tr><td>COS1 cell lines</td><td>ATTC</td><td>CRL-1570</td><td></td></tr><tr><td>D-(+)-Glucose</td><td>Sigma</td><td>16325</td><td></td></tr><tr><td>D-(+)-glucose (45% solution in water) for complete Neurobasal medium</td><td>Sigma</td><td>G8769</td><td></td></tr><tr><td>D-MEM (Dulbecco&#039;s Modified Eagle Medium 1x ) for COS1 culture medium</td><td>Invitrogen</td><td>41966-029</td><td></td></tr><tr><td>Dulbecco&amp;rsquo;s phosphate buffered saline 10x (without Ca&lt;sup&gt;2+&lt;/sup&gt; and Mg&lt;sup&gt;2+&lt;/sup&gt;+) (D-PBS) for cultures</td><td>Invitrogen</td><td>14200</td><td></td></tr><tr><td>Ethanol&amp;nbsp;</td><td>merck</td><td>108543</td><td></td></tr><tr><td>Ethylenediaminetetraacetic acid dihydrate disodium salt (EDTA)</td><td>Sigma</td><td>E5134</td><td></td></tr><tr><td>Fluorescence mounting media (e.g., Fluoromount-G or similar)</td><td>Electron Microscopy Sciences (EMS)</td><td>17984-25</td><td></td></tr><tr><td>Gelatin powder&amp;nbsp;</td><td>Sigma</td><td>G1890</td><td></td></tr><tr><td>Glacial acetic acid (Panreac, cat. no. 211008)</td><td>Panreac</td><td>211008</td><td></td></tr><tr><td>Hank&amp;rsquo;s balanced salt solution&amp;nbsp;</td><td>Invitrogen</td><td>24020083</td><td></td></tr><tr><td>Heat-inactivated foetal bovine serum&amp;nbsp;</td><td>Invitrogen</td><td>10108-165</td><td></td></tr><tr><td>Heat-inactivated horse serum&amp;nbsp;</td><td>Invitrogen</td><td>26050-088</td><td></td></tr><tr><td>Hydrogen peroxide (H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;, 32 to 33% in water)</td><td>Sigma</td><td>316989</td><td></td></tr><tr><td>L-glutamine 200 mM solution (100x) for complete Neurobasal and COS1 medium</td><td>Invitrogen</td><td>25030-024</td><td></td></tr><tr><td>Lipofectamine 2000 Reagent</td><td>Invitrogen</td><td>11668-019</td><td></td></tr><tr><td>Mice pregnant female (embryonic day 12.5 to 16.5; E12.5-16.5)&amp;nbsp;</td><td>Criffa-Credo, Lyon, France</td><td></td><td></td></tr><tr><td>Modified Minimum Essential Medium Eagle (MEM)</td><td>Invitrogen</td><td>11012-044</td><td></td></tr><tr><td>Monoclonal antibody against class III &amp;beta;-tubulin (clone TUJ-1)</td><td>Biolegend</td><td>801201</td><td></td></tr><tr><td>N-2 supplement 100x&amp;nbsp;</td><td>Invitrogen</td><td>17502-048</td><td></td></tr><tr><td>Neurobasal medium&amp;nbsp;</td><td>Invitrogen</td><td>21103049</td><td></td></tr><tr><td>Paraformaldehyde</td><td>Merck</td><td>1,040,051,000</td><td></td></tr><tr><td>Penicillin/streptomycin solution 100x&amp;nbsp;</td><td>Invitrogen</td><td>15140-22</td><td></td></tr><tr><td>Phosphate buffered saline 10x (PBS) for immunocytochemistry</td><td>Invitrogen</td><td>AM9624</td><td></td></tr><tr><td>Secondary antibody: biotinylated horse anti-mouse&amp;nbsp;</td><td>Vector Labs</td><td>BA-2000</td><td></td></tr><tr><td>Serum-free medium (Opti-MEM)</td><td>Invitrogen</td><td>11058-021</td><td></td></tr><tr><td>Sodium azide&amp;nbsp;</td><td>Panreac</td><td>162712</td><td></td></tr><tr><td>Sodium bicarbonate solution 7.5%&amp;nbsp;</td><td>Invitrogen</td><td>25080-094</td><td></td></tr><tr><td>Sterile culture grade H&lt;sub&gt;2&lt;/sub&gt;O&amp;nbsp;</td><td>Sigma</td><td>W3500</td><td></td></tr><tr><td>TritonTM X-100&amp;nbsp;</td><td>Sigma</td><td>X100</td><td></td></tr><tr><td>Trizma base&amp;nbsp;</td><td>Sigma</td><td>T1503</td><td></td></tr><tr><td>Trypsin-EDTA (Trypsin (0.05% (wt/vol) with EDTA (1x)</td><td>Invitrogen</td><td>25300-054</td><td></td></tr><tr><td>&lt;strong&gt;Equipment&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>1 large and 1 small curved scissors for dissection&amp;nbsp;</td><td>Fine tools Instruments or similar</td><td></td><td></td></tr><tr><td>1.5 mL conical centrifuge tubes&amp;nbsp;</td><td>Eppendorf or similar</td><td></td><td></td></tr><tr><td>15 mL conical centrifuge tubes&amp;nbsp;</td><td>Corning or similar</td><td></td><td></td></tr><tr><td>2 haemostats&amp;nbsp;&amp;nbsp;</td><td>Fine tools Instruments or similar</td><td></td><td></td></tr><tr><td>2 small straight dissecting scissors</td><td>Fine tools Instruments or similar</td><td></td><td></td></tr><tr><td>200 mL centrifuge tubes for centrifugation</td><td>Nalgene or similar</td><td></td><td></td></tr><tr><td>200 mL sterile glass conical flasks</td><td></td><td></td><td></td></tr><tr><td>2 L glass beaker</td><td></td><td></td><td></td></tr><tr><td>4- and 6-well culture plates&amp;nbsp;</td><td>Nunc</td><td>176740 and 140675</td><td></td></tr><tr><td>Automatic pipette pumps and disposable 10 mL and 25 mL filter-containing sterile plastic pipettes.</td><td>Gilson, Brand, Eppendorf or similar&amp;nbsp;</td><td></td><td></td></tr><tr><td>Automatic pipettes, sterile filter tips and current sterile tips&amp;nbsp;</td><td>Gilson, Eppendorf or similar</td><td></td><td></td></tr><tr><td>Bench top microcentrifuge with angle fixed rotor&amp;nbsp;</td><td>Eppendorf, Beckman Coulter or similar</td><td></td><td></td></tr><tr><td>Bench top refrigerated centrifuge with swing-bucket rotor (with 1.5, 15 and 50 mL tube adaptors)</td><td>Eppendorf, Beckman Coulter or similar</td><td></td><td></td></tr><tr><td>Cell culture incubator at 37 &amp;deg;C, 5% CO&lt;sub&gt;2&lt;/sub&gt; and 95% air</td><td></td><td></td><td></td></tr><tr><td>Dialysis tubing cellulose membrane</td><td>Sigma</td><td>D9402</td><td></td></tr><tr><td>Dialysis tubing closures&amp;nbsp;</td><td>Sigma</td><td>Z37101-7</td><td></td></tr><tr><td>Disposable glass pipettes</td><td></td><td></td><td></td></tr><tr><td>Dissecting microscope with dark field optics&amp;nbsp;</td><td>Olympus SZ51 or similar&amp;nbsp;</td><td></td><td></td></tr><tr><td>High-speed refrigerated Beckman Coulter centrifuge or similar with angle fixed rotor</td><td></td><td></td><td></td></tr><tr><td>Laminar flow hood</td><td></td><td></td><td></td></tr><tr><td>Large 100 mm, 60 mm and small 35 mm &amp;Oslash; cell culture dishes&amp;nbsp;</td><td>Nunc</td><td>&amp;nbsp;150679 , 150288 and 150318, respectively</td><td></td></tr><tr><td>Magnetic stirrer and magnetic spin bars</td><td>IKA or similar</td><td></td><td></td></tr><tr><td>McIlwain tissue chopper</td><td>Mickle Laboratory Engineering</td><td></td><td></td></tr><tr><td>One pair of fine straight forceps and one pair of curved forceps&amp;nbsp;</td><td>Fine tools Instruments or similar</td><td></td><td></td></tr><tr><td>Razor blades for the tissue chopper</td><td></td><td></td><td></td></tr><tr><td>Scalpels (number 15 and 11)</td><td></td><td></td><td></td></tr><tr><td>Two pairs of fine spatulas for transferring collagen and tissue pieces</td><td>Fine tools Instruments or similar</td><td></td><td></td></tr></tbody></table>

generation of 3-d collagen-based hydrogels to analyze axonal growth and behavior during nervous system development

This protocol uses natural type I collagen to generate three-dimensional (3-D) hydrogel for monitoring and analyzing the axonal growth. The protocol is centered on culturing small pieces of embryonic or early postnatal rodent brains inside a 3-D hydrogel formed by the rat tail tendon-derived type I collagen with specific porosity. Tissue pieces are cultured inside the hydrogel and confronted to specific brain fragments or genetically-modified cell aggregates to produce and secrete molecules suitable for creating a gradient inside the porous matrix. The steps of this protocol are simple and reproducible but include critical steps to be considered carefully during its development. Moreover, the behavior of growing axons can be monitored and analyzed directly using a phase-contrast microscope or mono/multiphoton fluorescence microscope after fixation by immunocytochemical methods.

Here, we present a widely accessible methodology to study axonal growth in 3-D hydrogel collagen cultures of embryonic mouse nervous system. To this end, we isolated collagen from adult rat tails to generate 3-D matrices in which we cultured genetically-modified cell aggregates expressing Netrin-1 or Sema3E confronted with embryonic neuronal tissue (e.g., CA region of the hippocampus). These cell aggregates formed a radially distributed gradient of the candidate molecule inside the collagen matrix. Finally, to evaluate t...

Watch this Scientific Journal Video about Generation of 3-D Collagen-based Hydrogels to Analyze Axonal Growth and Behavior During Nervous System Development at JoVE.com

Generation of 3-D Collagen-based Hydrogels to Analyze Axonal Growth and Behavior During Nervous System Development

Here, we provide a method for analyzing the behavior of growing axons in 3D matrices, mimicking their natural development.

This protocol uses natural type I collagen to generate three-dimensional (3-D) hydrogel for monitoring and analyzing the axonal growth. The protocol is ...

generation-3-d-collagen-based-hydrogels-to-analyze-axonal-growth

Universidad de Cartagena UDEC

Research

JoVE Journal

Neuroscience

5.6K Views.  Parc Científic de Barcelona. Here, we provide a method for analyzing the behavior of growing axons in 3D matrices, mimicking their natural development.

Video: Generation of 3-D Collagen-based Hydrogels to Analyze Axonal Growth and Behavior During Nervous System Development

Organotypic Collagen I Assay: A Malleable Platform to Assess Cell Behaviour in a 3-Dimensional Context

Cell migration is fundamental to many aspects of biology, including development, wound healing, the cellular responses of the immune system, and metastasis of tumor cells. Migration has been studied on glass coverslips in order to make cellular dynamics amenable to investigation by light microscopy. However, it has become clear that many aspects of cell migration depend on features of the local environment including its elasticity, protein composition, and pore size, which are not faithfully represented by rigid two dimensional substrates such as glass and plastic 1. Furthermore, interaction with other cell types, including stromal fibroblasts 2 and immune cells 3, has been shown to play a critical role in promoting the invasion of cancer cells. Investigation at the molecular level has increasingly shown that molecular dynamics, including response to drug treatment, of identical cells are significantly different when compared in vitro and in vivo 4. 
Ideally, it would be best to study cell migration in its naturally occurring context in living organisms, however this is not always possible. Intermediate tissue culture systems, such as cell derived matrix, matrigel, organotypic culture (described here) tissue explants, organoids, and xenografts, are therefore important experimental intermediates. These systems approximate certain aspects of an in vivo environment but are more amenable to experimental manipulation such as use of stably transfected cell lines, drug treatment regimes, long term and high-resolution imaging. Such intermediate systems are especially useful as proving grounds to validate probes and establish parameters required to image the dynamic response of cells and fluorescent reporters prior to undertaking imaging in vivo 5. As such, they can serve an important role in reducing the need for experiments on living animals.

A method is described for the preparation of a 3-dimensional matrix consisting of collagen type I and primary human fibroblasts. This organotypic gel serves as a useful substrate to assess invasive cell migration because it mimics basic features of tissue stroma and is amenable to many forms of microscopy.

Cell migration is fundamental to many aspects of biology, including development, wound healing, the cellular responses of the immune system, and ...

Bioengineering

Dissection and Culture of Chick Statoacoustic Ganglion and Spinal Cord Explants in Collagen Gels for Neurite Outgrowth Assays

The sensory organs of the chicken inner ear are innervated by the peripheral processes of statoacoustic ganglion (SAG) neurons. Sensory organ innervation depends on a combination of axon guidance cues1 and survival factors2 located along the trajectory of growing axons and/or within their sensory organ targets. For example, functional interference with a classic axon guidance signaling pathway, semaphorin-neuropilin, generated misrouting of otic axons3. Also, several growth factors expressed in the sensory targets of the inner ear, including Neurotrophin-3 (NT-3) and Brain Derived Neurotrophic Factor (BDNF), have been manipulated in transgenic animals, again leading to misrouting of SAG axons4. These same molecules promote both survival and neurite outgrowth of chick SAG neurons in vitro5,6.
Here, we describe and demonstrate the in vitro method we are currently using to test the responsiveness of chick SAG neurites to soluble proteins, including known morphogens such as the Wnts, as well as growth factors that are important for promoting SAG neurite outgrowth and neuron survival. Using this model system, we hope to draw conclusions about the effects that secreted ligands can exert on SAG neuron survival and neurite outgrowth. 
SAG explants are dissected on embryonic day 4 (E4) and cultured in three-dimensional collagen gels under serum-free conditions for 24 hours. First, neurite responsiveness is tested by culturing explants with protein-supplemented medium. Then, to ask whether point sources of secreted ligands can have directional effects on neurite outgrowth, explants are co-cultured with protein-coated beads and assayed for the ability of the bead to locally promote or inhibit outgrowth. We also include a demonstration of the dissection (modified protocol7) and culture of E6 spinal cord explants. We routinely use spinal cord explants to confirm bioactivity of the proteins and protein-soaked beads, and to verify species cross-reactivity with chick tissue, under the same culture conditions as SAG explants. These in vitro assays are convenient for quickly screening for molecules that exert trophic (survival) or tropic (directional) effects on SAG neurons, especially before performing studies in vivo. Moreover, this method permits the testing of individual molecules under serum-free conditions, with high neuron survival8.

We demonstrate how to dissect and culture chick E4 statoacoustic ganglion and E6 spinal cord explants. Explants are cultured under serum-free conditions in 3D collagen gels for 24 hours. Neurite responsiveness is tested with growth factor-supplemented medium and with protein-coated beads.

The sensory organs of the chicken inner ear are innervated by the peripheral processes of statoacoustic ganglion (SAG) neurons. Sensory organ innervation ...

Dissection and Culture of Mouse Dopaminergic and Striatal Explants in Three-Dimensional Collagen Matrix Assays

Midbrain dopamine (mdDA) neurons project via the medial forebrain bundle towards several areas in the telencephalon, including the striatum1. Reciprocally, medium spiny neurons in the striatum that give rise to the striatonigral (direct) pathway innervate the substantia nigra2. The development of these axon tracts is dependent upon the combinatorial actions of a plethora of axon growth and guidance cues including molecules that are released by neurites or by (intermediate) target regions3,4. These soluble factors can be studied in vitro by culturing mdDA and/or striatal explants in a collagen matrix which provides a three-dimensional substrate for the axons mimicking the extracellular environment. In addition, the collagen matrix allows for the formation of relatively stable gradients of proteins released by other explants or cells placed in the vicinity (e.g. see references 5 and 6). Here we describe methods for the purification of rat tail collagen, microdissection of dopaminergic and striatal explants, their culture in collagen gels and subsequent immunohistochemical and quantitative analysis. First, the brains of E14.5 mouse embryos are isolated and dopaminergic and striatal explants are microdissected. These explants are then (co)cultured in collagen gels on coverslips for 48 to 72 hours in vitro. Subsequently, axonal projections are visualized using neuronal markers (e.g. tyrosine hydroxylase, DARPP32, or &beta;III tubulin) and axon growth and attractive or repulsive axon responses are quantified. This neuronal preparation is a useful tool for in vitro studies of the cellular and molecular mechanisms of mesostriatal and striatonigral axon growth and guidance during development. Using this assay, it is also possible to assess other (intermediate) targets for dopaminergic and striatal axons or to test specific molecular cues.

Explants from the midbrain dopamine system and striatum are used in a collagen matrix assay for the in vitro analysis of mesostriatal and striatonigral pathway development. In this assay axonal outgrowth and guidance can be manipulated and quantified. It can also be modified for assessing other regions or molecular cues.

Midbrain dopamine (mdDA) neurons project via the medial forebrain bundle towards several areas in the telencephalon, including the striatum1. ...

Three-Dimensional In Vitro Biomimetic Model of Neuroblastoma Using Collagen-Based Scaffolds

Neuroblastoma is the most common extracranial solid tumor in children, accounting for 15% of overall pediatric cancer deaths. The native tumor tissue is a complex three-dimensional (3D) microenvironment involving layers of cancerous and non-cancerous cells surrounded by an extracellular matrix (ECM). The ECM provides physical and biological support and contributes to disease progression, patient prognosis, and therapeutic response.
This paper describes a protocol for assembling a 3D scaffold-based system to mimic the neuroblastoma microenvironment using neuroblastoma cell lines and collagen-based scaffolds. The scaffolds are supplemented with either nanohydroxyapatite (nHA) or glycosaminoglycans (GAGs), naturally found at high concentrations in the bone and bone marrow, the most common metastatic sites of neuroblastoma. The 3D porous structure of these scaffolds allows neuroblastoma cell attachment, proliferation and migration, and the formation of cell clusters. In this 3D matrix, the cell response to therapeutics is more reflective of the in vivo situation.
The scaffold-based culture system can maintain higher cell densities than conventional two-dimensional (2D) cell culture. Therefore, optimization protocols for initial seeding cell numbers are dependent on the desired experimental timeframes. The model is monitored by assessing cell growth via DNA quantification, cell viability via metabolic assays, and cell distribution within the scaffolds via histological staining.
This model&#39;s applications include the assessment of gene and protein expression profiles as well as cytotoxicity testing using conventional drugs and miRNAs. The 3D culture system allows for the precise manipulation of cell and ECM components, creating an environment more physiologically similar to native tumor tissue. Therefore, this 3D in vitro model will advance the understanding of the disease pathogenesis and improve the correlation between results obtained in vitro, in vivo in&#160;animal models, and human subjects.

Three-Dimensional In Vitro Biomimetic Model of Neuroblastoma Using Collagen-Based Scaffolds

This paper lists the steps required to seed neuroblastoma cell lines on previously described three-dimensional collagen-based scaffolds, maintain cell growth for a predetermined timeframe, and retrieve scaffolds for several cell growth and cell behavior analyses and downstream applications, adaptable to satisfy a range of experimental aims.

Neuroblastoma is the most common extracranial solid tumor in children, accounting for 15% of overall pediatric cancer deaths. The native tumor tissue is a ...

Cancer Research

Engineered 3D Silk-collagen-based Model of Polarized Neural Tissue

Despite huge efforts to decipher the anatomy, composition and function of the brain, it remains the least understood organ of the human body. To gain a deeper comprehension of the neural system scientists aim to simplistically reconstruct the tissue by assembling it in vitro from basic building blocks using a tissue engineering approach. Our group developed a tissue-engineered silk and collagen-based 3D brain-like model resembling the white and gray matter of the cortex. The model consists of silk porous sponge, which is pre-seeded with rat brain-derived neurons, immersed in soft collagen matrix. Polarized neuronal outgrowth and network formation is observed with separate axonal and cell body localization. This compartmental architecture allows for the unique development of niches mimicking native neural tissue, thus enabling research on neuronal network assembly, axonal guidance, cell-cell and cell-matrix interactions and electrical functions.

Insight into the complex actions of the brain requires advanced research tools. Here we demonstrate a novel silk-collagen-based 3D engineered model of neural tissue resembling brain-like architecture. The model can be used to study neuronal network assembly, axonal guidance, cell-cell interactions and electrical activity.

Despite huge efforts to decipher the anatomy, composition and function of the brain, it remains the least understood organ of the human body. To gain a ...

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Historically, most cellular processes have been studied in only 2 dimensions. While these studies have been informative about general cell signaling mechanisms, they neglect important cellular cues received from the structural and mechanical properties of the local microenvironment and extracellular matrix (ECM). To understand how cells interact within a physiological ECM, it is important to study them in the context of 3 dimensional assays. Cell migration, cell differentiation, and cell proliferation are only a few processes that have been shown to be impacted by local changes in the mechanical properties of a 3-dimensional ECM. Collagen I, a core fibrillar component of the ECM, is more than a simple structural element of a tissue. Under normal conditions, mechanical cues from the collagen network direct morphogenesis and maintain cellular structures. In diseased microenvironments, such as the tumor microenvironment, the collagen network is often dramatically remodeled, demonstrating altered composition, enhanced deposition and altered fiber organization. In breast cancer, the degree of fiber alignment is important, as an increase in aligned fibers perpendicular to the tumor boundary has been correlated to poorer patient prognosis1. Aligned collagen matrices result in increased dissemination of tumor cells via persistent migration2,3. The following is a simple protocol for embedding cells within a 3-dimensional, fibrillar collagen hydrogel. This protocol is readily adaptable to many platforms, and can reproducibly generate both aligned and random collagen matrices for investigation of cell migration, cell division, and other cellular processes in a tunable, 3-dimensional, physiological microenvironment.

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Collagen is a core component of the ECM, and provides essential cues for several cellular processes ranging from migration to differentiation and proliferation. Provided here is a protocol for embedding cells within 3D collagen hydrogels, and a more advanced technique for generating randomized or aligned collagen matrices using PDMS microchannels.

Historically, most cellular processes have been studied in only 2 dimensions.  While these studies have been informative about general cell signaling ...

Three-dimensional Tissue Engineered Aligned Astrocyte Networks to Recapitulate Developmental Mechanisms and Facilitate Nervous System Regeneration

Neurotrauma and neurodegenerative disease often result in lasting neurological deficits due to the limited capacity of the central nervous system (CNS) to replace lost neurons and regenerate axonal pathways. However, during nervous system development, neuronal migration and axonal extension often occur along pathways formed by other cells, referred to as &#34;living scaffolds&#34;. Seeking to emulate these mechanisms and to design a strategy that circumvents the inhibitory environment of the CNS, this manuscript presents a protocol to fabricate tissue engineered astrocyte-based &#34;living scaffolds&#34;. To create these constructs, we employed a novel biomaterial encasement scheme to induce astrocytes to self-assemble into dense three-dimensional bundles of bipolar longitudinally-aligned somata and processes. First, hollow hydrogel micro-columns were assembled, and the inner lumen was coated with collagen extracellular-matrix. Dissociated cerebral cortical astrocytes were then delivered into the lumen of the cylindrical micro-column and, at a critical inner diameter of &#60;350 &#181;m, spontaneously self-aligned and contracted to produce long fiber-like cables consisting of dense bundles of astrocyte processes and collagen fibrils measuring &#60;150 &#181;m in diameter yet extending several cm in length. These engineered living scaffolds exhibited &#62;97% cell viability and were virtually exclusively comprised of astrocytes expressing a combination of the intermediate filament proteins glial-fibrillary acidic protein (GFAP), vimentin, and nestin. These aligned astrocyte networks were found to provide a permissive substrate for neuronal attachment and aligned neurite extension. Moreover, these constructs maintain integrity and alignment when extracted from the hydrogel encasement, making them suitable for CNS implantation. These preformed constructs structurally emulate key cytoarchitectural elements of naturally occurring glial-based &#34;living scaffolds&#34; in vivo. As such, these engineered living scaffolds may serve as test-beds to study neurodevelopmental mechanisms in vitro or facilitate neuroregeneration by directing neuronal migration and/or axonal pathfinding following CNS degeneration in vivo.

We showcase the development of self-assembled, three-dimensional bundles of longitudinally aligned astrocytic somata and processes within a novel biomaterial encasement. These engineered &#34;living scaffolds&#34;, exhibiting micron-scale diameter yet extending centimeters in length, may serve as test-beds to study neurodevelopmental mechanisms or facilitate neuroregeneration by directing neuronal migration and/or axonal pathfinding.

Neurotrauma and neurodegenerative disease often result in lasting neurological deficits due to the limited capacity of the central nervous system (CNS) to ...

Improved 3D Hydrogel Cultures of Primary Glial Cells for In Vitro Modelling of Neuroinflammation

In the central nervous system, numerous acute injuries and neurodegenerative disorders, as well as implanted devices or biomaterials engineered to enhance function result in the same outcome: excess inflammation leads to gliosis, cytotoxicity, and/or formation of a glial scar that collectively exacerbate injury or prevent healthy recovery. With the intent of creating a system to model glial scar formation and study inflammatory processes, we have generated a 3D cell scaffold capable of housing primary cultured glial cells: microglia that regulate the foreign body response and initiate the inflammatory event, astrocytes that respond to form a fibrous scar, and oligodendrocytes that are typically vulnerable to inflammatory injury. The present work provides a detailed step-by-step method for the fabrication, culture, and microscopic characterization of a hyaluronic acid-based 3D hydrogel scaffold with encapsulated rat brain-derived glial cells. Further, protocols for characterization of cell encapsulation and the hydrogel scaffold by confocal immunofluorescence and scanning electron microscopy are demonstrated, as well as the capacity to modify the scaffold with bioactive substrates, with incorporation of a commercial basal lamina mixture to improved cell integration.

Improved 3D Hydrogel Cultures of Primary Glial Cells for In Vitro Modelling of Neuroinflammation

Herein, we present a protocol for the 3D culture of rat brain-derived glia cells, including astrocytes, microglia, and oligodendrocytes. We demonstrate primary cell culture, methacrylated hyaluronic acid (HAMA) hydrogel synthesis, HAMAphoto-polymerization and cell encapsulation, and sample processing for confocal and scanning electron microscopic imaging.

In the central nervous system, numerous acute injuries and neurodegenerative disorders, as well as implanted devices or biomaterials engineered to enhance ...

Production of Elastin-like Protein Hydrogels for Encapsulation and Immunostaining of Cells in 3D

Two-dimensional (2D) tissue culture techniques have been essential for our understanding of fundamental cell biology. However, traditional 2D tissue culture systems lack a three-dimensional (3D) matrix, resulting in a significant disconnect between results collected in vitro and in vivo. To address this limitation, researchers have engineered 3D hydrogel tissue culture platforms that can mimic the biochemical and biophysical properties of the in vivo cell microenvironment. This research has motivated the need to develop material platforms that support 3D cell encapsulation and downstream biochemical assays. Recombinant protein engineering offers a unique toolset for 3D hydrogel material design and development by allowing for the specific control of protein sequence and therefore, by extension, the potential mechanical and biochemical properties of the resultant matrix. Here, we present a protocol for the expression of recombinantly-derived elastin-like protein (ELP), which can be used to form hydrogels with independently tunable mechanical properties and cell-adhesive ligand concentration. We further present a methodology for cell encapsulation within ELP hydrogels and subsequent immunofluorescent staining of embedded cells for downstream analysis and quantification.

Recombinant protein-engineered hydrogels are advantageous for 3D cell culture as they allow for complete tunability of the polymer backbone and therefore, the cell microenvironment. Here, we describe the process of recombinant elastin-like protein purification and its application in 3D hydrogel cell encapsulation.

Two-dimensional (2D) tissue culture techniques have been essential for our understanding of fundamental cell biology. However, traditional 2D tissue ...

In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures

During neuronal development, axons navigate the cortical environment to reach their final destinations and establish synaptic connections. Growth cones -the sensory structures located at the distal tips of developing axons- execute this process. Studying the structure and dynamics of the growth cone is crucial to understanding axonal development and the interactions with the surrounding central nervous system (CNS) that enable it to form neural circuits. This is essential when devising methods to reintegrate axons into neural circuits following injury in fundamental research and pre-clinical contexts. Thus far, the general understanding of growth cone dynamics is primarily founded on studies of neurons cultured in two dimensions (2D). Although undoubtedly fundamental to the current knowledge of growth cone structural dynamics and response to stimuli, 2D studies misrepresent the physiological three-dimensional (3D) environment encountered by neuronal growth cones in intact CNS tissue. More recently, collagen gels were employed to overcome some of these limitations, enabling the investigation of neuronal development in 3D. However, both synthetic 2D and 3D environments lack signaling cues within CNS tissue, which direct the extension and pathfinding of developing axons. This protocol provides a method for studying axons and growth cones using organotypic brain slices, where developing axons encounter physiologically relevant physical and chemical cues. By combining fine-tuned in utero and ex utero electroporation to sparsely deliver fluorescent reporters along with super-resolution microscopy, this protocol presents a methodological pipeline for the visualization of axon and growth cone dynamics in situ. Furthermore, a detailed toolkit description of the analysis of long-term and live-cell imaging data is included.

In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures

This protocol demonstrates a straightforward and robust method to study in situ axon growth and growth cone dynamics. It describes how to prepare ex vivo physiologically relevant acute brain slices and provides a user-friendly analysis pipeline.

During neuronal development, axons navigate the cortical environment to reach their final destinations and establish synaptic connections. Growth cones ...

Generation of 3-D Collagen-based Hydrogels to Analyze Axonal Growth and Behavior During Nervous System Development

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Chapters in this video

Organotypic Collagen I Assay: A Malleable Platform to Assess Cell Behaviour in a 3-Dimensional Context

Dissection and Culture of Chick Statoacoustic Ganglion and Spinal Cord Explants in Collagen Gels for Neurite Outgrowth Assays

Dissection and Culture of Mouse Dopaminergic and Striatal Explants in Three-Dimensional Collagen Matrix Assays

Three-Dimensional In Vitro Biomimetic Model of Neuroblastoma Using Collagen-Based Scaffolds

Engineered 3D Silk-collagen-based Model of Polarized Neural Tissue

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Three-dimensional Tissue Engineered Aligned Astrocyte Networks to Recapitulate Developmental Mechanisms and Facilitate Nervous System Regeneration

Improved 3D Hydrogel Cultures of Primary Glial Cells for In Vitro Modelling of Neuroinflammation

Production of Elastin-like Protein Hydrogels for Encapsulation and Immunostaining of Cells in 3D

In Situ Visualization of Axon Growth and Growth Cone Dynamics in Acute Ex Vivo Embryonic Brain Slice Cultures