This research was supported by the California Institute for Regenerative Medicine (CIRM)&#160;&#160;(DISC2-COVID19-12022).

This study protocol was approved by the Institutional Review Board of UCSD&#39;s Human Research Protections Program (181180).
1. Definitive endoderm induction from induced pluripotent stem cells (Day 1 - 3)
<ol>
	<li>Slowly thaw growth factor reduced (GFR)-basement membrane (BM) matrix medium on ice 30 minutes prior to use. In cold DMEM/F12, mixture, dilute the GFR BM matrix medium 1:1 such that it constitutes 50% of this medium. Place P1000 pipette tips in the freezer to chill prior to use.</li>
	<li>Coat each well of a 12-well plate with 500 &#181;L of 50% GFR-basement membrane matrix medium prepared in ice-cold DMEM/F12. Once the desired number of wells are coated, remove any excess medium mixture and/or bubbles from wells and place the plate on ice or refrigerator at 4 &#176;C for 20 min to set. Then, move the plate to the incubator at 37 &#176;C overnight to gel and dry.</li>
	<li>Once hiPSCs reach 70-90% confluency, add 10 &#181;M of Rho-associated kinase (ROCK)&#160;Inhibitor Y-27632 an hour prior to dissociation. Aspirate off the media and wash once with Phosphate buffered saline (PBS). Dissociate hiPSCs by adding cell detachment medium (0.5 mL/ well of a 12-well plate) and incubate for 20 min at 37 &#176;C in a 5% CO2 incubator.</li>
	<li>Remove plates from the incubator and add 0.5 mL/12-well of stem cell passaging medium (Table 1) to the wells; gently triturate&#160;cells using a P1000 tip to obtain single-cell suspension. Transfer dissociated cells into a 15 mL conical centrifuge tube; centrifuge for 5 min at 300 x g.</li>
	<li>Aspirate off the medium and resuspend the cell pellet with 1 mL of mTeSR Plus media supplemented with 10 &#181;M ROCK inhibitor (Y-27632). Perform a cell count. Add 2.0 x 105&#160;hiPSCs in 1 mL of mTeSR supplemented with ROCK Inhibitor Y-27632 per well of a 12-well GFR-basement membrane medium coated plate. Incubate at 37 &#176;C overnight. 
	NOTE: Cell seeding number must be optimized per cell line. 24 h after plating, wells should be 50%-70% confluent.</li>
	<li>On day 1, aspirate off the mTeSR Plus and add Definitive Endoderm (DE) induction media (Table 1) supplemented with 100 ng/mL of human activin A and 5 &#181;M of GSK3&#946; inhibitor/Wnt activator CHIR99021. 
	&#8203;NOTE: DE media with GSK3&#946; inhibitor/Wnt activator CHIR99021 should be removed within 20-24 h of day 1 DE induction for successful differentiation.</li>
	<li>On day 2 and day 3, change to DE induction media supplemented with 100 ng/mL of activin A only. 
	&#8203;NOTE: DE differentiation should not exceed a total of 72 h, or efficacy will decrease. On day 4, if large cell die-off is observed, decrease total DE media exposure time by 6-12 h.</li>
	<li>To analyze DE efficiency, confirm greater than 90% CXCR4 and/or cKit expression via flow cytometry or immunofluorescence analysis of FOXA2 and/or SOX17 (Figure 2a).</li>
</ol>
2. Anterior foregut endoderm (AFE) induction (Day 4 - 6)
<ol>
	<li>On day 4, change media to serum free basal medium (SFBM) (Table 1) supplemented with 10 &#181;M SB431542 and 2 &#181;M Dorsomorphin for AFE induction. Change AFE media daily for 3 days (day 4, day 5, and day 6).</li>
	<li>To analyze AFE efficiency, confirm robust expression of SOX2, TBX1, and FOXA2 via immunofluorescence staining (Figure 2b).</li>
</ol>
3. Lung progenitor cell (LPC) differentiation (Day 7 - 16)
<ol>
	<li>On day 7, thaw GFR-basement membrane matrix medium on ice. Aspirate off the AFE media and wash well with 1x PBS. Add 1 mL of cell detachment solution and incubate for 10 min at 37 &#176;C.</li>
	<li>Add 1 mL of quenching medium (2% FBS in DMEM/F12) to the wells containing cell detachment solution. Keep cells as aggregates by pipetting up and down gently. Make sure all cells are dislodged and transferred into a 15 mL conical centrifuge tube. Centrifuge for 5 min at 300 x g.</li>
	<li>Remove the supernatant and resuspend the cell pellet in Quenching medium&#160;supplemented with 10 ng/mL of human recombinant bone morphogenic protein-4 (BMP4), 0.1 &#181;M of all-trans retinoic acid (RA), 3 &#181;M of GSK3&#946; inhibitor/Wnt activator CHIR99021, and 10 &#181;M of Rock Inhibitor Y-27632.</li>
	<li>Perform a cell count. Add 2.5 x 105 cells to 100 &#181;L of cold GFR-basement membrane matrix medium, mix well, and place droplet into a well of a 12-well plate. Incubate the plate at 37 &#176;C for 30-60 min to allow the medium to polymerize. Add 1 mL of LPC media supplemented with 10 &#181;M of ROCK Inhibitor Y-27632 per well ensuring the medium drop is fully submerged and incubate at 37 &#176;C overnight.</li>
	<li>On day 8, 24 h after LPC induction, change LPC medium to remove ROCK Inhibitor Y-27632. Change the LPC medium every other day for a total of 9-11 days. 
	NOTE: If the medium becomes yellow within 24 h, change medium every day.</li>
	<li>To analyze LPC efficiency, confirm robust expression of the intracellular transcription factor NKX2-1 or perform flow cytometry for surface markers CD47hi/CD26low15 or CPM18 (Figure 2c). Grossly, the LPC spheroids should be round and transparent (Figure 2c). 
	&#8203;NOTE: Do not proceed with lung organoid differentiation if efficiency of NKX2-1 is below 30%.</li>
</ol>
4. 3D lung organoid induction (Day 16 - 22)
<ol>
	<li>On day 17, thaw GFR-basement membrane matrix medium on ice. Aspirate the LPC induction medium. Then add 2 &#181;g/mL of dispase (1&#160;mL) to the well and resuspend the medium/dispase mixture with a P1000 pipette. Incubate at&#160;37 &#176;C for 15 min. Triturate the mixture again and incubate at&#160;37 &#176;C for another 15 min.</li>
	<li>Transfer the dispase and cells into a 15 mL conical centrifuge tube. Use chilled PBS (2-3 mL) to wash the well and resuspend the dispase/cell mixture. Centrifuge for 5 min at 400 x g. Manually remove the supernatant, being careful not to distub the medium/cell pellet layer. Repeat the chilled PBS wash, and&#160;centrifuge the conical centrifuge tube for another 5 min at 400 x g.</li>
	<li>Manually remove the supernatant, and then add 2 mL of trypsin- based dissociation solution to the conical centrifuge tube. Incubate at 37 &#176;C for 12 min.</li>
	<li>After incubation, resuspend cells with a P1000 pipette tip. Then add an equal volume of quenching media to the conical centrifuge tube and spin down at 400 x g for 5 min. Aspirate the supernatant and resuspend cells&#160; in quenching medium + 10 &#181;M of ROCK Inhibitor Y-27632. 
	NOTE: Successful lung organoid induction occurs when cells are embedded as aggregates, not single cells, adjust pipetting accordingly.</li>
	<li>Perform a cell count. Calculate the volume needed to obtain 5.0-8.0 x 104 cells per well. Aliquot the LPC cell aggregates into 1.5 mL microcentrifuge tubes and centrifuge for 5 min at 400 x g. Remove excess supernatant, being careful to not agitate the cell pellet. Leave only 10 &#181;L of residual media.</li>
	<li>Re-suspend the cell pellet in 200 &#181;L of cold GFR-basement membrane matrix medium and add to cell culture membrane inserts (6.5 mm diameter, 0.4 &#181;m pore, polyester membrane). Incubate the plate at 37 &#176;C for 30-60 min to allow GFR-basement membrane matrix medium to polymerize.</li>
	<li>Add 1 mL of 3D organoid induction medium (Table 1) supplemented with&#160;fibroblast growth factor-7&#160;(FGF7) (10 ng/mL), FGF10 (10 ng/mL), GSK3&#946; inhibitor/Wnt activator CHIR (3 &#181;M), epidermal growth factor (EGF) (10 ng/mL), and 10 &#181;M of ROCK&#160;Inhibitor Y-27632 to the basolateral chamber of the membrane insert. Change the medium every other day for 6 days.</li>
</ol>
5. 3D Lung organoid branching (Day 23 - 28)
<ol>
	<li>On day 23 change to 3D branching medium (Table 1) supplemented with FGF7 (10 ng/mL), FGF10 (10 ng/mL), GSK3&#946; inhibitor/Wnt activator CHIR99021 (3 &#181;M), RA (0.1 &#181;M), EGF (10 ng/mL), and vascular endothelial growth factor (VEGF) / placental growth factor (PlGF)&#160;(10 ng/mL). Change the medium every other day for 6 days. 
	NOTE: At day 6 of 3D branching differentiation, there should be multiple branching organoids (Figure 2).</li>
</ol>
6. 3D lung organoid maturation (Day 29 - 34)
<ol>
	<li>On day 29, change to 3D maturation medium (Table 1), which is the same as 3D branching medium but with the addition of dexamethasone (50 nM), cAMP (100 &#181;M), and and 3-isobutyl-1-methylxanthine (IBMX), a phosphodiesterase inhibitor also termed isobutylxanthine&#160;(100 &#181;M). Change the medium every other day for 6 days. 
	&#8203;NOTE: Within 24 h after 3D maturation, the branching organoids should expand and change into transparent spheres.</li>
</ol>
7. 3D Lung organoid immunocytochemistry
<ol>
	<li>For 3D whole lung organoid analysis, fix GFR-basement membrane matrix medium in the membrane inserts with 4% paraformaldehyde (PFA) for 1 h at 4 &#176;C. Embed in paraffin wax and mount onto slides per standard published protocols.</li>
	<li>Perform antigen retrieval prior to staining. Airway markers include KRT5, MUC5AC, and SCGB3A2. Alveolar markers include SP-C, SP-B, HTII-280, HTI-56, and HOPX (Figure 3).</li>
</ol>
8. Removal of whole lung organoids from GFR-basement membrane matrix medium for passage, FACS, or cryopreservation
<ol>
	<li>To dissociate the organoids from the GFR-basement membrane matrix medium, remove media from the basal chamber and add 2 &#181;g/mL of dispase (1 mL) in the apical chamber.</li>
	<li>Gently triturate the medium /dispase mixture with a P1000 pipette and place in the incubator for 15 min. Gently triturate the mixture again and incubate for another 15 min.</li>
	<li>Add 1 mL of chilled PBS (4 &#176;C) and transfer organoids with the matrix medium into a 15 mL conical centrifuge tube. Spin at 400 x g for 5 min. Remove the supernatant carefully, not to disturb the cell pellet.</li>
	<li>Wash once more with 1 mL chilled PBS and spin down at 400 x g for 5 min. Remove the supernatant carefully, not to disturb the medium/cell mixture.</li>
	<li>Add 1 mL of cell detachment solution to the conical centrifuge tube, gently triturate resuspend the GFR-Basement membrane matrix medium/cell mixture. Place in the incubator for 12 min for passaging cells as aggregates or for cryopreservation), or 20 min for single cell suspension.</li>
	<li>Add equal volume of quenching media and spin down at 400 x g for 5 min. Resuspend in quenching medium + 10 &#181;M of ROCK Inhibitor Y-27632. 
	NOTE: At this step, no residual basement membrane medium should be seen in the tube. If residual medium remains, repeat steps 8.5 and 8.6.</li>
	<li>Perform a cell count. Calculate the volume needed for downstream applications.</li>
</ol>

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The authors have nothing to disclose.

The successful differentiation of 3D whole lung organoids (WLO) relies on a multi-step, 6-week protocol with attention to detail, including time of exposure to growth factors and small molecules, cellular density after passaging, and the quality of hiPSCs. For troubleshooting, see Table 2. hiPSCs should be approximately 70%-80% confluent, with less than 5% spontaneous differentiation prior to dissociation. This protocol calls for &#34;mTeSR plus&#34; medium; however,&#160; plain &#34;mTeSR&#34; medium&#1...

The lung is a complicated, heterogeneous, dynamic organ that develops in six distinct stages - embryonic, pseudoglandular, canalicular, saccular, alveolar, and microvascular maturation1,2. The latter two phases occur pre and postnatally in human development while the first four stages occur exclusively during fetal development unless preterm birth occurs3. The embryonic phase begins in the endodermal germ layer and concludes with the budding of the trachea and lung buds. Lung development occurs in part via signaling between the epithelial and mesenchymal cells4. These interactions result in lung branching, proliferation, cellular fate determination and cellular differentiation of the developing lung. The lung is divided into conducting zones (trachea to the terminal bronchioles) and respiratory zones (respiratory bronchioles to the alveoli). Each zone contains unique epithelial cell types; including basal, secretory, ciliated, brush, neuroendocrine, and ionocyte cells in the conducting airway5, followed by alveolar type I and II cells in the respiratory epithelium6. Much is still unknown about the development and response to injury of the various cell types. iPSC derived lung organoid models enable the study of mechanisms that drive human lung development, the effects of genetic mutations on pulmonary function, and the response of both the epithelium and mesenchyme to infectious agents without the need for primary human lung tissue.
Markers corresponding to the various stages of embryonic differentiation include CXCR4, cKit, FOXA2, and SOX17 for definitive endoderm (DE)7, FOXA2, TBX1, and SOX2 for anterior foregut endoderm (AFE)8, and NKX2-1 for early lung progenitor cells9. In embryonic lung development, the foregut divides into the dorsal esophagus and ventral trachea. The buds of the right and left lungs appear as two independent outpouchings around the tracheal bud10. During branching morphogenesis, the mesenchyme surrounding the epithelium produces elastic tissue, smooth muscle, cartilage, and vasculature11. The interaction between the epithelium and mesenchyme is essential for normal lung development. This includes the secretion of FGF1012 by the mesenchyme and SHH13 produced by the epithelium.
Here, we describe a protocol for the directed differentiation of hiPSCs into three-dimensional (3D) whole lung organoids (WLO). While there are similar approaches that incorporate isolation of lung progenitor cells via sorting at the LPC stage to make alveolar-like14,15 (distal) organoids or airway16 (proximal) organoids, or generate ventral-anterior foregut spheroids to make human lung organoids expressing alveolar-cell and mesenchymal markers and bud tip progenitor organoids17, the strength of this method is the inclusion of both lung epithelial and mesenchymal cell types to pattern and orchestrate lung branching morphogenesis, maturation, and expansion in vitro.
This protocol uses small molecules and growth factors to direct the differentiation of pluripotent stem cells through definitive endoderm, anterior foregut endoderm, and lung progenitor cells. These cells are then induced into 3D whole lung organoids through important developmental steps, including branching and maturation. The summary of the differentiation protocol is shown in Figure 1a with representative brightfield images of endodermal and organoid differentiation shown in Figure 1b. Figure 1c,d show the gene expression details of endodermal differentiation as well as the gene expression of both the proximal and distal populations of lung epithelial cells after completing the differentiation.

<table><tbody><tr><td>&lt;strong&gt;Cell Culture&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>12 well plates</td><td>Corning</td><td>3512</td><td></td></tr><tr><td>12-well inserts, 0.4um, translucent</td><td>VWR</td><td>10769-208</td><td></td></tr><tr><td>2-mercaptoethanol</td><td>Sigma-Aldrich</td><td>M3148</td><td></td></tr><tr><td>Accutase</td><td>Innovative Cell Tech</td><td>AT104</td><td></td></tr><tr><td>ascorbic acid</td><td>Sigma</td><td>A4544</td><td></td></tr><tr><td>B27 without retinoic acid</td><td>ThermoFisher</td><td>12587010</td><td></td></tr><tr><td>Bovine serum albumin (BSA) Fraction V, 7.5% solution</td><td>Gibco</td><td>15260-037</td><td></td></tr><tr><td>Dispase</td><td>StemCellTech</td><td>7913</td><td></td></tr><tr><td>DMEM/F12</td><td>Gibco</td><td>10565042</td><td></td></tr><tr><td>FBS</td><td>Gibco</td><td>10082139</td><td></td></tr><tr><td>Glutamax</td><td>Life Technologies</td><td>35050061</td><td></td></tr><tr><td>Ham&amp;rsquo;s F12</td><td>Invitrogen</td><td>11765-054</td><td></td></tr><tr><td>HEPES</td><td>Gibco</td><td>15630-080</td><td></td></tr><tr><td>Iscove&amp;rsquo;s Modified Dulbecco&amp;rsquo;s Medium (IMDM) + Glutamax</td><td>Invitrogen</td><td>31980030</td><td></td></tr><tr><td>Knockout Serum Replacement (KSR)</td><td>Life Technologies</td><td>10828028</td><td></td></tr><tr><td>Matrigel</td><td>Corning</td><td>354230</td><td></td></tr><tr><td>Monothioglycerol</td><td>Sigma</td><td>M6145</td><td></td></tr><tr><td>mTeSR plus Kit (10/case)</td><td>Stem Cell Tech</td><td>5825</td><td></td></tr><tr><td>N2</td><td>ThermoFisher</td><td>17502048</td><td></td></tr><tr><td>NEAA</td><td>Life Technologies</td><td>11140050</td><td></td></tr><tr><td>Pen/strep</td><td>Lonza</td><td>17-602F</td><td></td></tr><tr><td>ReleSR</td><td>Stem Cell Tech</td><td>5872</td><td></td></tr><tr><td>RPMI1640 + Glutamax</td><td>Life Technologies</td><td>12633012</td><td></td></tr><tr><td>TrypLE</td><td>Gibco</td><td>12605-028</td><td></td></tr><tr><td>Y-27632 (Rock Inhibitor)</td><td>R&amp;amp;D Systems</td><td>1254/1</td><td></td></tr><tr><td>&lt;strong&gt;Growth Factors/Small Molecules&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Activin A</td><td>R&amp;amp;D Systems</td><td>338-AC</td><td></td></tr><tr><td>All-trans retinoic acid (RA)</td><td>Sigma-Aldrich</td><td>R2625</td><td></td></tr><tr><td>BMP4</td><td>R&amp;amp;D Systems</td><td>314-BP/CF</td><td></td></tr><tr><td>Br-cAMP</td><td>Sigma-Aldrich</td><td>B5386</td><td></td></tr><tr><td>CHIR99021</td><td>Abcam</td><td>ab120890</td><td></td></tr><tr><td>Dexamethasone</td><td>Sigma-Aldrich</td><td>D4902</td><td></td></tr><tr><td>Dorsomorphin</td><td>R&amp;amp;D Systems</td><td>3093</td><td></td></tr><tr><td>EGF</td><td>R&amp;amp;D Systems</td><td>236-EG</td><td></td></tr><tr><td>FGF10</td><td>R&amp;amp;D Systems</td><td>345-FG/CF</td><td></td></tr><tr><td>FGF7</td><td>R&amp;amp;D Systems</td><td>251-KG/CF</td><td></td></tr><tr><td>IBMX (3-Isobtyl-1-methylxanthine)</td><td>Sigma-Aldrich</td><td>I5879</td><td></td></tr><tr><td>SB431542</td><td>R&amp;amp;D Systems</td><td>1614</td><td></td></tr><tr><td>VEGF/PIGF</td><td>R&amp;amp;D Systems</td><td>297-VP/CF</td><td></td></tr><tr><td>&lt;strong&gt;Primary antibodies&lt;/strong&gt;</td><td></td><td></td><td>&lt;strong&gt;Dilution rate&lt;/strong&gt;</td></tr><tr><td>CXCR4-PE</td><td>R&amp;amp;D Systems</td><td>FAB170P</td><td>1:200 (F)</td></tr><tr><td>HOPX</td><td>Santa Cruz Biotech</td><td>sc-398703</td><td>0.180555556</td></tr><tr><td>HTII-280</td><td>Terrace Biotech</td><td>TB-27AHT2-280</td><td>0.145833333</td></tr><tr><td>KRT5</td><td>Abcam</td><td>ab52635</td><td>0.180555556</td></tr><tr><td>NKX2-1</td><td>Abcam</td><td>ab76013</td><td>0.25</td></tr><tr><td>NKX2-1-APC</td><td>LS-BIO</td><td>LS-C264437</td><td>1:1000 (F)</td></tr><tr><td>proSPC</td><td>Abcam</td><td>ab40871</td><td>0.215277778</td></tr><tr><td>SCGB3A2</td><td>Abcam</td><td>ab181853</td><td>0.25</td></tr><tr><td>SOX2</td><td>Invitrogen</td><td>MA1-014</td><td>0.180555556</td></tr><tr><td>SOX9</td><td>R&amp;amp;D Systems</td><td>AF3075</td><td>0.180555556</td></tr><tr><td>SPB (mature)</td><td>7 Hills</td><td>48604</td><td>1: 1500 (F) 1:500 (W)&lt;sup&gt;a&lt;/sup&gt;</td></tr><tr><td>SPC (mature)</td><td>LS Bio</td><td>LS-B9161</td><td>1:100 (F); 1:500 (W)&lt;sup&gt; a&lt;/sup&gt;</td></tr></tbody></table>

generation of 3d whole lung organoids from induced pluripotent stem cells for modeling lung developmental biology and disease

Human lung development and disease has been difficult to study due to the lack of biologically relevant in vitro model systems. Human induced pluripotent stem cells (hiPSCs) can be differentiated stepwise into 3D multicellular lung organoids, made of both epithelial and mesenchymal cell populations. We recapitulate embryonic developmental cues by temporally introducing a variety of growth factors and small molecules to efficiently generate definitive endoderm, anterior foregut endoderm, and subsequently lung progenitor cells. These cells are then embedded in growth factor reduced (GFR)-basement membrane matrix medium, allowing them to spontaneously develop into 3D lung organoids in response to external growth factors. These whole lung organoids (WLO) undergo early lung developmental stages including branching morphogenesis and maturation after exposure to dexamethasone, cyclic AMP and isobutylxanthine. WLOs possess airway epithelial cells expressing the markers KRT5 (basal), SCGB3A2 (club) and MUC5AC (goblet) as well as alveolar epithelial cells expressing HOPX (alveolar type I) and SP-C (alveolar type II). Mesenchymal cells are also present, including smooth muscle actin (SMA), and platelet-derived growth factor receptor A (PDGFR&#945;). iPSC derived WLOs can be maintained in 3D culture conditions for many months and can be sorted for surface markers to purify a specific cell population. iPSC derived WLOs can also be utilized to study human lung development, including signaling between the lung epithelium and mesenchyme, to model genetic mutations on human lung cell function and development, and to determine the cytotoxicity of infective agents.

24 hours after plating, day 1, iPSCs should be 50%-90% confluent. On day 2, DE should be 90%-95% confluent. During DE induction, it is common to observe significant cell death on day 4 but attached cells will retain a compact cobblestone morphology (Figure 2b). Discontinue differentiation if the majority of adherent cells detach and consider shortening exposure to DE media with activin A by 6-12 h. During AFE induction, cell death is minimal, and cells remain adherent, but will appear smalle...

Watch this Scientific Journal Video about Generation of 3D Whole Lung Organoids from Induced Pluripotent Stem Cells for Modeling Lung Developmental Biology and Disease at JoVE.com

Generation of 3D Whole Lung Organoids from Induced Pluripotent Stem Cells for Modeling Lung Developmental Biology and Disease

The article describes step wise directed differentiation of induced pluripotent stem cells to three-dimensional whole lung organoids containing both proximal and distal epithelial lung cells along with mesenchyme.

Human lung development and disease has been difficult to study due to the lack of biologically relevant in vitro model systems. Human induced pluripotent ...

generation-3d-whole-lung-organoids-from-induced-pluripotent-stem

Universidad San Sebastian

Research

JoVE Journal

Developmental Biology

7.8K Views.  University of California, San Diego School of Medicine. The article describes step wise directed differentiation of induced pluripotent stem cells to three-dimensional whole lung organoids containing both proximal and distal epithelial lung cells along with mesenchyme.

Video: Generation of 3D Whole Lung Organoids from Induced Pluripotent Stem Cells for Modeling Lung Developmental Biology and Disease

Generation of ESC-derived Mouse Airway Epithelial Cells Using Decellularized Lung Scaffolds

Lung lineage differentiation requires integration of complex environmental cues that include growth factor signaling, cell-cell interactions and cell-matrix interactions. Due to this complexity, recapitulation of lung development in vitro to promote differentiation of stem cells to lung epithelial cells has been challenging. In this protocol, decellularized lung scaffolds are used to mimic the 3-dimensional environment of the lung and generate stem cell-derived airway epithelial cells. Mouse embryonic stem cell are first differentiated to the endoderm lineage using an embryoid body (EB) culture method with activin A. Endoderm cells are then seeded onto decellularized scaffolds and cultured at air-liquid interface for up to 21 days. This technique promotes differentiation of seeded cells to functional airway epithelial cells (ciliated cells, club cells, and basal cells) without additional growth factor supplementation. This culture setup is defined, serum-free, inexpensive, and reproducible. Although there is limited contamination from non-lung endoderm lineages in culture, this protocol only generates airway epithelial populations and does not give rise to alveolar epithelial cells. Airway epithelia generated with this protocol can be used to study cell-matrix interactions during lung organogenesis and for disease modeling or drug-discovery platforms of airway-related pathologies such as cystic fibrosis.

This protocol efficiently directs mouse embryonic stem cell-derived definitive endoderm to mature airway epithelial cells. This differentiation technique uses 3-dimensional decellularized lung scaffolds to direct lung lineage specification, in a defined, serum-free culture setting.

Lung lineage differentiation requires integration of complex environmental cues that include growth factor signaling, cell-cell interactions and ...

Bioengineering

Generating Self-Assembling Human Heart Organoids Derived from Pluripotent Stem Cells

The ability to study human cardiac development in health and disease is highly limited by the capacity to model the complexity of the human heart in vitro. Developing more efficient organ-like platforms that can model complex in vivo phenotypes, such as organoids and organs-on-a-chip, will enhance the ability to study human heart development and disease. This paper describes a protocol to generate highly complex human heart organoids (hHOs) by self-organization using human pluripotent stem cells and stepwise developmental pathway activation using small molecule inhibitors. Embryoid bodies (EBs) are generated in a 96-well plate with round-bottom, ultra-low attachment wells, facilitating suspension culture of individualized constructs.
The EBs undergo differentiation into hHOs by a three-step Wnt signaling modulation strategy, which involves an initial Wnt pathway activation to induce cardiac mesoderm fate, a second step of Wnt inhibition to create definitive cardiac lineages, and a third Wnt activation step to induce proepicardial organ tissues. These steps, carried out in a 96-well format, are highly efficient, reproducible, and produce large amounts of organoids per run. Analysis by immunofluorescence imaging from day 3 to day 11 of differentiation reveals first and second heart field specifications and highly complex tissues inside hHOs at day 15, including myocardial tissue with regions of atrial and ventricular cardiomyocytes, as well as internal chambers lined with endocardial tissue. The organoids also exhibit an intricate vascular network throughout the structure and an external lining of epicardial tissue. From a functional standpoint, hHOs beat robustly and present normal calcium activity as determined by Fluo-4 live imaging. Overall, this protocol constitutes a solid platform for in vitro studies in human organ-like cardiac tissues.

Here, we describe a protocol to create developmentally relevant human heart organoids (hHOs) efficiently using human pluripotent stem cells by self-organization. The protocol relies on the sequential activation of developmental cues and produces highly complex, functionally relevant human heart tissues.

The ability to study human cardiac development in health and disease is highly limited by the capacity to model the complexity of the human heart in ...

Biochemistry

Generating 3D Spheres and 2D Air-Liquid Interface Cultures of Human Induced Pluripotent Stem Cell-Derived Type 2 Alveolar Epithelial Cells

In the lung, the alveolar epithelium is a physical barrier from environmental stimuli and plays an essential role in homeostasis and disease. Type 2 alveolar epithelial cells (AT2s) are the facultative progenitors of the distal lung epithelium. Dysfunction and injury of AT2s can result from and contribute to various lung diseases. Improved understanding of AT2 biology is, thus, critical for understanding lung biology and disease; however, primary human AT2s are generally difficult to isolate and limited in supply. To overcome these limitations, human induced pluripotent stem cell (iPSC)-derived type 2 alveolar epithelial cells (iAT2s) can be generated through a directed differentiation protocol that recapitulates in vivo lung development. iAT2s grow in feeder-free conditions, share a transcriptomic program with human adult primary AT2s, and execute key functions of AT2s such as production, packaging, and secretion of surfactant. This protocol details the methods for maintaining self-renewing iAT2s through serial passaging in three-dimensional (3D) culture or adapting iAT2s to air-liquid interface (ALI) culture. A single-cell suspension of iAT2s is generated before plating in 3D solubilized basement membrane matrix (hereafter referred to as &#34;matrix&#34;), where they self-assemble into monolayered epithelial spheres. iAT2s in 3D culture can be serially dissociated into single-cell suspensions to be passaged or plated in 2D ALI culture. In ALI culture, iAT2s form a polarized monolayer with the apical surface exposed to air, making this platform readily amenable to environmental exposures. Hence, this protocol generates an inexhaustible supply of iAT2s, producing upwards of 1 x 1030 cells per input cell over 15 passages while maintaining the AT2 program indicated by SFTPCtdTomato expression. The resulting cells represent a reproducible and relevant platform that can be applied to study genetic mutations, model environmental exposures, or screen drugs.

The present protocol describes human induced pluripotent stem cell-derived type 2 alveolar epithelial-like cells (iAT2s). These cells can be cultured as self-renewing spheres in 3D culture or adapted to air-liquid interface (ALI) culture.

In the lung, the alveolar epithelium is a physical barrier from environmental stimuli and plays an essential role in homeostasis and disease. Type 2 ...

Generation of 3D Midbrain Organoids from Human-Induced Pluripotent Stem Cells

The development of midbrain organoids (MOs) from human pluripotent stem cells (hPSCs) represents a significant advancement in understanding brain development, facilitating precise disease modeling, and advancing therapeutic research. This protocol outlines a method for generating midbrain-specific organoids using induced pluripotent stem cells (iPSCs), employing a strategic differentiation approach. Key techniques include dual-SMAD inhibition to suppress SMAD signaling, administration of fibroblast growth factor 8b (FGF-8b), and activation of the Sonic Hedgehog pathway using the agonist purmorphamine, guiding iPSCs towards a midbrain fate.
The organoids produced by this method achieve diameters up to 2 mm and incorporate a diverse array of neuroepithelial cell types, reflecting the midbrain&#39;s inherent cellular diversity. Validation of these organoids as authentic midbrain structures involves the expression of midbrain-specific markers, confirming their identity. A notable outcome of this methodology is the effective differentiation of iPSCs into dopaminergic neurons, which are characteristic of the midbrain.
The significance of this protocol lies in its ability to produce functionally mature, midbrain-specific organoids that closely replicate essential aspects of the midbrain, offering a valuable model for in-depth exploration of midbrain developmental processes and the pathophysiology of related disorders such as Parkinson&#39;s disease. Thus, this protocol serves as a crucial resource for researchers seeking to enhance our understanding of the human brain and develop new treatments for neurodegenerative diseases, making it an indispensable tool in the field of neurological research.

This protocol describes a novel method for creating 3D midbrain organoids from human induced pluripotent stem cells, guiding their formation to mimic native midbrain tissue, thereby aiding in the study of development and disorders.

The development of midbrain organoids (MOs) from human pluripotent stem cells (hPSCs) represents a significant advancement in understanding brain ...

Generation of Human 3D Lung Tissue Cultures (3D-LTCs) for Disease Modeling

Translation of novel discoveries to human disease is limited by the availability of human tissue-based models of disease. Precision-cut lung slices (PCLS) used as 3D lung tissue cultures (3D-LTCs) represent an elegant and biologically highly relevant 3D cell culture model, which highly resemble in situ tissue due to their complexity, biomechanics and molecular composition. Tissue slicing is widely applied in various animal models. 3D-LTCs derived from human PCLS can be used to analyze responses to novel drugs, which might further help to better understand the mechanisms and functional effects of drugs in human tissue. The preparation of PCLS from surgically resected lung tissue samples of patients, who experienced lung lobectomy, increases the accessibility of diseased and peritumoral tissue. Here, we describe a detailed protocol for the generation of human PCLS from surgically resected soft-elastic patient lung tissue. Agarose was introduced into the bronchoalveolar space of the resectates, thus preserving lung structure and increasing the tissue&#39;s stiffness, which is crucial for subsequent slicing. 500 &#181;m thick slices were prepared from the tissue block with a vibratome. Biopsy punches taken from PCLS ensure comparable tissue sample sizes and further increase the amount of tissue samples. The generated lung tissue cultures can be applied in a variety of studies in human lung biology, including the pathophysiology and mechanisms of different diseases, such as fibrotic processes at its best at (sub-)cellular levels. The highest benefit of the 3D-LTC ex vivo model is its close representation of the in situ human lung in respect of 3D tissue architecture, cell type diversity and lung anatomy as well as the potential for assessment of tissue from individual patients, which is relevant to further develop novel strategies for precision medicine.

Generation of Human 3D Lung Tissue Cultures 3D-LTCs for Disease Modeling

Here, we present a protocol for the preparation of agarose-filled human precision-cut lung slices from resected patient tissue that are suitable for generating 3D lung tissue cultures to model human lung diseases in biological and biomedical studies.

Translation of novel discoveries to human disease is limited by the availability of human tissue-based models of disease. Precision-cut lung slices (PCLS) ...

Medicine

hiPSC-Derived Vascular Organoids for Drug Screening and Disease Modeling

Vascular Organoid Generation from Human-Induced Pluripotent Stem Cells

Vascular organoids derived from human induced pluripotent stem cells (hiPSCs) recapitulate the cell type diversity and complex architecture of human vascular networks. This three-dimensional (3D) model holds substantial potential for vascular pathology modeling and in vitro drug screening. Despite recent advances, a key technical challenge remains in reproducibly generating organoids with consistent quality, which is crucial for downstream assays and applications. Here, a modified protocol is presented that improves both the homogeneity and reproducibility of vascular organoid generation. The modified protocol incorporates the use of microwells and the CEPT cocktail (chroman 1, emricasan, polyamines, and the integrated stress response inhibitor, trans-ISRIB) to improve embryoid body formation and cell survival. Differentiated, mature vascular organoids generated using this protocol are characterized by whole-mount 3D immunofluorescence microscopy to analyze their morphology and complex vasculature. This protocol enables the production of high-quality vascular organoids in a scalable manner, potentially facilitating their use in disease modeling and drug screening applications.

Author Spotlight: Improving Reproducibility in Vascular Organoids Using ROCK Inhibitors and Microwell Confinement

This protocol presents a method for generating vascular organoids using human pluripotent stem cells.

Vascular organoids derived from human induced pluripotent stem cells (hiPSCs) recapitulate the cell type diversity and complex architecture of human ...

Single-Cell Resolution Three-Dimensional Imaging of Intact Organoids

Organoid technology, in vitro 3D culturing of miniature tissue, has opened a new experimental window for cellular processes that govern organ development and function as well as disease. Fluorescence microscopy has played a major role in characterizing their cellular composition in detail and demonstrating their similarity to the tissue they originate from. In this article, we present a comprehensive protocol for high-resolution 3D imaging of whole organoids upon immunofluorescent labeling. This method is widely applicable for imaging of organoids differing in origin, size and shape. Thus far we have applied the method to airway, colon, kidney, and liver organoids derived from healthy human tissue, as well as human breast tumor organoids and mouse mammary gland organoids. We use an optical clearing agent, FUnGI, which enables the acquisition of whole 3D organoids with the opportunity for single-cell quantification of markers. This three-day protocol from organoid harvesting to image analysis is optimized for 3D imaging using confocal microscopy.

The entire 3D structure and cellular content of organoids, as well as their phenotypic resemblance to the original tissue can be captured using the single-cell resolution 3D imaging protocol described here. This protocol can be applied to a wide range of organoids varying in origin, size and shape.

Organoid technology, in vitro 3D culturing of miniature tissue, has opened a new experimental window for cellular processes that govern organ development ...

Biology

Isolation and Enrichment of Human Lung Epithelial Progenitor Cells for Organoid Culture

Epithelial organoid models serve as valuable tools to study the basic biology of an organ system and for disease modeling. When grown as organoids, epithelial progenitor cells can self-renew and generate differentiating progeny that exhibit cellular functions similar to those of their in vivo counterparts. Herein we describe a step-by-step protocol to isolate region-specific progenitors from human lung and generate 3D organoid cultures as an experimental and validation tool. We define proximal and distal regions of the lung with the goal of isolating region-specific progenitor cells. We utilized a combination of enzymatic and mechanical dissociation to isolate total cells from the lung and trachea. Specific progenitor cells were then fractionated from the proximal or distal origin cells using fluorescence associated cell sorting (FACS) based on cell type-specific surface markers, such as NGFR&#160;for sorting basal cells and HTII-280 for sorting alveolar type II cells. Isolated basal or alveolar type II progenitors were used to generate 3D organoid cultures. Both distal and proximal progenitors formed organoids with a colony forming efficiency of 9-13% in distal region and 7-10% in proximal region when plated 5000 cell/well on day 30. Distal organoids maintained HTII-280+ alveolar type II cells in culture whereas proximal organoids differentiated into ciliated and secretory cells by day 30. These 3D organoid cultures can be used as an experimental tool for studying the cell biology of lung epithelium and epithelial mesenchymal interactions, as well as for the development and validation of therapeutic strategies targeting epithelial dysfunction in a disease.

This article provides a detailed methodology for tissue dissociation and cellular fractionation approaches allowing enrichment of viable epithelial cells from proximal and distal regions of the human lung. Herein these approaches are applied for the functional analysis of lung epithelial progenitor cells through the use of 3D organoids culture models.

Epithelial organoid models serve as valuable tools to study the basic biology of an organ system and for disease modeling. When grown as organoids, ...

Establishing Human Lung Organoids and Proximal Differentiation to Generate Mature Airway Organoids

The lack of a robust in vitro model of the human respiratory epithelium hinders the understanding of the biology and pathology of the respiratory system. We describe a defined protocol to derive human lung organoids from adult stem cells in the lung tissue and induce proximal differentiation to generate mature airway organoids. The lung organoids are then consecutively expanded for over 1 year with high stability, while the differentiated airway organoids are used to morphologically and functionally simulate human airway epithelium to a near-physiological level. Thus, we establish a robust organoid model of the human airway epithelium. The long-term expansion of lung organoids and differentiated airway organoids generates a stable and renewable source, enabling scientists to reconstruct and expand the human airway epithelial cells in culture dishes. The human lung organoid system provides a unique and physiologically active in vitro model for various applications, including studying virus-host interaction, drug testing, and disease modeling.

The protocol presents a method to derive human lung organoids from primary lung tissues, expand the lung organoids and induce proximal differentiation to generate 3D and 2D airway organoids that faithfully phenocopy the human airway epithelium.

The lack of a robust in vitro model of the human respiratory epithelium hinders the understanding of the biology and pathology of the respiratory system. ...

A High-Throughput Platform for Culture and 3D Imaging of Organoids

The characterization of a large number of three-dimensional (3D) organotypic cultures (organoids) at different resolution scales is currently limited by standard imaging approaches. This protocol describes a way to prepare microfabricated organoid culture chips, which enable multiscale, 3D live imaging on a user-friendly instrument requiring minimal manipulations and capable of up to 300 organoids/h imaging throughput. These culture chips are compatible with both air and immersion objectives (air, water, oil, and silicone) and a wide range of common microscopes (e.g., spinning disk, point scanner confocal, wide field, and brightfield). Moreover, they can be used with light-sheet modalities such as the single-objective, single-plane illumination microscopy (SPIM) technology (soSPIM). 
The protocol described here gives detailed steps for the preparation of the microfabricated culture chips and the culture and staining of organoids. Only a short length of time is required to become familiar with, and consumables and equipment can be easily found in normal biolabs. Here, the 3D imaging capabilities will be demonstrated only with commercial standard microscopes (e.g., spinning disk for 3D reconstruction and wide field microscopy for routine monitoring).

This paper presents a fabrication protocol for a new type of culture substrate with hundreds of microcontainers per mm2, in which organoids can be cultured and observed using high-resolution microscopy. The cell seeding and immunostaining protocols are also detailed.

The characterization of a large number of three-dimensional (3D) organotypic cultures (organoids) at different resolution scales is currently limited by ...