KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal to activated caspase 3 | Sigma Aldrich | Cat# C8487; RRID:AB_476884 |
| Mouse monoclonal to β actin | Sigma Aldrich | Cat# A1978; RRID:AB_476692 |
| Mouse monoclonal to CD26, PE conjugated (clone BA5b) | BioLegend | Cat# 302705; RRID:AB_314289 |
| Mouse monoclonal to CD47, PerCP-Cy5.5 conjugated (clone CC2C6) | BioLegend | Cat# 323110; RRID:AB_940461 |
| Rabbit polyclonal to CRB3 | Szymaniak et al., 2015 | N/A |
| Mouse IgG1 isotype, PE conjugated | BioLegend | Cat# 400113; RRID:AB_326435 |
| Mouse IgG1 isotype, PerCP-Cy5.5 conjugated | BioLegend | Cat# 400149; RRID:AB_893680 |
| Mouse monoclonal to E-Cadherin/CDH1 | BD Biosciences | Cat# 610181; RRID:AB_397580 |
| Mouse monoclonal to EPCAM | Santa Cruz | Cat# Sc-73491; RRID:AB_1122569 |
| Mouse monoclonal to GAPDH | Chemicon | Cat# MAB374; RRID:AB_2107445 |
| Rabbit monoclonal to NKX2-1 (clone EP15847) | Abcam | Cat# ab76013; RRID:AB_1310784 |
| Rabbit monoclonal to Phospho-Ezrin/Radixin/Moesin (p-ERM) | Cell Signaling | Cat# 3726; RRID:AB_10560513 |
| Mouse monoclonal to pro-SFTPC | Santa Cruz | Cat# sc-518029 |
| Rabbit polyclonal to pro-SFTPC | Seven Hills | Cat# WRAB-9337; RRID:AB_2335890 |
| Rabbit polyclonal to mature SFTPC | Seven Hills | Cat# WRAB-76694 |
| Rabbit polyclonal anti-NPRO-SFTPC | Beers et al., 1994 | N/A |
| Rabbit polyclonal anti-mature SFTPB (PT3) | Beers et al., 1992 | N/A |
| Rabbit monoclonal to MUC1 | Abcam | Cat# Ab218998 |
| Rabbit polyclonal to HA tag | Abcam | Cat# Ab20084; RRID:AB_445319 |
| Mouse monoclonal to RAGE | Abcam | Cat# Ab54741; RRID:AB_2242462 |
| Rabbit polyclonal to LC3B | Cell Signaling | Cat# 2775; RRID:AB_915950 |
| Mouse monoclonal to SQSTM1/p62 | Abcam | Cat# Ab56416; RRID:AB_945626 |
| Mouse monoclonal to CPM | Wako | Cat# 014-27501; RRID:AB_2801482 |
| Mouse monoclonal to SLC34A2 | Yin et al., 2008 | N/A |
| AffiniPure Donkey Anti-Rabbit IgG (H+L), AlexaFluor 488 conjugated | Jackson ImmunoResearch | Cat# 711-545-152; RRID:AB_2313584 |
| AffiniPure Donkey Anti-Rabbit IgG (H+L), AlexaFluor 647 conjugated | Jackson ImmunoResearch | Cat# 711-605-152; RRID:AB_2492288 |
| AffiniPure Donkey Anti-Mouse IgG (H+L), AlexaFluor 488 conjugated | Jackson ImmunoResearch | Cat# 715-545-150; RRID:AB_2340846 |
| AffiniPure Donkey Anti-Mouse IgG (H+L), AlexaFluor 647 conjugated | Jackson ImmunoResearch | Cat# 715-605-150; RRID:AB_2340862 |
| AffiniPure Goat Anti-Mouse IgG (H+L), AlexaFluor 488 conjugated | Jackson ImmunoResearch | Cat# 115-545-062; RRID:AB_2338845 |
| AffiniPure Goat Anti-Rabbit IgG (H+L), AlexaFluor 488 conjugated | Jackson ImmunoResearch | Cat# 111-545-144; RRID:AB_2338052 |
| AffiniPure Goat Anti-Mouse IgG (H+L), AlexaFluor 594 conjugated | Jackson ImmunoResearch | Cat# 115-585-146; RRID:AB_2338881 |
| AffiniPure Goat Anti-Rabbit IgG (H+L), AlexaFluor 594 conjugated | Jackson ImmunoResearch | Cat# 111-585-144; RRID:AB_2307325 |
| Goat Anti-Mouse IgG (H+L), HRP conjugated | BioRad | Cat# 0300-0108P; RRID:AB_808614 |
| Goat Anti-Rabbit IgG (H+L), HRP conjugated | BioRad | Cat# 5196-2504; RRID:AB_619908 |
| Chemicals, peptides and recombinant proteins | ||
| Human embryonic stem cell (hESC)- qualified (2D) Matrigel | Corning | Cat# 354277 |
| Growth Factor Reduced (3D) Matrigel | Corning | Cat# 356231 |
| SB431542 | Tocris | Cat# 1614 |
| Dorsomorphin | Stemgent | Cat# 04-0024 |
| CHIR99021 (CHIR) | Tocris | Cat# 4423 |
| Recombinant human FGF10 | R&D Systems | Cat# 345-FG-025 |
| Recombinant Human Keratinocyte Growth Factor (KGF) | R&D Systems | Cat# 251-KG-010 |
| Recombinant Human BMP4 (rhBMP4) | R&D Systems | Cat# 314-BP |
| Retinoic acid | Sigma Aldrich | Cat# R2625 |
| Y-27632 dihydrochloride | Tocris | Cat# 1254 |
| Ascorbic Acid | Sigma Aldrich | Cat# A4544 |
| 1-Thioglycerol (MTG) | Sigma Aldrich | Cat# M6145 |
| BSA 7.5% Stock | Thermo Fisher Scientific | Cat# 15260037 |
| 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (EDTA) | Sigma Aldrich | Cat# E7889 |
| N-(2-Hydroxyethyl)piperazine-N’-(2- ethanesulfonic acid) Solution (HEPES) | Sigma Aldrich | Cat# H0887 |
| Dexamethasone | Sigma Aldrich | Cat# D4902 |
| 8-bromoadenosine 30,50-cyclic monophosphate sodium salt (cAMP) | Sigma Aldrich | Cat# B7880 |
| 3-Isobutyl-1-methylxanthine (IBMX) | Sigma Aldrich | Cat# I5879 |
| Puromycin Dihydrochloride | Thermo Fisher Scientific | Cat# A1113802 |
| Geneticin Sulfate | Life Technologies | Cat# 11811-023 |
| 0.05% trypsin-EDTA | Invitrogen | Cat# 25300-120 |
| Defined Fetal Bovine Serum | Thermo Fisher Scientific | Cat# NC0652331 |
| Dimethyl Sulfoxide (DMSO) | Sigma Aldrich | Cat# D2650 |
| Calcein blue | Life Technologies | Cat# C1429 |
| Hoechst 33342 | Thermo Fisher Scientific | Cat#H3570 |
| DAPI, FluoroPure grade | Invitrogen | D21490 |
| ProLong Diamond Antifade Mountant | Invitrogen | Cat# P36965 |
| LysoTracker Green DND-26 | Thermo Fisher Scientific | Cat# L7526 |
| MitoTracker Green FM | Thermo Fisher Scientific | Cat# M7514 |
| BODIPY-493/503 | Thermo Fisher Scientific | Cat# D3922 |
| LysoSensor Yellow/Blue Dextran | Thermo Fisher Scientific | Cat# L22460 |
| Dispase II | Thermo Fisher Scientific | Cat# 17105-041 |
| Glutaraldehyde | Ladd Research | Cat# 20100 |
| Osmium Tetroxide | Polysciences | Cat# 0223D |
| Uranyl Acetate | Electron Microscopy Sciences | Cat# 22400 |
| EMbed 812 | Electron Microscopy Sciences | Cat# 14120 |
| Paraformaldehyde | Electron Microscopy Sciences | Cat# 19208 |
| Oligomycin | Millipore | Cat# 495455 |
| FCCP | Sigma Aldrich | Cat# C2920 |
| Antimycin A | Sigma Aldrich | Cat# A8674 |
| Bafilomycin A1 | Sigma Aldrich | Cat# B1793 |
| Torin | Tocris | Cat# 4247 |
| Critical commercial assays | ||
| RNeasy Mini Kit | QIAGEN | Cat# 74104 |
| QIAzol Lysis Reagent QIAGEN | QIAGEN | Cat# 79306 |
| TaqMan Fast Universal PCR Master Mix (2X) | Thermo Fisher | Cat# 4364103 |
| High-Capacity cDNA Reverse Transcription Kit | Applied Biosystems | Cat# 4368814 |
| EZ-TAL TALE Assembly Kit | System Bioscience | Cat# GE120A-1 |
| Click-iT EdU Alexa Fluor 647 Flow Cytometry Assay Kit | Thermo Fisher Scientific | Cat# C10424 |
| Lipofectamine LTX Kit | Thermo Fisher Scientific | Cat# 15338100 |
| P3 Primary Cell 4D-NucleofectorO X Kit S | Lonza | Cat# V4XP-3032 |
| Magnetic Luminex® Performance Assay Human HighSensitivity | R&D Systems | Cat# LXSAHM-31 |
| Deposited data | ||
| Single cell transcriptomic profiling of patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells expressing the SFTPCI73T variant and their gene-edited corrected counterparts | This paper | GEO (GSE160801) |
| Proteomic and phosphoproteomic profiling of SFTPCI73T expressing patient-specific pluripotent stem cell-derived alveolar epithelial type 2 cells and their gene-edited corrected counterparts. | This paper | PRIDE: PXD022334 |
| Experimental models: Cell lines | ||
| Human: SFTPCI73T/WT donor iPSC line (SPC2) | This paper | http://stemcellbank.bu.edu/Catalog/Item/Home |
| Human: Corrected SFTPC donor iPSC line (SPC2-CorrC1; SFTPCwt/wt) | This paper | http://stemcellbank.bu.edu/Catalog/Item/Home |
| Human: Donor iPSC line targeted with SFTPCtdTomato (SPC2-ST-C11; SFTPCI73T/tdT) | This paper | http://stemcellbank.bu.edu/Catalog/Item/Home |
| Human: Donor iPSC line targeted with SFTPCtdTomato (SPC2-ST-B2; SFTPCtdT/WT) | Kotton Lab; Hurley et al., 2020 | http://stemcellbank.bu.edu/Catalog/Item/Home |
| Oligonucleotides | ||
| See Table S3 | This paper | N/A |
| Recombinant DNA | ||
| EF1a-TALEN_HD; SFTPC recognition sequence of right TALEN 5′-TCA CCG GCG GGC TCT CCA TC-3′. | Kotton Lab; Jacob et al., 2017 | http://www.kottonlab.com |
| EF1a-TALEN_NN; SFTPC recognition sequence of left TALEN: 5’-TAG CAC CTG CAG CAA GAT GG-3′. | Kotton Lab; Jacob et al., 2017 | http://www.kottonlab.com |
| p1303-DV-SFTPC-tdTomato | Kotton Lab; Jacob et al., 2017 | http://www.kottonlab.com |
| pHAGE2 EF1a-Cre-IRES-NeoR-W | Kotton Lab; Jacob et al., 2017 | http://www.kottonlab.com |
| pHAGE2-Cre-IRES-PuroR | Kotton Lab; Somers et al., 2010 | Addgene #30205 |
| Software and algorithms | ||
| FlowJo version 10.5.3 | Becton, Dickinson & Company | https://www.flowjo.com/ |
| ImageJ | National Institutes of Health | https://imagej.nih.gov/ij/ |
| CellProfiler v2.0 | Broad Institute | https://cellprofiler.org |
| Prism | GraphPad | https://www.graphpad.com/ |
| Original code | This paper | https://github.com/CReM-BU/Alysandratos_iAEC2s |
| Other | ||
| StemDiff Definitive Endoderm Kit | StemCell Technologies | Cat# 05110 |
| mTeSR1 | StemCell Technologies | Cat# 05850 |
| Glutamax | Life Technologies | Cat# 35050-061 |
| Gentle Cell Dissociation Reagent | StemCell Technologies | Cat# 07174 |
| Seahorse XF Base Medium Minimal DMEM | Agilent Technologies | Cat# 103193-100 |
| Hank’s Buffered Saline Solution (HBSS; no calcium, no magnesium, no phenol red) | GIBCO | Cat# 14175095 |
| Ham’s F12 Medium | Cellgro | Cat# 10-080-CV |
| Iscove’s Modified Dulbecco’s Medium (IMDM) | Thermo Fisher Scientific | Cat# 12440053 |
| N2 Supplement | Invitrogen | Cat# 17502-048 |
| B27 Supplement | Invitrogen | Cat# 15260-037 |
| Primocin | Invitrogen | Cat# NC9141851 |