This study was supported by the Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Scientific Research 17H05661 and 18K19903, Core-2-core program, and Beyond AI institute.

<ol>
	<li>Raper, J., Mason, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+strategies+of+axonal+pathfinding.">Cellular strategies of axonal pathfinding.</a> Cold Spring Harbor Perspective Biology. 2 (9), 001933 (2010).</li><li>Ito, Y., 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=RIPK1+mediates+axonal+degeneration+by+promoting+inflammation+and+necroptosis+in+ALS.">RIPK1 mediates axonal degeneration by promoting inflammation and necroptosis in ALS.</a> Science. 353 (6299), 603-608 (2016).</li><li>Fujimori, K., 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=Modeling+sporadic+ALS+in+iPSC-derived+motor+neurons+identifies+a+potential+therapeutic+agent.">Modeling sporadic ALS in iPSC-derived motor neurons identifies a potential therapeutic agent.</a> Nature Medicine. 24 (10), 1579-1589 (2018).</li><li>Chen, H., 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=Modeling+ALS+with+iPSCs+Reveals+that+Mutant+SOD1+Misregulates+Neurofilament+Balance+in+Motor+Neurons.">Modeling ALS with iPSCs Reveals that Mutant SOD1 Misregulates Neurofilament Balance in Motor Neurons.</a> Cell Stem Cell. 14 (6), 796-809 (2014).</li><li>Osaki, T., Uzel, S. G. M., Kamm, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microphysiological+3D+model+of+amyotrophic+lateral+sclerosis+(ALS)+from+human+iPS-derived+muscle+cells+and+optogenetic+motor+neurons.">Microphysiological 3D model of amyotrophic lateral sclerosis (ALS) from human iPS-derived muscle cells and optogenetic motor neurons.</a> Science Advances. 4 (10), (2018).</li><li>Imamura, K., 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=The+Src/c-Abl+pathway+is+a+potential+therapeutic+target+in+amyotrophic+lateral+sclerosis.">The Src/c-Abl pathway is a potential therapeutic target in amyotrophic lateral sclerosis.</a> Science Translational Medicine. 9 (391), (2017).</li><li>Wang, L., Marquardt, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+axons+tell+each+other:+axon-axon+signaling+in+nerve+and+circuit+assembly.">What axons tell each other: axon-axon signaling in nerve and circuit assembly.</a> Current Opinion in Neurobiology. 23 (6), 974-982 (2013).</li><li>Kawada, 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=Generation+of+a+Motor+Nerve+Organoid+with+Human+Stem+Cell-Derived+Neurons.">Generation of a Motor Nerve Organoid with Human Stem Cell-Derived Neurons.</a> Stem Cell Reports. 9 (5), 1441-1449 (2017).</li><li>Nagendran, T., Poole, V., Harris, J., Taylor, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+Pre-Assembled+Plastic+Microfluidic+Chips+for+Compartmentalizing+Primary+Murine+Neurons.">Use of Pre-Assembled Plastic Microfluidic Chips for Compartmentalizing Primary Murine Neurons.</a> JoVE. (141), e58421 (2018).</li><li>Paranjape, S. R., Nagendran, T., Poole, V., Harris, J., Taylor, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartmentalization+of+Human+Stem+Cell-Derived+Neurons+within+Pre-Assembled+Plastic+Microfluidic+Chips.">Compartmentalization of Human Stem Cell-Derived Neurons within Pre-Assembled Plastic Microfluidic Chips.</a> JoVE. (147), e59250 (2019).</li><li>Chambers, S. 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=Combined+small-molecule+inhibition+accelerates+developmental+timing+and+converts+human+pluripotent+stem+cells+into+nociceptors.">Combined small-molecule inhibition accelerates developmental timing and converts human pluripotent stem cells into nociceptors.</a> Nature Biotechnology. 30 (7), 715-720 (2012).</li><li>Rimington, R. P., Fleming, J. W., Capel, A. J., Wheeler, P. C., Lewis, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bioengineered+model+of+the+human+motor+unit+with+physiologically+functional+neuromuscular+junctions.">Bioengineered model of the human motor unit with physiologically functional neuromuscular junctions.</a> bioRxiv. , (2020).</li><li>Cullen, D. K., 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=Bundled+Three-Dimensional+Human+Axon+Tracts+Derived+from+Brain+Organoids.">Bundled Three-Dimensional Human Axon Tracts Derived from Brain Organoids.</a> iScience. 21, 57-67 (2019).</li><li>Giandomenico, S. 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=Cerebral+organoids+at+the+air-liquid+interface+generate+diverse+nerve+tracts+with+functional+output.">Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output.</a> Nature Neurosciences. 22 (4), 669-679 (2019).</li><li>Egawa, N., 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=Drug+screening+for+ALS+using+patient-specific+induced+pluripotent+stem+cells.">Drug screening for ALS using patient-specific induced pluripotent stem cells.</a> Science Translational Medicine. 4 (145), (2012).</li><li>Sances, S., 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=Modeling+ALS+with+motor+neurons+derived+from+human+induced+pluripotent+stem+cells.">Modeling ALS with motor neurons derived from human induced pluripotent stem cells.</a> Nature Neurosciences. 19 (4), 542-553 (2016).</li><li>Qu, Q., 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=High-efficiency+motor+neuron+differentiation+from+human+pluripotent+stem+cells+and+the+function+of+Islet-1.">High-efficiency motor neuron differentiation from human pluripotent stem cells and the function of Islet-1.</a> Nature Communications. 5 (1), 3449 (2014).</li><li>Kirihara, T., 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+Human+Induced+Pluripotent+Stem+Cell-Derived+Tissue+Model+of+a+Cerebral+Tract+Connecting+Two+Cortical+Regions.">A Human Induced Pluripotent Stem Cell-Derived Tissue Model of a Cerebral Tract Connecting Two Cortical Regions.</a> iScience. 14, 301-311 (2019).</li><li>Rigamonti, A., 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=Large-Scale+Production+of+Mature+Neurons+from+Human+Pluripotent+Stem+Cells+in+a+Three-Dimensional+Suspension+Culture+System.">Large-Scale Production of Mature Neurons from Human Pluripotent Stem Cells in a Three-Dimensional Suspension Culture System.</a> Stem Cell Reports. 6 (6), 993-1008 (2016).</li><li>Yan, Y., Song, L., Madinya, J., Ma, T., Li, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Derivation+of+Cortical+Spheroids+from+Human+Induced+Pluripotent+Stem+Cells+in+a+Suspension+Bioreactor.">Derivation of Cortical Spheroids from Human Induced Pluripotent Stem Cells in a Suspension Bioreactor.</a> Tissue Engineering Part A. 24 (5-6), 418-431 (2017).</li></ol>

In part of this protocol, a patent has been licensed to Jiksak Bioengineering, Inc. which was founded by Jiro Kawada.

This protocol describes the formation of a motor nerve organoid (MNO) which has an axon bundle extended from a motor neuron spheroid generated from human iPS cells. The formed axon bundle is thick, flexible, and well-organized in unidirectional structures. By dissecting the axon bundle, high-purity axonal protein and RNA can be obtained sufficiently for biochemical analyses. Neuronal activity can be measured in axon bundles and spheroids with calcium imaging. Contamination of nuclear and dendritic proteins in the axonal lysate was not detected by western blotting, demonstrating that our method efficiently separated axons from cell bodies and dendrites.
One of the advantages of this protocol is the rapid differentiation and generation of MNO equipped with an axon bundle, in which all processes can be done in 4 weeks with the 3D protocol and 5-6 weeks using the 2D protocol. This is short compared to other protocols which typically take 3-4 weeks to simply differentiate into MN from embryonic stem cells and iPS cells17 and it takes an additional 2-4 weeks to obtain axonal elongation. The 3D protocol is generally preferred over the 2D protocol because of the shorter differentiation time, fewer steps, and reduced technical risks without the dissociation step compared to the 2D protocol. The microfluidic-based tissue culture chip was designed in a manner so that the axons of MNS can elongate toward the other compartment through the microchannel, which facilitates formation of a bundle of axons by inducing axo-axonal interactions and affinity between axons. Because of the simple experimental set-up, all the protocols described here can not only be performed by bioengineers, who are familiar with the manipulation of a tissue culture chip, but also biologists and neuroscientists who are not familiar with microfluidics and microfabrication techniques. It should be noted that Steps 1 and 2 can be also performed by using an external fabrication service.
One of the critical steps to accomplish the protocol is a sequential change of culture medium. It is advised to completely change the culture medium at each step during the differentiation so that factors in the spent medium do not disturb the MN differentiation. Another critical point of this protocol is to maintain undifferentiated iPS cells in good quality. Quality of the initial iPS cell culture significantly affects the efficiency to obtain motor neurons and MNO. Another point is that the diameter of MNS should be smaller than the size of the hole of the chip (1.5 mm). Larger spheroids cannot enter the chamber, and potentially experience severe hypoxic necrosis in the center part. The size of MNSs can be controlled by changing an initial seeding number of iPS cells (in 3D protocol) or motor neurons (in 2D protocol). The seeding density of cells should be optimized for each iPS cell line.
Compartmentalized microfluidic devices with microgrooves and small pore filters have been widely used to separate axons from cell bodies and dendrites. This technique can also separate axons from cell bodies and dendrite, with superior abundance of axons in bundled tissues. Compared to the other methods, one major limitation of this method is that it cannot separate two different culture media in the current design of the tissue culture chip, which hinders capability of co-culture of two different cells that require two distinct media. Another limitation is that the PDMS chip put predetermined restriction on size of the tissue. A spheroid larger than the hole cannot enter the chamber, and the axon bundle cannot grow thicker than the width of microfluidic channel.
This method can be applied to other types of neurons. Our group has shown capability to model a cerebral tract by using a modified method combined with cerebral organoid techniques18. Cortical spheroids were introduced into both compartments and the axons spontaneously elongated reciprocally toward each spheroid, and subsequently an axon bundle formed spontaneously. As a result, two cortical spheroids can be connected through an axon bundle, and the tissue could be obtained as one piece. This demonstrates that the approach is highly versatile to form axon bundle tissues regardless of neuronal cell types. In this protocol, human iPS cells were used, however, other stem cells including human ES cells and human neural stem cells may be used with modifications to the presented protocol. 3D spheroids of neurons can be generated by diverse protocols19,20. This method of making tissues with an axon bundle can potentially be combined in the future with the other differentiation protocols for making 3D MN spheroid. In addition, the thickness and the length of the axon bundle can be controlled by simply changing the width and height of microchannels of the tissue culture chip for future developments.
We believe that this protocol can be used for drug testing and screening and can contribute to the understanding of mechanisms underlying the development and diseases of axon fascicles.

Spinal motor neurons (MN) extend axons to skeletal muscles to control body motion. Their axonal trajectories are highly organized and regulated in the developmental process. Despite many studies on axon extension and guidance1, mechanisms for organized axon bundle formation are still under investigation. Axons of motor neurons are often damaged by neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS)2, but pathophysiological mechanisms of the damage on axon fascicles are poorly understood. Thus, a physiological and pathological model to recapitulate axon bundle formation and regression is required in the field.
A human stem cell-derived motor neuron is a promising platform for understanding the development and diseases such as ALS3. Human induced pluripotent stem cells (iPS cells) can be used to model diseases using patient-derived cells. To date, various differentiation methods from pluripotent stem cells into MN have been reported4,5,6. However, axons of neurons in two-dimensional culture are randomly oriented and do not recapitulate in vivo microenvironment within developing nerves in which axons are unidirectionally assembled through dense axo-axonal interactions7. To overcome this issue, we have developed a technique to generate a three-dimensional tissue resembling motor nerve from human iPS cells8, and named the tissue as motor nerve organoid (MNO). The MNO consists of cell bodies located in a motor neuron spheroid (MNS) and an axonal fascicle extended out from the spheroid. The axons in the fascicle are unidirectionally oriented, which resembles axons in developing motor nerves. Hence, MNOs uniquely provide a physiological axonal microenvironment, which was not done by any other previously developed neuronal culture methods.
In this protocol, we describe methods for tissue culture chips fabrication, rapid motor neuron differentiation, and motor nerve organoid formation in developed chips. Our tissue culture chip is very simple, and it only contains a compartment for accepting a spheroid, a microchannel for forming an axon bundle, and a compartment for housing axon terminals. The device does not contain complex structures including microgrooves or micropore filters that are often used to separate axons and cell bodies by size9,10. Hence our devices can be easily fabricated by following the steps described in this protocol if a photolithography setup is available.
Rapid differentiation of human iPS cells is achieved with an optimized combination of inducing and patterning factors (SB431542, LDN-193189, retinoic acid (RA), and smoothened agonist (SAG)) and acceleration factors (SU5402 and DAPT). It has been reported that the combination of SU5402 and DAPT accelerates the differentiation of peripheral neurons and neural crest cells11. In this protocol, we offer three different methods to generate MNOs, so that readers can decide on a method most suited to their needs. We recommend performing differentiation of human iPS cells after forming a spheroid (the 3D method), since the differentiated MNS can be transferred directly into a tissue culture chip. Alternatively, human iPS cells can be differentiated into motor neurons in monolayer (2D) culture, and then created into three-dimensional motor neuron spheroids as we previously reported8. We have updated the protocol, and with the three-dimensional differentiation method described in this protocol, the transition from 2D to 3D can be avoided and MNOs can be obtained with shorter differentiation time, fewer steps, and reduced technical risks without the dissociation step. Commercially available neurons can be also used to generate MNS to reduce the time for differentiation.
To generate an MNO, we cultured an MNS in the tissue culture chip. The axons elongate from the spheroid and extend into the microchannel in which axons gather and align unidirectionally. This facilitates axo-axonal interaction and spontaneous formation of a tightly assembled unidirectional bundle tissue of axons in the microchannel, which is uniquely achieved by this protocol, whereas either spontaneous bundle formation or guided axonal orientation alone can be achieved by other protocols12,13,14. In a typical experiment, few cells migrate out from spheroids to the microchannel and most cells stay nearby spheroids. This method allows axons to be spontaneously separated out from the spheroids without using size-dependent physical barriers (e.g., microgrooves or micropore filters) to separate axons from cell bodies.
The resultant MNO can be subjected to various examinations, including morphological, biochemical, and physical analyses. The cell body and extended axon bundle can be physically isolated by cutting and can be separately analyzed for downstream experiments, e.g., biochemical assays. Biological materials including RNA and protein can be isolated from just a few axon bundles for regular biochemical assays including RT-PCR and western blotting. Here, we describe a protocol for generating motor nerve organoid from iPS cells, which offers an attractive physiological and pathological model to study the mechanism underlying development and disease of axon fascicles.

<table>
	<tbody>
		<tr>
			<td>(Tridecafluoro-1,1,2,2-tetrahydrooctyl)-1-trichlorosilane</td>
			<td>Sigma</td>
			<td>440302</td>
			<td></td>
		</tr>
		<tr>
			<td>16% Paraformaldehyde (formaldehyde) aqueous solution</td>
			<td>Electron Microscopy Sciences</td>
			<td>15710</td>
			<td></td>
		</tr>
		<tr>
			<td>200&#181;l Wide Bore Pipet Tips</td>
			<td>BMBio</td>
			<td>BMT-200WRS</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well plates</td>
			<td>Violamo</td>
			<td>2-8588-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Accutase</td>
			<td>ICT</td>
			<td>AT104</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement (50X)</td>
			<td>Gibco</td>
			<td>17504044</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Sigma</td>
			<td>A6003</td>
			<td></td>
		</tr>
		<tr>
			<td>Brain-derived neurotrophic factor (BDNF)</td>
			<td>Wako</td>
			<td>020-12913</td>
			<td></td>
		</tr>
		<tr>
			<td>CO2 incubator</td>
			<td>Panasonic</td>
			<td>MCO-18AIC</td>
			<td></td>
		</tr>
		<tr>
			<td>Cryostor CS10</td>
			<td>Stem Cell Technologies</td>
			<td>07959</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPT</td>
			<td>Sigma</td>
			<td>D5942</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F12</td>
			<td>Sigma</td>
			<td>D8437</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluo-4 AM</td>
			<td>Dojindo Laboratories</td>
			<td>CS22</td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX Supplement</td>
			<td>Gibco</td>
			<td>35050-061</td>
			<td></td>
		</tr>
		<tr>
			<td>Growth factor reduced Matrigel (basement membrane matrix)</td>
			<td>Corning</td>
			<td>354230</td>
			<td></td>
		</tr>
		<tr>
			<td>HB9 Antibody</td>
			<td>Santa Cruz</td>
			<td>sc-22542</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Wako</td>
			<td>085-09355</td>
			<td></td>
		</tr>
		<tr>
			<td>Hoechst 33342</td>
			<td>Sigma</td>
			<td>14533</td>
			<td></td>
		</tr>
		<tr>
			<td>iCell motor neuron (commercially available human iPS cell-derived motor neurons)</td>
			<td>Cellular Dynamics</td>
			<td>R1051</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropyl alcohol (IPA)</td>
			<td>Wako</td>
			<td>166-04836</td>
			<td></td>
		</tr>
		<tr>
			<td>Knock Out Serum Replacement</td>
			<td>Gibco</td>
			<td>10828028</td>
			<td></td>
		</tr>
		<tr>
			<td>LDN193189</td>
			<td>Sigma</td>
			<td>SML0559</td>
			<td></td>
		</tr>
		<tr>
			<td>MEA probe</td>
			<td>Alpha MED Scientific inc</td>
			<td>MED-P5004A</td>
			<td></td>
		</tr>
		<tr>
			<td>MEM Non-essential Amino Acid Solution (100x) (NEAA)</td>
			<td>Sigma</td>
			<td>M7145</td>
			<td></td>
		</tr>
		<tr>
			<td>Microscope Glass</td>
			<td>Matsunami</td>
			<td>S9111</td>
			<td></td>
		</tr>
		<tr>
			<td>mTeSR Plus</td>
			<td>Stem Cell Technologies</td>
			<td>05825</td>
			<td></td>
		</tr>
		<tr>
			<td>N2 supplement</td>
			<td>Wako</td>
			<td>141-08941</td>
			<td></td>
		</tr>
		<tr>
			<td>Neurobasal medium</td>
			<td>Gibco</td>
			<td>21103049</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-streptomycin</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Photoresist SU-8 2100</td>
			<td>Microchem</td>
			<td>#SU-8 2100</td>
			<td></td>
		</tr>
		<tr>
			<td>Prime surface 96U</td>
			<td>Sumitomo Bakelite</td>
			<td>MS-9096U</td>
			<td></td>
		</tr>
		<tr>
			<td>ReLeSR (passaging reagent)</td>
			<td>Stem Cell Technologies</td>
			<td>05872</td>
			<td></td>
		</tr>
		<tr>
			<td>Retinoic acid</td>
			<td>Wako</td>
			<td>186-01114</td>
			<td></td>
		</tr>
		<tr>
			<td>SAG</td>
			<td>Sigma</td>
			<td>SML1314</td>
			<td></td>
		</tr>
		<tr>
			<td>SB431542</td>
			<td>Wako</td>
			<td>192-16541</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicon wafer</td>
			<td>SUMCO</td>
			<td>PW-100-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Silpot 184 w/c kit</td>
			<td>Dow Toray</td>
			<td>Silpot 184 w/c kit</td>
			<td></td>
		</tr>
		<tr>
			<td>Smi32 Antibody</td>
			<td>Biolegend</td>
			<td>801701</td>
			<td></td>
		</tr>
		<tr>
			<td>SU5402</td>
			<td>Sigma</td>
			<td>SML0443</td>
			<td></td>
		</tr>
		<tr>
			<td>SU-8 Developer</td>
			<td>Microchem</td>
			<td>Y020100</td>
			<td></td>
		</tr>
		<tr>
			<td>Synapsin I Antibody</td>
			<td>Millipore</td>
			<td>Ab1543</td>
			<td></td>
		</tr>
		<tr>
			<td>TrypLE Express liquid without phenol red (dissociation solution)</td>
			<td>Gibco</td>
			<td>12604-021</td>
			<td></td>
		</tr>
		<tr>
			<td>Tuj1 Antibody</td>
			<td>Biolegend</td>
			<td>801202</td>
			<td></td>
		</tr>
		<tr>
			<td>Y-27632</td>
			<td>Wako</td>
			<td>030-24021</td>
			<td></td>
		</tr>
	</tbody>
</table>

three-dimensional motor nerve organoid generation

A fascicle of axons is one of the major structural motifs observed in the nervous system. Disruption of axon fascicles could cause developmental and neurodegenerative diseases. Although numerous studies of axons have been conducted, our understanding of formation and dysfunction of axon fascicles is still limited due to the lack of robust three-dimensional in vitro models. Here, we describe a step-by-step protocol for the rapid generation of a motor nerve organoid (MNO) from human induced pluripotent stem (iPS) cells in a microfluidic-based tissue culture chip. First, fabrication of chips used for the method is described. From human iPS cells, a motor neuron spheroid (MNS) is formed. Next, the differentiated MNS is transferred into the chip. Thereafter, axons spontaneously grow out of the spheroid and assemble into a fascicle within a microchannel equipped in the chip, which generates an MNO tissue carrying a bundle of axons extended from the spheroid. For the downstream analysis, MNOs can be taken out of the chip to be fixed for morphological analyses or dissected for biochemical analyses, as well as calcium imaging and multi-electrode array recordings. MNOs generated with this protocol can facilitate drug testing and screening and can contribute to understanding of mechanisms underlying development and diseases of axon fascicles.

Motor neurons were differentiated within 12-14 days in 3D differentiation procedures (Figure 4 and Figure 5). Importantly, more than 60% of cells expressed motor neuron marker HB9 during the differentiation. Immunohistochemistry revealed that approximately 80% of the cells in the MNS were SMI32-positive motor neurons. HB9 and SMI32 are the established early-stage motor neuron markers15,16. The expression of HB9 and SMI32 are the key parameters that need to be confirmed to ensure cellular identity of motor neurons. After the introduction of an MNS into the culture chip, axons extend into the channel and an axon bundle forms. Due to microchannels serving as physical guides, axons elongate from the MNS and form a bundle by axo-axonal interaction (Figure 6A). It is essential to confirm the formation of the axon bundle by microscopic observation to confirm the generation of an MNO. A successful MNO bears an axon bundle wider than 50 &#956;m and few isolated axons out of the bundle in the channel. Initial elongation of axons can be observed 24 hours after the introduction of the spheroid. Within the next 3-4 days, the axons reached to the center of the microchannel and then reaches to the other end within an additional 10 days (Figure 6A). Consequently, the axons assembled and formed a straight and unidirectional bundle in 2-3 weeks in a chip, and neuronal activities were observed thereafter.
Motor nerve organoids can be collected from the chip by detaching the PDMS from the microscope glass for biological analysis (Figure 6B). Axon bundles and cell bodies can be dissected and isolated by cutting using a surgical knife or tweezer under a microscope (Figure 6B). These biological materials including RNA and protein can be used for regular biochemical assays such as RT-PCR and western blotting. In axon bundles of MNOs, nuclear or dendritic maker proteins are not detected in western blotting (Figure 6C).
In combination with a calcium indicator (Fluo-4 AM), neuronal activity can be captured in the tissue culture chip. Spontaneous activity of motor neurons in the spheroid and the axon bundle were observed within the MNO. Also, the neural activities were observed by using a multi-electrode array system.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61544/61544fig01.jpg" /> 
Figure 1: The dimension of PDMS tissue culture chip. 
(A) Photomask of the tissue culture chip. (B) Dimensions of microchannel in the tissue culture chip. The diameter of the base chamber for holding motor neuron spheroid is 2 mm and the hole of PDMS above the chamber is 1.5 mm. The width and height of a microchannel bridging two chambers are both 150 &#956;m. <a href="https://www.jove.com/files/ftp_upload/61544/61544fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/61544/61544fig02.jpg" /> 
Figure 2: Schematic illustration of motor neuron differentiation. 
(A) The differentiation steps involved neural induction, patterning into motor neuron lineage, and maturation of motor neurons. (B) Two options to create motor neuron spheroid (MNS) from iPS cells: 3D protocol, and a 2D protocol with dissociation step of motor neurons. Motor nerve organoid (MNO) can be obtained by both protocols. <a href="https://www.jove.com/files/ftp_upload/61544/61544fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/61544/61544fig03.jpg" /> 
Figure 3: Step by step protocol for basement membrane matrix coating and motor neuron spheroid introduction. 
(A) Basement membrane matrix coating in the channel of the tissue culture chip. (B) MNS introduction into the hole of the chip. (C) Culture medium change by aspiration of exhausted medium. <a href="https://www.jove.com/files/ftp_upload/61544/61544fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/61544/61544fig04.jpg" /> 
Figure 4: 2D and 3D motor neuron differentiation. 
(A) Time course of representative 3D MNS differentiation (3D protocol). The size of the MNS gradually increased over time. Scale bar: 500 &#956;m. (B) Time course of 2D differentiation on -D2, D0, D1, D6, D12 (2D protocol). Scale bar: 500 &#956;m. <a href="https://www.jove.com/files/ftp_upload/61544/61544fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/61544/61544fig05.jpg" /> 
Figure 5: Characterization of motor neurons. 
(A) (Left) A cryosection of a MNS stained with SMI-32 antibody and DAPI. (Middle) A phase-contrast image of replated MNS on a basement membrane matrix-coated surface. Axonal elongation was observed. (Right) Axons of replated MNS stained with Synapsin I and Tuj1 antibodies. Scale bar: 500 &#956;m (Left and Middle) and 50&#956;m (Right). (B) A representative image of 2D motor neurons immunostained with Tuj and HB9 antibodies. Scale bar: 200 &#956;m. <a href="https://www.jove.com/files/ftp_upload/61544/61544fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/61544/61544fig06.jpg" /> 
Figure 6: Characterization of a motor nerve organoid (MNO) generated in a culture chip. 
(A) Representative images of axon elongation and thick axon bundle formation on D32. Scale bar: 500 &#956;m. (B) Immunostaining of motor nerve organoid (MNO) by SMI-32 and DAPI. Axons and cell bodies can be isolated by physically cutting. Scale bar: 1 mm. (C) Purity of the protein from axons and cell bodies quantified by western blotting. MAP2, a dendritic marker, was not detected in axonal protein, whereas axonal marker Tau1 is enriched in the axonal protein. <a href="https://www.jove.com/files/ftp_upload/61544/61544fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

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Three-Dimensional Motor Nerve Organoid Generation

This protocol provides a comprehensive procedure to fabricate human iPS cell-derived motor nerve organoid through spontaneous assembly of a robust bundle of axons extended from a spheroid in a tissue culture chip.

A fascicle of axons is one of the major structural motifs observed in the nervous system. Disruption of axon fascicles could cause developmental and ...

three-dimensional-motor-nerve-organoid-generation

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JoVE Journal

Neuroscience

8.8K Views.  The University of Tokyo. This protocol provides a comprehensive procedure to fabricate human iPS cell-derived motor nerve organoid through spontaneous assembly of a robust bundle of axons extended from a spheroid in a tissue culture chip.

Video: Three-Dimensional Motor Nerve Organoid Generation

Motor Nerve Transection and Time-lapse Imaging of Glial Cell Behaviors in Live Zebrafish

The nervous system is often described as a hard-wired component of the body even though it is a considerably fluid organ system that reacts to external stimuli in a consistent, stereotyped manner, while maintaining incredible flexibility and plasticity. Unlike the central nervous system (CNS), the peripheral nervous system (PNS) is capable of significant repair, but we have only just begun to understand the cellular and molecular mechanisms that govern this phenomenon. Using zebrafish as a model system, we have the unprecedented opportunity to couple regenerative studies with in vivo imaging and genetic manipulation. Peripheral nerves are composed of axons surrounded by layers of glia and connective tissue. Axons are ensheathed by myelinating or non-myelinating Schwann cells, which are in turn wrapped into a fascicle by a cellular sheath called the perineurium. Following an injury, adult peripheral nerves have the remarkable capacity to remove damaged axonal debris and re-innervate targets. To investigate the roles of all peripheral glia in PNS regeneration, we describe here an axon transection assay that uses a commercially available nitrogen-pumped dye laser to axotomize motor nerves in live transgenic zebrafish. We further describe the methods to couple these experiments to time-lapse imaging of injured and control nerves. This experimental paradigm can be used to not only assess the role that glia play in nerve regeneration, but can also be the platform for elucidating the molecular mechanisms that govern nervous system repair.

Although the peripheral nervous system (PNS) is capable of significant repair after injury, little is known about the cellular and molecular mechanisms that govern this phenomenon. Using live, transgenic zebrafish and a reproducible nerve transection assay, we can study dynamic glial cell behaviors during nerve degeneration and regeneration.

The  nervous system is often described as a hard-wired component of the body even  though it is a considerably fluid organ system that reacts to external ...

Protocol for Three-dimensional Confocal Morphometric Analysis of Astrocytes

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify their functional and structural properties, a condition called reactive astrogliosis. Here, a protocol for assessment of the morphological properties of astrocytes is presented. This protocol includes quantification of 12 different parameters i.e. the surface area and volume of the tissue covered by an astrocyte (astrocyte territory), the entire astrocyte including branches, cell body, and nucleus, as well as total length and number of branches, the intensity of fluorescence immunoreactivity of antibodies used for astrocyte detection, and astrocyte density (number/1,000 &#181;m2). For this purpose three-dimensional (3D) confocal microscopic images were created, and 3D image analysis software such as Volocity 6.3 was used for measurements. Rat brain tissue exposed to amyloid beta1-40 (A&#946;1-40) with or without a therapeutic&#160;intervention was used to present the method. This protocol can also be used for 3D morphometric analysis of other cells from either in vivo or in vitro conditions.

Astrocytes in the CNS change their functional and structural properties in response to harmful stimuli. This report presents a protocol for assessment of three-dimensional astrocyte morphology in diseased conditions or after therapeutic interventions.

As glial cells in the brain, astrocytes have diverse functional roles in the central nervous system. In the presence of harmful stimuli, astrocytes modify ...

Three-dimensional Imaging and Analysis of Mitochondria within Human Intraepidermal Nerve Fibers

The goal of this protocol is to study mitochondria within intraepidermal nerve fibers. Therefore, 3D imaging and analysis techniques were developed to isolate nerve-specific mitochondria and evaluate disease-induced alterations of mitochondria in the distal tip of sensory nerves. The protocol combines fluorescence immunohistochemistry, confocal microscopy and 3D image analysis techniques to visualize and quantify nerve-specific mitochondria. Detailed parameters are defined throughout the procedures in order to provide a concrete example of how to use these techniques to isolate nerve-specific mitochondria. Antibodies were used to label nerve and mitochondrial signals within tissue sections of skin punch biopsies, which was followed by indirect immunofluorescence to visualize nerves and mitochondria with a green and red fluorescent signal respectively. Z-series images were acquired with confocal microscopy and 3D analysis software was used to process and analyze the signals. It is not necessary to follow the exact parameters described within, but it is important to be consistent with the ones chosen throughout the staining, acquisition and analysis steps. The strength of this protocol is that it is applicable to a wide variety of circumstances where one fluorescent signal is used to isolate other signals that would otherwise be impossible to study alone.

This protocol uses three-dimensional (3D) imaging and analysis techniques to visualize and quantify nerve-specific mitochondria. The techniques are applicable to other situations where one fluorescent signal is used to isolate a subset of data from another fluorescent signal.

The goal of this protocol is to study mitochondria within intraepidermal nerve fibers. Therefore, 3D imaging and analysis techniques were developed to ...

Fiber Connections of the Supplementary Motor Area Revisited: Methodology of Fiber Dissection, DTI, and Three Dimensional Documentation

The purpose of this study is to show the methodology for the examination of the white matter connections of the supplementary motor area (SMA) complex (pre-SMA and SMA proper) using a combination of fiber dissection techniques on cadaveric specimens and magnetic resonance (MR) tractography. The protocol will also describe the procedure for a white matter dissection of a human brain, diffusion tensor tractography imaging, and three-dimensional documentation. The fiber dissections on human brains and the 3D documentation were performed at the University of Minnesota, Microsurgery and Neuroanatomy Laboratory, Department of Neurosurgery. Five postmortem human brain specimens and two whole heads were prepared in accordance with Klingler's method. Brain hemispheres were dissected step by step from lateral to medial and medial to lateral under an operating microscope, and 3D images were captured at every stage. All dissection results were supported by diffusion tensor imaging. Investigations on the connections in line with Meynert's fiber tract classification, including association fibers (short, superior longitudinal fasciculus I and frontal aslant tracts), projection fibers (corticospinal, claustrocortical, cingulum, and frontostriatal tracts), and commissural fibers (callosal fibers) were also conducted.

The purpose of this study is to show each step of the fiber dissection technique on human cadaveric brains, the 3D documentation of these dissections, and the diffusion tensor imaging of the anatomically dissected fiber pathways.

The purpose of this study is to show the methodology for the examination of the white matter connections of the supplementary motor area (SMA) complex ...

Generation and Long-term Maintenance of Nerve-free Hydra

The interstitial cell lineage of Hydra includes multipotent stem cells, and their derivatives: gland cells, nematocytes, germ cells, and nerve cells. The interstitial cells can be eliminated through two consecutive treatments with colchicine, a plant-derived toxin that kills dividing cells, thus erasing the potential for renewal of the differentiated cells that are derived from the interstitial stem cells. This allows for the generation of Hydra that lack nerve cells. A nerve-free polyp cannot open its mouth to feed, egest, or regulate osmotic pressure. Such animals, however, can survive and be cultured indefinitely in the laboratory if regularly force-fed and burped. The lack of nerve cells allows for studies of the role of the nervous system in regulating animal behavior and regeneration. Previously published protocols for nerve-free Hydra maintenance involve outdated techniques such as mouth-pipetting with hand-pulled micropipette tips to feed and clean the Hydra. Here, an improved protocol for maintenance of nerve-free Hydra is introduced. Fine-tipped forceps are used to force open the mouth and insert freshly killed Artemia. Following force-feeding, the body cavity of the animal is flushed with fresh medium using a syringe and hypodermic needle to remove undigested material, referred to here as "burping". This new method of force-feeding and burping nerve-free Hydra through the use of forceps and syringes eliminates the need for mouth-pipetting using hand-pulled micropipette tips. It thus makes the process safer and significantly more time efficient. To ensure that the nerve cells in the hypostome have been eliminated, immunohistochemistry using anti-tyrosine-tubulin is conducted.

Generation and Long-term Maintenance of Nerve-free Hydra

Through a double treatment with colchicine, a plant-derived toxin that kills dividing cells, nerve-free Hydra vulgaris can be generated. These Hydra cannot feed or egest on their own. This paper describes an improved method for long-term maintenance of nerve free Hydra vulgaris in the laboratory.

The interstitial cell lineage of Hydra includes multipotent stem cells, and their derivatives: gland cells, nematocytes, germ cells, and nerve cells. The ...

In Vivo Single-Molecule Tracking at the Drosophila Presynaptic Motor Nerve Terminal

An increasing number of super-resolution microscopy techniques are helping to uncover the mechanisms that govern the nanoscale cellular world. Single-molecule imaging is gaining momentum as it provides exceptional access to the visualization of individual molecules in living cells. Here, we describe a technique that we developed to perform single-particle tracking photo-activated localization microscopy (sptPALM) in Drosophila larvae. Synaptic communication relies on key presynaptic proteins that act by docking, priming, and promoting the fusion of neurotransmitter-containing vesicles with the plasma membrane. A range of protein-protein and protein-lipid interactions tightly regulates these processes and the presynaptic proteins therefore exhibit changes in mobility associated with each of these key events. Investigating how mobility of these proteins correlates with their physiological function in an intact live animal is essential to understanding their precise mechanism of action. Extracting protein mobility with high resolution in vivo requires overcoming limitations such as optical transparency, accessibility, and penetration depth. We describe how photoconvertible fluorescent proteins tagged to the presynaptic protein Syntaxin-1A can be visualized via slight oblique illumination and tracked at the motor nerve terminal or along the motor neuron axon of the third instar Drosophila larva.

In Vivo Single-Molecule Tracking at the Drosophila Presynaptic Motor Nerve Terminal

Here we illustrate how single molecule photo-activated localization microscopy can be carried out on the motor nerve terminal of a live Drosophila melanogaster third instar larva.

An increasing number of super-resolution microscopy techniques are helping to uncover the mechanisms that govern the nanoscale cellular world. ...

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical properties, synaptic connections, and in vivo functions, but their basic functional and anatomical organization from cellular to network scale is poorly understood. Here we describe a method for the three-dimensional imaging of fluorescently-labeled neurons across large areas of the brain for the investigation of the cortical cellular organization. Specific types of neurons are labeled by the injection of fluorescent retrograde neuronal tracers or expression of fluorescent proteins in transgenic mice. Block brain samples, e.g., a hemisphere, are prepared after fixation, made transparent with tissue clearing methods, and subjected to fluorescent immunolabeling of the specific cell types. Large areas are scanned using confocal or two-photon microscopes equipped with large working distance objectives and motorized stages. This method can resolve the periodic organization of the cell type-specific microcolumn functional modules in the mouse neocortex. The procedure can be useful for the study of three-dimensional cellular architecture in the diverse brain areas and other complex tissues.

Here we describe a procedure for tissue clearing, fluorescent labeling, and large-scale imaging of mouse brain tissue which, thereby, enables visualization of the three-dimensional organization of cell types in the neocortex.

The mammalian neocortex is composed of many types of excitatory and inhibitory neurons, each with specific electrophysiological and biochemical ...

Three-Dimensional Shape Modeling and Analysis of Brain Structures

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. We have developed a software package for accurate and robust shape modeling and group-wise analysis. Here, we introduce an pipeline for the shape analysis, from individual 3D shape modeling to quantitative group shape analysis. We also describe the pre-processing and segmentation steps using open software packages. This practical guide would help researchers save time and effort in 3D shape analysis on brain structures.

We introduce a semi-automatic protocol for shape analysis on brain structures, including image segmentation using open software, and further group-wise shape analysis using an automated modeling package. Here, we demonstrate each step of the 3D shape analysis protocol with hippocampal segmentation from brain MR images.

Statistical shape analysis of brain structures has been used to investigate the association between their structural changes and pathological processes. ...

3D Kinematic Analysis for the Functional Evaluation in the Rat Model of Sciatic Nerve Crush Injury

Compared to the Sciatic Functional Index (SFI), kinematic analysis is a more reliable and sensitive method for performing functional evaluations of sciatic nerve injury rodent models. In this protocol, we describe a novel kinematic analysis method that uses a three-dimensional (3D) motion capture apparatus for functional evaluations using a rat sciatic nerve crush injury model. First, the rat is familiarized with treadmill walking. Markers are then attached to the designated bone landmarks and the rat is made to walk on the treadmill at the desired speed. Meanwhile, the posterior limb movements of the rat are recorded using four cameras. Depending on the software used, marker tracings are created using both automatic and manual modes and the desired data are produced after subtle adjustments. This method of kinematic analysis, which uses a 3D motion capture apparatus, offers numerous advantages, including superior precision and accuracy. Many more parameters can be investigated during the comprehensive functional evaluations. This method has several shortcomings that require consideration: The system is expensive, can be complicated to operate, and may produce data deviations due to skin shifting. Nevertheless, kinematic analysis using a 3D motion capture apparatus is useful for performing functional anterior and posterior limb evaluations. In the future, this method may become increasingly useful for generating accurate assessments of various traumas and diseases.

We introduce a kinematic analysis method that uses a three-dimensional motion capture apparatus containing four cameras and data processing software for performing functional evaluations during fundamental research involving rodent models.

Compared to the Sciatic Functional Index (SFI), kinematic analysis is a more reliable and sensitive method for performing functional evaluations of ...

Purification of Fibroblasts and Schwann Cells from Sensory and Motor Nerves in Vitro

The principal cells in the peripheral nervous system are the Schwann cells (SCs) and the fibroblasts. Both these cells distinctly express the sensory and motor phenotypes involved in different patterns of neurotrophic factor gene expression and other biological processes, affecting nerve regeneration. The present study has established a protocol to obtain highly purified rat sensory and motor SCs and fibroblasts more rapidly. The ventral root (motor nerve) and the dorsal root (sensory nerve) of neonatal rats (7-days-old) were dissociated and the cells were cultured for 4-5 days, followed by isolation of sensory and motor fibroblasts and SCs by combining differential digestion and differential adherence methods sequentially. The results of immunocytochemistry and flow cytometry analyses showed that the purity of the sensory and motor SCs and fibroblasts were &#62;90%. This protocol can be used to obtain a large number of sensory and motor fibroblasts/SCs more rapidly, contributing to the exploration of sensory and motor nerve regeneration.

Here, we present a method to purify fibroblasts and Schwann cells from sensory and motor nerves in vitro.

The principal cells in the peripheral nervous system are the Schwann cells (SCs) and the fibroblasts. Both these cells distinctly express the sensory and ...