KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Alexa Fluor 488 Goat anti-Rabbit secondary antibody | ThermoScientific | Cat# A11008 |
| Alexa Fluor 647 Donkey anti-Mouse secondary antibody | ThermoScientific | Cat# A-31571 |
| anti-FGF1 neutralizing antibody | R&D System | Cat# AF232 |
| anti-FGF2 neutralizing antibody | R&D System | Cat# AF-233-NA |
| anti-FGF5 neutralizing antibody | R&D System | Cat# AF-237-NA |
| anti-FGF7 neutralizing antibody | R&D System | Cat# AF-251-NA |
| anti-FGF9 neutralizing antibody | R&D System | Cat# MAB273–100 |
| anti-Mouse IgG HRP-linked secondary antibody | Cell Signaling Technology | Cat# 7076 |
| anti-Rabbit IgG HRP-linked secondary antibody | Cell Signaling Technology | Cat# 7074 |
| CD8 | Leica Biosystems | RTU Clone 4B11 |
| Cytokeratin 8/18 | Dako | Cat# M3652 |
| EGFR | Santa Cruz | Cat# sc-373746 |
| Erk1/2 | Cell Signaling Technology | Cat# 9102 |
| Histone H3 | Cell Signaling Technology | Cat# 4499 |
| Ki67 | Leica Biosystems | IVT Clone K2 |
| Normal IgG Control | R&D System | Cat# AB-108-C |
| Normal IgG Control | R&D System | Cat# MAB002 |
| phospho-EGFR (Y1068) | Abcam | Cat# ab5644 |
| phospho-Erk 1/2 (Thr202/Tyr204) | Cell Signaling Technology | Cat# 9101 |
| phospho-MET (Tyr1234/1235) | Cell Signaling Technology | Cat# 3129 |
| phospho-S6 (Ser240/244) | Cell Signaling Technology | Cat# 5364 |
| phospho-SMAD2 (Ser465/467) | Cell Signaling Technology | Cat# 3108 |
| phospho-STAT3 (Tyr705) | Cell Signaling Technology | Cat# 9145 |
| phosphor-SMAD3 (Ser423/425) | Invitrogen | Cat# 710756 |
| S6 | Cell Signaling Technology | Cat# 2217 |
| SMAD2 | Cell Signaling Technology | Cat# 3103 |
| SMAD3 | Abcam | Cat# ab40854 |
| TBX2 | Abnova | Cat# H00006909-M01 |
| Vimentin | Dako | Cat# M0725 |
| α-SMA | Abcam | Cat# ab5694 |
| β-Actin | Cell Signaling Technology | Cat# 4970 |
| Biological samples | ||
| NSCLC biopsy tissue | Massachusetts General Hospital, Boston, MA | IRB #13–416 |
| Human peripheral blood mononuclear cell | STEMCELL | Cat# 70025 |
| Human peripheral blood CD8+ T-cells | STEMCELL | Cat# 200–0164 |
| Chemicals, peptides, and recombinant proteins | ||
| Osimertinib | Selleckchem | Cat# S7297 |
| INC280 | Selleckchem | Cat# S2788 |
| BGJ398 | Selleckchem | Cat# S2183 |
| Lorlatinib | Selleckchem | Cat# S7536 |
| SH-4–54 | Selleckchem | Cat# S7337 |
| GDC0941 | Selleckchem | Cat# S1065 |
| R406 | Selleckchem | Cat# S2194 |
| SB431542 | Selleckchem | Cat# S1067 |
| ABT263 | Selleckchem | Cat# S1001 |
| AEW541 | Selleckchem | Cat# S1034 |
| AZD0530 | Selleckchem | Cat# S1006 |
| LEE011 | Selleckchem | Cat# S7440 |
| MLN8237 | Selleckchem | Cat# S1133 |
| Ruxolitinib | Selleckchem | Cat# S1378 |
| TAE226 | Selleckchem | Cat# S2820 |
| TP0903 | Selleckchem | Cat# S7846 |
| Rapamycin | Selleckchem | Cat# S1039 |
| Trametinib | Selleckchem | Cat# S2673 |
| Vactosertib | Selleckchem | Cat# S7530 |
| Cilengitide | MedChemExpress | Cat# HY-16141 |
| HGF | Peprotech | Cat# 100–39 |
| FGF1 | Peprotech | Cat# 100–17A |
| FGF2 | Peprotech | Cat# 100–18C |
| FGF5 | Peprotech | Cat# 100–34 |
| FGF7 | Peprotech | Cat# 100–19 |
| FGF9 | Peprotech | Cat# 100–23 |
| TGF-β1 | Peprotech | Cat# 100–21 |
| IL-2 | STEMCELL | Cat# 78036.1 |
| DNase I | STEMCELL | Cat# 07900 |
| Type-I collagen | Nitta Gelatin | Cat# 631–00651 |
| Liberase | Roche | Cat# LIBDH-RO |
| Blasticidin | Gibico | Cat# A1113903 |
| Critical commercial assays | ||
| Tumor Dissociation Kit, human | Miltenyi Biotec | Cat# 130–095-929 |
| Anti-fibroblast microbeads, human | Miltenyi Biotec | Cat# 130–050-601 |
| pLenti6/V5 Directional TOPO Cloning Kit | Invitrogen | Cat# K495510 |
| ViraPower Lentiviral Directional TOPO Expression Kit | Invitrogen | Cat# K495000 |
| Lenti-X Concentrator | TaKaRa | Cat# 631232 |
| 3D Cell Culture Chips | AIMbiotech | Cat# DAX-1, HOL-1 |
| CellTracker Green CMFDA Dye | Invitrogen | Cat# C7025 |
| CellTracker Red CMTPX Dye | Invitrogen | Cat# C34552 |
| Hoechst 33342 | ThermoScientific | Cat# H3570 |
| BioCoat Transwell (0.4 µm) | Corning | Cat# 354570 |
| RNeasy Micro Kit | Qiagen | Cat# 74004 |
| TRAPeze Telomerase Detection Kit | Millipore | Cat# S7700 |
| Nunc Lab-Tek Chamber Slide System | ThermoScientific | Cat# 177429PK |
| RNAscope 2.5 HD Detection Kit-Brown | Advanced Cell Diagnostics | Cat# 322370 |
| RNAscope 2.5 HD Duplex Reagent Kit | Advanced Cell Diagnostics | Cat# 322430 |
| Nuclear Extraction Kit | Abcam | Cat# ab113474 |
| ELISA tests for HGF, FGF7 | RayBiotech | Cat# ELH-HGF-1, EHFGF7 |
| ELISA tests for IGFBP6 | Invitrogen | Cat# EHIGFBP6 |
| Customized quantitative proteomics array | RayBiotech | NA |
| Deposited data | ||
| NSCLC sc-RNAseq | (Lambrechts et al., 2018) | https://gbiomed.kuleuven.be/english/research/50000622/laboratories/54213024/scrnaseq_tutorial/fibroblasts |
| NSCLC sc-RNAseq | (N. Kim et al., 2020) | GSE131907 |
| NSCLC sc-RNAseq | (Laughney et al., 2020) | GSE123904 |
| NSCLC sc-RNAseq | (Maynard et al., 2020) | PRJNA591860 |
| Normal lung sc-RNAseq | (Travaglini et al., 2020) | EGAS00001004344 |
| RNAseq of NSCLC biopsies | (Roper et al., 2020) | NA |
| Stromal score in TCGA LUAD tumors | (Yoshihara et al., 2013) | NA |
| TCGA lung adenocarcinoma RNAseq (LUAD) | cBioPortal | http://www.cbioportal.org |
| Experimental models: Cell lines | ||
| 293FT | Invitrogen | Cat# R70007 |
| CCD-19Lu | ATCC | Cat# CCL-210 |
| Jurkat | ATCC | Cat# TIB-152 |
| THP-1 | ATCC | Cat# TIB-202 |
| NCI-H1975 | MGH Center for Molecular Therapeutics Cell Bank | NA |
| NCI-H3122 | MGH Center for Molecular Therapeutics Cell Bank | NA |
| HCC4006 | MGH Center for Molecular Therapeutics Cell Bank | NA |
| HCC827 | MGH Center for Molecular Therapeutics Cell Bank | NA |
| PC9 | MGH Center for Molecular Therapeutics Cell Bank | NA |
| MGH006–1 | MGH patient-derived cell line (Crystal et al., 2014) | NA |
| MGH021–5 | MGH patient-derived cell line (Crystal et al., 2014) | NA |
| MGH048–1 | MGH patient-derived cell line | NA |
| MGH119–1 | MGH patient-derived cell line (Jia et al., 2016) | NA |
| MGH121–1 | MGH patient-derived cell line (Jia et al., 2016; Niederst et al., 2015) | NA |
| MGH134–1 | MGH patient-derived cell line (Jia et al., 2016) | NA |
| MGH154–1 | MGH patient-derived cell line | NA |
| MGH164–1 | MGH patient-derived cell line | NA |
| MGH707–1 | MGH patient-derived cell line (Kodack et al., 2017) | NA |
| MGH708–1 | MGH patient-derived cell line | NA |
| MGH805–1 | MGH patient-derived cell line | NA |
| PDF cell lines | MGH patient-derived cell line | NA |
| Experimental models: Organisms/strains | ||
| Female athymic nude (Nu/Nu) mice | MGH Gnotobiotic Mouse Core | NA |
| Oligonucleotides | ||
| Individual siRNA for FGFR1 | Ambion | Cat# s5164, s5165, s5166 |
| Individual siRNA for FGFR2 | Ambion | Cat# s5173, s5174, s5175 |
| Individual siRNA for FGFR3 | Ambion | Cat# s5167, s5168, s5169 |
| Negative control siRNA | Ambion | Cat# 4390844 |
| ON-TARGETplus Human ETV1 siRNA Pool | Horizon | Cat# L-003801–00-0005 |
| ON-TARGETplus Human TBX2 siRNA Pool | Horizon | Cat# L-012196–00-0005 |
| ON-TARGETplus Non-targeting Control Pool | Horizon | Cat# D-001810–10-05 |
| Individual siRNA for ETV1 | Qiagen | Cat# 1027416-GS2115 |
| Individual siRNA for TBX2 | Qiagen | Cat# 1027416-GS6909 |
| Negative control siRNA | Qiagen | Cat# 1022076 |
| RNAscope probe for ACTA2 | Advanced Cell Diagnostics | Cat# 311811 |
| RNAscope probe for S100A4 | Advanced Cell Diagnostics | Cat# 422071 |
| RNAscope probe for HGF | Advanced Cell Diagnostics | Cat# 310761 |
| RNAscope probe for FGF7 | Advanced Cell Diagnostics | Cat# 443441 |
| RNAscope probe for FGFR2 | Advanced Cell Diagnostics | Cat# 311171 |
| RNAscope probe for KRT18 | Advanced Cell Diagnostics | Cat# 310211 |
| q-PCR primers | This paper (Table S7) | NA |
| Recombinant DNA | ||
| hTERT (NM_198253) | Applied Biological Materials | Cat# LV808298 |
| pLenti6/V5-hTERT | This paper | NA |
| Lenti ORF clone: TBX2 | Origene | Cat# RC208558 |
| Lenti ORF clone: ETV1 | Origene | Cat# RC210533 |
| Lenti ORF clone: vehicle | Origene | Cat# PS100001 |
| Software and algorithms | ||
| HALO ISH v2.2 | Indica Labs | NA |
| HALO Cytonuclear IHC v1.6 | Indica Labs | NA |
| iDEP.91 | (Ge et al., 2018) | http://bioinformatics.sdstate.edu/idep |
| ShinyGo v0.61 | (Ge et al., 2020) | http://bioinformatics.sdstate.edu/go/ |
| GraphPad Prism v7.0 | GraphPad Software Inc. | NA |
| Other | ||
| Bel-Art™ Cloning Cylinders | FisherScientific | Cat# 07–907-10 |
| Polybrene | Millipore | Cat# TR-1003-G |
| Lipofectamine RNAiMAX | Invitrogen | Cat# 13778150 |
| T-cell Media | STEMCELL | Cat# 10981 |
| 40μm Strainer | FisherScientific | Cat# 08–771-1 |