The authors thank Michael Ward for providing the WTC11 hNIL iPSC line for motor neuron differentiation and the Jackson Laboratories for supplying the KOLF2.1J WT clone B03 iPSC line used for microglia differentiation. We also thank Dorothy Schafer for her support during the implementation of the protocols, Anthony Giampetruzzi and John Landers for their help with the live-cell imaging system as well as Hayden Gadd for his technical contributions during revisions and Jonathan Jung for his collaboration in this study. This work was supported by the Dan and Diane Riccio Fund for Neuroscience from UMASS Chan Medical School and the Angel Fund, Inc.

NOTE: All the reagents used in this protocol must be sterile, and all the steps must be performed in a biosafety cabinet under sterile conditions. All the iPSC lines, as well as maintenance and differentiation media, are described in the Table of Materials. The microglia differentiation method illustrated below is based on previously published protocols7,8,12 with new modifications described herein.
<p class...

<ol>
	<li>Heider, J., Vogel, S., Volkmer, H., Breitmeyer, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+iPSC-derived+glia+as+a+tool+for+neuropsychiatric+research+and+drug+development.">Human iPSC-derived glia as a tool for neuropsychiatric research and drug development.</a> International Journal of Molecular Sciences. 22 (19), 10254 (2021).</li><li>Muzio, L., Viotti, A., Martino, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microglia+in+neuroinflammation+and+neurodegeneration:+from+understanding+to+therapy.">Microglia in neuroinflammation and neurodegeneration: from understanding to therapy.</a> Frontiers in Neuroscience. 15, 742065 (2021).</li><li>Galatro, T. F., 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=Transcriptomic+analysis+of+purified+human+cortical+microglia+reveals+age-associated+changes.">Transcriptomic analysis of purified human cortical microglia reveals age-associated changes.</a> Nature Neuroscience. 20 (8), 1162-1171 (2017).</li><li>Gosselin, D., 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=An+environment-dependent+transcriptional+network+specifies+human+microglia+identity.">An environment-dependent transcriptional network specifies human microglia identity.</a> Science. 356 (6344), (2017).</li><li>Haimon, Z., 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=Re-evaluating+microglia+expression+profiles+using+RiboTag+and+cell+isolation+strategies.">Re-evaluating microglia expression profiles using RiboTag and cell isolation strategies.</a> Nature Immunology. 19 (6), 636-644 (2018).</li><li>Abud, E. 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=iPSC-derived+human+microglia-like+cells+to+study+neurological+diseases.">iPSC-derived human microglia-like cells to study neurological diseases.</a> Neuron. 94 (2), 278-293 (2017).</li><li>Brownjohn, P. W., 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=Functional+studies+of+missense+TREM2+mutations+in+human+stem+cell-derived+microglia.">Functional studies of missense TREM2 mutations in human stem cell-derived microglia.</a> Stem Cell Reports. 10 (4), 1294-1307 (2018).</li><li>Haenseler, W., 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+highly+efficient+human+pluripotent+stem+cell+microglia+model+displays+a+neuronal-co-culture-specific+expression+profile+and+inflammatory+response.">A highly efficient human pluripotent stem cell microglia model displays a neuronal-co-culture-specific expression profile and inflammatory response.</a> Stem Cell Reports. 8 (6), 1727-1742 (2017).</li><li>McQuade, 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=Development+and+validation+of+a+simplified+method+to+generate+human+microglia+from+pluripotent+stem+cells.">Development and validation of a simplified method to generate human microglia from pluripotent stem cells.</a> Molecular Neurodegeneration. 13 (1), 1-13 (2018).</li><li>Muffat, 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=Efficient+derivation+of+microglia-like+cells+from+human+pluripotent+stem+cells.">Efficient derivation of microglia-like cells from human pluripotent stem cells.</a> Nature Medicine. 22 (11), 1358-1367 (2016).</li><li>Haenseler, W., Rajendran, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Concise+review:+modeling+neurodegenerative+diseases+with+human+pluripotent+stem+cell-derived+microglia.">Concise review: modeling neurodegenerative diseases with human pluripotent stem cell-derived microglia.</a> Stem Cells. 37 (6), 724-730 (2019).</li><li>Wilgenburg, B. v., Browne, C., Vowles, J., Cowley, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Efficient,+long+term+production+of+monocyte-derived+macrophages+from+human+pluripotent+stem+cells+under+partly-defined+and+fully-defined+conditions.">Efficient, long term production of monocyte-derived macrophages from human pluripotent stem cells under partly-defined and fully-defined conditions.</a> PloS One. 8 (8), 71098 (2013).</li><li>Hoeffel, G., Ginhoux, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ontogeny+of+tissue-resident+macrophages.">Ontogeny of tissue-resident macrophages.</a> Frontiers in Immunology. 6, 486 (2015).</li><li>Janda, E., Boi, L., Carta, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microglial+phagocytosis+and+its+regulation:+a+therapeutic+target+in+Parkinson's+disease.">Microglial phagocytosis and its regulation: a therapeutic target in Parkinson's disease.</a> Frontiers in Molecular Neuroscience. 11, 144 (2018).</li><li>Schafer, D. P., Stevens, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microglia+function+in+central+nervous+system+development+and+plasticity.">Microglia function in central nervous system development and plasticity.</a> Cold Spring Harbor Perspectives in Biology. 7 (10), 020545 (2015).</li><li>Nau, R., Ribes, S., Djukic, M., Eiffert, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strategies+to+increase+the+activity+of+microglia+as+efficient+protectors+of+the+brain+against+infections.">Strategies to increase the activity of microglia as efficient protectors of the brain against infections.</a> Frontiers in Cellular Neuroscience. 8, 138 (2014).</li><li>Fernandopulle, M. 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=Transcription+factor-mediated+differentiation+of+human+iPSCs+into+neurons.">Transcription factor-mediated differentiation of human iPSCs into neurons.</a> Current Protocols in Cell Biology. 79 (1), 51 (2018).</li><li>Gutbier, 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=Large-scale+production+of+human+IPSC-derived+macrophages+for+drug+screening.">Large-scale production of human IPSC-derived macrophages for drug screening.</a> International Journal of Molecular Sciences. 21 (13), 4808 (2020).</li><li>Sellgren, C., 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=Patient-specific+models+of+microglia-mediated+engulfment+of+synapses+and+neural+progenitors.">Patient-specific models of microglia-mediated engulfment of synapses and neural progenitors.</a> Molecular Psychiatry. 22 (2), 170-177 (2017).</li><li>Schmidt, E. 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=ALS-linked+PFN1+variants+exhibit+loss+and+gain+of+functions+in+the+context+of+formin-induced+actin+polymerization.">ALS-linked PFN1 variants exhibit loss and gain of functions in the context of formin-induced actin polymerization.</a> Proceedings of the National Academy of Sciences of the United States of America. 118 (23), (2021).</li><li>Miksa, M., Komura, H., Wu, R., Shah, K. G., Wang, P. <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+method+to+determine+the+engulfment+of+apoptotic+cells+by+macrophages+using+pHrodo+succinimidyl+ester.">A novel method to determine the engulfment of apoptotic cells by macrophages using pHrodo succinimidyl ester.</a> Journal of Immunological Methods. 342 (1-2), 71-77 (2009).</li></ol>

The authors have no conflicts of interest to declare.

The differentiation protocol described here provides an efficient method to obtain iPSC-derived microglia-like cells in ~6-8 weeks with high purity and in a sufficient yield to perform immunofluorescence experiments and other assays that require a higher number of cells. This protocol has yielded up to 1 &#215; 106 iMGs in 1 week, which allows for protein and RNA extraction and corresponding downstream analyses (e.g., RNASeq, qRT-PCR, western blot, mass spectrometry). That said, a limitation of this protocol i...

Microglia are the resident immune cells in the central nervous system (CNS) and play a crucial role in developing the CNS. Microglia are also important in the adult brain for maintaining homeostasis and actively responding to trauma and disease processes. Cumulative evidence shows that microglia are key contributors to the pathogenesis of multiple neurodevelopmental and neurodegenerative diseases1,2. Although current knowledge about microglial biology has been predominately derived from mouse models, recent studies have elucidated important differences between murine and human microglia, underscoring the need for developing technologies to study the genetics and biological functions of human microglia3,4. Isolation of microglia from dissected primary tissue can severely modify microglia properties5, potentially confounding results acquired with such cells. The overall goal of this method is to differentiate human iPSCs into iMGs, thereby providing a cell culture system to study human microglia under basal conditions. Furthermore, a phagocytosis assay using a fully human model system is included herein as a means to study the functionality of iMGs, both as a quality control measure and to assess iMG dysfunction in the context of disease.
Multiple protocols for microglia differentiation from iPSCs have recently emerged in the literature6,7,8,9,10. Potential disadvantages of some protocols include extended or long periods of differentiation, the addition of multiple growth factors, and/or complex experimental procedures6,9,10. Here, a &#34;user-friendly&#34; differentiation method is demonstrated that recapitulates aspects of microglia ontogeny through differentiation of iPSCs into precursor cells termed primitive macrophage precursors (PMPs)7,11. PMPs are generated as described previously, with some optimizations presented herein12. The PMPs mimic MYB-independent yolk-sac-derived macrophages, which give rise to microglia during embryonic development by invading the brain before blood-brain barrier closure13. To terminally differentiate PMPs into iMGs, we used a fast and simplified monoculture method based on protocols by Haenseler et al. and Brownjohn et al., with some modifications to generate an efficient microglia differentiation method in which iMGs robustly express microglia-enriched markers7,8. This differentiation method can be reproduced in laboratories with expertise in the culture of iPSCs and with research goals aiming to study microglia biology using a human model system.
iPSC-derived microglia represent a biologically relevant source of human microglia for in vitro experimentation and are an important tool to investigate microglial canonical functions, including phagocytosis. Microglia are the professional phagocytes of the brain and CNS, where they clear cell debris, aggregated proteins, and degraded myelin14. Microglia also function in synaptic remodeling by engulfing synapses and in the defense against external infections through phagocytosis of pathogens15,16. In this protocol, phagocytosis by iMGs is assessed using human synaptosomes as material for iMG engulfment. To this end, a description for isolating synaptosomes derived from human i3LMNs is described. The i3LMN-derived human synaptosomes are labeled with a pH-sensitive dye that allows for quantification of synaptosomes localized within acidic compartments during phagosome processing and degradation in vitro. A phagocytosis assay using live-cell microscopy is shown for monitoring the dynamic process of microglia engulfment in real-time. This functional assay establishes a basis to investigate possible defects in microglial phagocytosis in health and disease using a complete human system.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Antibodies for immunofluorescence analysis</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>anti-IBA1 rabbit antibody</td>
			<td>Wako Chemical USA</td>
			<td>NC9288364</td>
			<td>1:350 dilution</td>
		</tr>
		<tr>
			<td>anti-P2RY12 rabbit antibody</td>
			<td>Sigma-Aldrich</td>
			<td>HPA014518</td>
			<td>1:50 dilution</td>
		</tr>
		<tr>
			<td>anti-TMEM119 rabbit antibody</td>
			<td>Sigma-Aldrich</td>
			<td>HPA051870</td>
			<td>1:100 dilution</td>
		</tr>
		<tr>
			<td>Antibodies for Western blot analysis</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>anti-&#946;-Tubulin rabbit antibody</td>
			<td>Abcam</td>
			<td>ab6046</td>
			<td>1:500 dilution</td>
		</tr>
		<tr>
			<td>anti-Synaptophysin (SYP) rabbit antibody</td>
			<td>Abclonal</td>
			<td>A6344</td>
			<td>1:1,000 dilution</td>
		</tr>
		<tr>
			<td>anti-PSD95 mouse antibody</td>
			<td>Millipore</td>
			<td>MAB1596</td>
			<td>1:500 dilution</td>
		</tr>
		<tr>
			<td>Borate buffer components</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Boric acid (100 mM)</td>
			<td>Sigma</td>
			<td>B6768</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium bicarbonate (NaHCO3) BioXtra</td>
			<td>Sigma-Aldrich</td>
			<td>S6297-250G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium chloride (75 mM)</td>
			<td>Sigma</td>
			<td>&#160;S7653</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium tetraborate (25 mM)</td>
			<td>Sigma</td>
			<td>221732</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell culture materials</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>6-well plates</td>
			<td>Greiner Bio-One</td>
			<td>657160</td>
			<td></td>
		</tr>
		<tr>
			<td>40 &#956;m Cell Strainers</td>
			<td>&#160;Falcon</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>100 mm x 20 mm Tissue Culture Treated</td>
			<td>CELLTREAT</td>
			<td>229620</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Lifter, Double End, Flat Blade &#38; Narrow Blade, Sterile</td>
			<td>CELLTREAT</td>
			<td>229305</td>
			<td></td>
		</tr>
		<tr>
			<td>low adherence round-bottom 96-well plate</td>
			<td>Corning</td>
			<td>7007</td>
			<td></td>
		</tr>
		<tr>
			<td>Primaria 24-well Flat Bottom Surface Modified Multiwell Cell Culture Plate</td>
			<td>Corning</td>
			<td>353847,</td>
			<td></td>
		</tr>
		<tr>
			<td>Primaria 6-well Cell Clear Flat Bottom Surface-Modified Multiwell Culture Plate</td>
			<td>Corning</td>
			<td>353846</td>
			<td></td>
		</tr>
		<tr>
			<td>Primaria 96-well Clear Flat Bottom Microplate</td>
			<td>Corning</td>
			<td>353872</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell dissociation reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Accutase</td>
			<td>&#160;Corning</td>
			<td>25058CI</td>
			<td>dissociation reagents used for lower motor neuron differentiation</td>
		</tr>
		<tr>
			<td>TrypLE reagent</td>
			<td>Life Technologies</td>
			<td>12-605-010</td>
			<td>dissociation reagents used for microglia differentiation</td>
		</tr>
		<tr>
			<td>UltraPure 0.5 M EDTA, pH 8.0</td>
			<td>Invitrogen</td>
			<td>15575020</td>
			<td></td>
		</tr>
		<tr>
			<td>Coating reagents for cell culture</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Matrigel GFR Membrane Matrix</td>
			<td>Corning&#8482;</td>
			<td>354230</td>
			<td>Referred as to extracellular matrix coating reagent</td>
		</tr>
		<tr>
			<td>CellAdhere Laminin-521</td>
			<td>STEMCELL Technology</td>
			<td>77004</td>
			<td>Referred as to laminin 521</td>
		</tr>
		<tr>
			<td>Poly-D-Lysine</td>
			<td>Sigma</td>
			<td>P7405</td>
			<td>Reconstitute to 0.1 mg/mL in borate buffer</td>
		</tr>
		<tr>
			<td>Poly-L-Ornithine</td>
			<td>Sigma</td>
			<td>&#160;P3655</td>
			<td>Reconstitute to 1 mg/mL in borate buffer</td>
		</tr>
		<tr>
			<td>Components of iPSC media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>&#160;mTeSR Plus Kit</td>
			<td>STEMCELL Technology</td>
			<td>100-0276</td>
			<td>To prepare iPSC media mixed the components to 1x</td>
		</tr>
		<tr>
			<td>Components of EB media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>BMP-4</td>
			<td>Fisher Scientific</td>
			<td>PHC9534</td>
			<td>final concentration 50 ng/mL</td>
		</tr>
		<tr>
			<td>iPSC media</td>
			<td></td>
			<td></td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>ROCK inhibitor Y27632</td>
			<td>Fisher Scientific</td>
			<td>BD 562822</td>
			<td>final concentration 10 &#181;M</td>
		</tr>
		<tr>
			<td>SCF</td>
			<td>PeproTech</td>
			<td>300-07</td>
			<td>final concentration 20 ng/mL</td>
		</tr>
		<tr>
			<td>VEGF</td>
			<td>PeproTech</td>
			<td>100-20A</td>
			<td>final concentration 50 ng/mL</td>
		</tr>
		<tr>
			<td>Components of PMP base media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>GlutaMAX</td>
			<td>Gibco</td>
			<td>35050061</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (10,000 U/mL)</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td>final concentration 100 U/mL</td>
		</tr>
		<tr>
			<td>X-VIVO 15</td>
			<td>Lonza</td>
			<td>12001-988</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Components of PMP complete media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>55 mM 2-mercaptoethanol</td>
			<td>Gibco</td>
			<td>21985023</td>
			<td>final concentration 55 &#181;M</td>
		</tr>
		<tr>
			<td>IL-3</td>
			<td>PeproTech</td>
			<td>200-03</td>
			<td>final concentration 25 ng/mL</td>
		</tr>
		<tr>
			<td>M-CSF</td>
			<td>PeproTech</td>
			<td>300-25</td>
			<td>final concentration 100 ng/mL</td>
		</tr>
		<tr>
			<td>PMP base media</td>
			<td></td>
			<td></td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Components of iMG base media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Advanced DMEM/F12</td>
			<td>Gibco</td>
			<td>12634010</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>GlutaMAX</td>
			<td>Gibco</td>
			<td>35050061</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>N2 supplement, 100x</td>
			<td>Gibco</td>
			<td>17502-048</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (10,000 U/mL)</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td>final concentration 100 U/mL</td>
		</tr>
		<tr>
			<td>Components of iMG complete media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>55 mM 2-mercaptoethanol</td>
			<td>Gibco</td>
			<td>21985023</td>
			<td>final concentration 55 &#181;M</td>
		</tr>
		<tr>
			<td>IL-34</td>
			<td>PeproTech or Biologend</td>
			<td>200-34 or 577904</td>
			<td>final concentration 100 ng/mL</td>
		</tr>
		<tr>
			<td>iMG base media</td>
			<td></td>
			<td></td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>M-CSF</td>
			<td>PeproTech</td>
			<td>300-25</td>
			<td>final concentration 5 ng/mL</td>
		</tr>
		<tr>
			<td>TGF-&#946;</td>
			<td>PeproTech</td>
			<td>100-21</td>
			<td>final concentration 50 ng/mL</td>
		</tr>
		<tr>
			<td>Components of Induction base media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F12 with HEPES</td>
			<td>Gibco</td>
			<td>11330032</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>GlutaMAX</td>
			<td>Gibco</td>
			<td>35050061</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>N2 supplement, 100x</td>
			<td>Gibco</td>
			<td>17502-048</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Non-essential amino acids (NEAA), 100x</td>
			<td>Gibco</td>
			<td>11140050</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Components of Complete induction media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Compound E</td>
			<td>Calbiochem</td>
			<td>565790</td>
			<td>final concentration 0.2 &#956;M and reconstitute stock reagent to 2 mM in 1:1 ethanol and DMSO</td>
		</tr>
		<tr>
			<td>Doxycycline</td>
			<td>Sigma</td>
			<td>D9891</td>
			<td>final concentration 2 &#956;g/mL and reconstitute stock reagent to 2 mg/mL in DPBS</td>
		</tr>
		<tr>
			<td>Induction base media</td>
			<td></td>
			<td></td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>ROCK inhibitor Y27632</td>
			<td>Fisher Scientific</td>
			<td>BD 562822</td>
			<td>final concentration 10 &#956;M</td>
		</tr>
		<tr>
			<td>Components of Neuron media</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Plus Neuronal Culture System</td>
			<td>Gibco</td>
			<td>A3653401</td>
			<td>final concentration 1x for media and suplemment</td>
		</tr>
		<tr>
			<td>GlutaMAX</td>
			<td>Gibco</td>
			<td>35050061</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>N2 supplement, 100x</td>
			<td>Gibco</td>
			<td>17502-048</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>Non-essential amino acids (NEAA), 100x</td>
			<td>Gibco</td>
			<td>11140050</td>
			<td>final concentration 1x</td>
		</tr>
		<tr>
			<td>iPSC lines used in this study</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>KOLF2.1J: WT clone B03</td>
			<td>The Jackson Laboratories</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>WTC11 hNIL</td>
			<td>National Institute of Health</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Synaptosome isolation reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>BCA Protein Assay Kit</td>
			<td>Thermo Scientific Pierce</td>
			<td>23227</td>
			<td></td>
		</tr>
		<tr>
			<td>dimethyl sulfoxide (DMSO)</td>
			<td>Sigma</td>
			<td>D2650</td>
			<td></td>
		</tr>
		<tr>
			<td>Syn-PER Synaptic Protein Extraction Reagent</td>
			<td>Thermo Scientific</td>
			<td>87793</td>
			<td>Referred as to cell lysis reagent for isolation of synaptosomes</td>
		</tr>
		<tr>
			<td>Phagocytosis assay dyes</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NucBlue Live Ready reagent</td>
			<td>Invitrogen</td>
			<td>&#160;R37605</td>
			<td></td>
		</tr>
		<tr>
			<td>pHrodo Red, succinimidyl ester</td>
			<td>ThermoFisher Scientific</td>
			<td>&#160;P36600</td>
			<td>Referred as to pH-sensitive dye</td>
		</tr>
		<tr>
			<td>Other cell-culture reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue, 0.4% Solution</td>
			<td>AMRESCO INC</td>
			<td>K940-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA)</td>
			<td>Sigma</td>
			<td>22144-77-0</td>
			<td></td>
		</tr>
		<tr>
			<td>BrdU</td>
			<td>Sigma</td>
			<td>B9285</td>
			<td>Reconstitute to 40 mM in sterile water</td>
		</tr>
		<tr>
			<td>Cytochalasin D</td>
			<td>Sigma</td>
			<td></td>
			<td>final concentration 10 &#181;M</td>
		</tr>
		<tr>
			<td>DPBS with Calcium and magnesium</td>
			<td>Corning</td>
			<td>21-030-CV</td>
			<td></td>
		</tr>
		<tr>
			<td>DPBS without calcium and magnesium</td>
			<td>Corning</td>
			<td>21-031-CV</td>
			<td>Referred as to DPBS</td>
		</tr>
		<tr>
			<td>KnockOut&#160; DMEM/F-12</td>
			<td>Gibco</td>
			<td>12660012</td>
			<td>Referred as to DMEM-F12 optimized for growth of human embryonic and induced pluripotent stem cells</td>
		</tr>
		<tr>
			<td>Laminin Mouse Protein, Natural</td>
			<td>Gibco</td>
			<td>23017015</td>
			<td>Referred as to laminin</td>
		</tr>
		<tr>
			<td>Software and Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf</td>
			<td>Model 5810R</td>
			<td></td>
		</tr>
		<tr>
			<td>Cytation 5 live cell imaging reader</td>
			<td>Biotek</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Gen5 Microplate Reader and Imager Software</td>
			<td>Biotek</td>
			<td>version 3.03</td>
			<td></td>
		</tr>
		<tr>
			<td>Multi-Therm Heat-Shake</td>
			<td>Benchmark</td>
			<td></td>
			<td>refer as tube shaker</td>
		</tr>
		<tr>
			<td>Water sonicator</td>
			<td>Elma</td>
			<td>Mode Transsonic 310</td>
			<td></td>
		</tr>
	</tbody>
</table>

human microglia-like cells: differentiation from induced pluripotent stem cells and in vitro live-cell phagocytosis assay using human synaptosomes

Microglia are the resident immune cells of myeloid origin that maintain homeostasis in the brain microenvironment and have become a key player in multiple neurological diseases. Studying human microglia in health and disease represents a challenge due to the extremely limited supply of human cells. Induced pluripotent stem cells (iPSCs) derived from human individuals can be used to circumvent this barrier. Here, it is demonstrated how to differentiate human iPSCs into microglia-like cells (iMGs) for in vitro experimentation. These iMGs exhibit the expected and physiological properties of microglia, including microglia-like morphology, expression of proper markers, and active phagocytosis. Additionally, documentation for isolating and labeling synaptosome substrates derived from human iPSC-derived lower motor neurons (i3LMNs) is provided. A live-cell, longitudinal imaging assay is used to monitor engulfment of human synaptosomes labeled with a pH-sensitive dye, allowing for investigations of iMG's phagocytic capacity. The protocols described herein are broadly applicable to different fields that are investigating human microglia biology and the contribution of microglia to disease.

To generate iMGs using this protocol, it is important to start with undifferentiated iPSCs that show compact colony morphology with well-defined edges (Figure 2A). Dissociated iPSCs maintained as described in the EB formation section will form spherical aggregates, termed EBs, which will grow in size until day 4 of differentiation (Figure 2B). Once the EBs are collected and plated in the appropriate conditions for PMP generation, they attach to the Matrigel-coat...

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Human Microglia-like Cells: Differentiation from Induced Pluripotent Stem Cells and In Vitro Live-cell Phagocytosis Assay using Human Synaptosomes

This protocol describes the differentiation process of human induced pluripotent stem cells (iPSCs) into microglia-like cells for in vitro experimentation. We also include a detailed procedure for generating human synaptosomes from iPSC-derived lower motor neurons that can be used as a substrate for in vitro phagocytosis assays using live-cell imaging systems.

Human Microglia-like Cells: Differentiation from Induced Pluripotent Stem Cells and In Vitro Live-cell Phagocytosis Assay using Human Synaptosomes

Microglia are the resident immune cells of myeloid origin that maintain homeostasis in the brain microenvironment and have become a key player in multiple ...

iPS-derived microglia represent a biologically relevant source of human microglia for in vitro experimentation, and are an important tool to investigate microglia biology in health and disease. We present a simple microglia differentiation protocol that requires minimal use of growth factors and achieves high purity and yield. Also, we demonstrate a fully humanized phagocytosis assay.iPSC-derived microglia-like cells are very sensitive to media evaporation. You should avoid using the wells in the corner of the cell culture plate, and fill all empty wells with water to improve survival. Once Induced Pluripotent Stem Cells, or iPSCs, have reached 80%confluency, dissociate the colonies by washing with one milliliter of DPBS, and adding one milliliter of a dissociation reagent for two minutes at 37 degrees Celsius.Dislodge the colonies using a cell lifter by scraping multiple times to create a single cell suspension. Collect the suspension, and transfer them to a 15-milliliter conical tube containing nine milliliters of DPBS. Then centrifuge the cells at 500 times g for one minute, remove the supernatant, and resuspend in one milliliter of the Embryoid Body, or EB, medium.Take 10 microliters of cells, and dilute one to two with trypan blue. Count the cells on a hemocytometer, and based on the cell count, dilute the cell stock to a final dilution of 10, 000 cells per 100 microliters. For plating cells, add 100 microliters of the diluted cells per well into a low adherence round-bottom 96-well plate.Centrifuge the plate at 125 times g for three minutes, and incubate at 37 degrees Celsius and 5%carbon dioxide for four days. On day two, using a multi-channel pipette, replace the old half-EB medium with a fresh medium. To generate Primitive Macrophage Precursors, or PMPs, coat the wells of a six-well plate by adding one milliliter of ice cold Matrigel coating solution.Then incubate the plate at 37 degrees Celsius and 5%carbon dioxide for two hours, or overnight. On day four of EB differentiation, using a one-milliliter pipette tip, transfer the EBs to the Matrigel-coated wells. Pipette up and down to dislodge the EBs from the well.Then hold the plate tilted to allow the EBs to settle down at the edge of the well. Once all the EBs have settled down, gently pipette and replace the old medium, while keeping the EB at the edge of the well with three milliliters of freshly prepared PMP complete medium. Evenly distribute the cells in the wells by manually shuffling the plate side to side and back to front.Then incubate the plate for seven days to allow the EBs to attach to the bottom of the well. After seven days, inspect the EBs under a light field microscope at four times magnification to ensure that they are attached to the bottom of the wells. Perform a half medium change, and on day 21, replace the complete medium with three milliliters of PMP complete medium.On day 28, look for round cells referred to as PMPs in the supernatant. Then collect the medium containing the PMPs using a 10-milliliter pipette and automatic pipetter without disturbing the EBs. Transfer the PMPs in the medium to a 15-milliliter conical tube.Centrifuge the collected PMPs at 200 times g for four minutes and aspirate the supernatant before re-suspending them in one to two milliliters of microglia-like cells, or IMG basal medium. Then count the cells on the hemocytometer as described previously. Centrifuge the rest of the cells, and dilute the PMPs to the desired concentration.Then plate the cells at a density of 10 to the fifth cells per square centimeter on cell culture-treated plates using freshly prepared IMG complete medium. For live cell phagocytosis assay, plate 20 to 30 times 10 to the fourth PMPs into a 96-well plate and 100 microliters of IMG complete medium and follow the differentiation process for 10 days. On the day of the assay, remove 40 microliters of medium per well, and add 10 microliters of the nuclear staining solution.Incubate the plate for two hours. Thaw the labeled synaptosomes on ice, and gently sonicate using a water sonicator for one minute. Again, immediately place the synaptosomes on ice.Dilute the labeled synaptosomes in IMG complete medium at one microliter of synaptosomes per 50 microliters of medium. For negative control, prepare 60 micromolar Cytochalasin D in IMG complete medium to inhibit actin polymerization, and thus phagocytosis. Then add 10 microliters of this solution to each well for a final concentration of 10 micromolar, and incubate for 30 minutes.Remove the plate from the incubator, and incubate at 10 degrees Celsius for 10 minutes. Maintain the plate on ice, and add 50 microliters of medium containing synaptosomes. Centrifuge the plate at 270 times g for three minutes at 10 degrees Celsius, and maintain the plate on ice until imaging acquisition.Insert the plate into a live cell imaging reader, and select the wells to be analyzed. Then select a 20X objective lens. Next, adjust the focus, Light Emitting Diode, or LED, intensity, integration time, and gain of the bright-field and blue channels.The synaptosome fluorescence should be negligible at the initial time point. Select the number of individual tiles to be acquired in a montage per well. Acquire 16 tiles at the center of the well, imaging approximately 5%of the total well area.Set the temperature to 37 degrees Celsius, and the desired time interval for imaging. Next, open the analysis software. Then open the experiment that contains the images, and click on the Data Reduction icon.In the menu, pick Imaging Stitching under Imaging Processing to create a complete image from the four by four individual tiles in the montage with the parameters described in the text manuscript. Define an intensity threshold using the DAPI and RFP channels for these images. Open an image, and click on Analyze.Under Analysis, select Cellular Analysis, and under Detection Channel, pick a stitched image either in the DAPI, or RFP channels. Next, go to the Primary Mask and Count tab, and establish a threshold value and object size values that properly select the cell nuclei in the DAPI channel, or the synaptosome signal in the RFP channel. To count the number of nuclei, go to the Data Reduction menu, and under Image Analysis, select Cellular Analysis.Again, go to the Primary Mask and Count tab, and under Channel, select the DAPI stitched images, and use the parameters described in the text manuscript. Next, go to the Calculated Metrics tab, and select Cell Count. Then to obtain the area of the synaptosome signal, go to the Data Reduction menu, and under Analysis, select Cellular Analysis.Again, go to the Primary Mask and Count tab, and under Channel, select RFP stitched images, and use the parameters detailed in the text manuscript. Next, go to the Calculated Metrics tab, and select Object Sum Area. In the Data Reduction tab, click on OK to allow the software to analyze all the acquired images.Once the images are analyzed, export the Object Sum Area and Cell Count values for each time point. Then divide the Object Sum Area by the Cell Count to calculate the normalized area per time point. If comparing multiple treatments, or genotypes, calculate the phagocytosis index using the given equation.Undifferentiated iPSCs show compact colony morphology with well-defined edges. Dissociated iPSCs formed spherical aggregates termed EBs, and grow in size until day four of differentiation. When the EBs are plated for PMP generation, they attach to the Matrigel-coated plates, and a layer of cells spreads and surrounds the spherical aggregates.On day 28, round cells with a large cytoplasm to nucleus ratio appear in the suspension. It is strongly recommended to culture iPSCs in Laminin 521-coated plates instead of Matrigel, because of the higher PMP yield in Laminin 521-coated plates. After the exposure of PMPs to IMG medium, cells acquire a microglia-like morphology with a small cytoplasm in the presence of elongated processes.Further, microglia identity was verified by immunofluorescent staining. Typically, more than 95%of the cells express IB1 and approximately 90%of the cells express P2RY12 and TMEM119. Western blot analysis confirmed that iPSC derived lower motor neurons for human synaptosomes'expressed synaptic markers, synaptophysin and postsynaptic density protein 95.In control compared to the initial time point, by 10 hours, the red fluorescent signal was robust, as most of the synaptosomes had been engulfed, and were localized to acidic intracellular compartments. In Cytochalasin D-treated IMGs, a strong reduction of the red signal for zero and 10 hours indicated that the detected signal results from phagocytic events. The area of engulfed synaptosomes increased with time until 16 hours.However, the area of red signal from Cytochalasin D-treated cells did not increase with time. iPS-derived Microglia like cells can be used for various applications, including phagocytosis, and inflammatory response in the study of neurodevelopmental and neurodegenerative diseases.

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Neuroscience

3.4K Views.  University of Massachusetts Chan Medical School. Le microglia derivate da iPS rappresentano una fonte biologicamente rilevante di microglia umana per la sperimentazione in vitro e sono uno strumento importante per studiare la biologia delle microglia in salute e malattia. Presentiamo un semplice protocollo di differenziazione della microglia che richiede un uso minimo di fattori di crescita e raggiunge un'elevata purezza e resa. Inoltre, dimostriamo un test di fagocitosi completamente umanizzato.Le cellule simili a microglia derivate...

Video: Human Microglia-like Cells: Differentiation from Induced Pluripotent Stem Cells and In Vitro Live-cell Phagocytosis Assay using Human Synaptosomes