KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
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| Mouse monoclonal anti-YAP/TAZ (clone 63.7) | Santa Cruz Biotechnology | Cat# sc-101199; RRID: AB_1131430 |
| Rabbit monoclonal anti-YAP/TAZ (clone D24E4) | Cell Signaling Technology | Cat# 8418; RRID: AB_10950494 |
| Rabbit monoclonal anti-YAP (clone D8H1X) | Cell Signaling Technology | Cat# 14074; RRID: AB_2650491 |
| Mouse monoclonal anti-YAP (clone 1A12) | Cell Signaling Technology | Cat# 12395; RRID: AB_2797897 |
| Mouse monoclonal anti-GFP (clone B-2) | Santa Cruz Biotechnology | Cat# sc-9996; RRID: AB_627695 |
| Goat polyclonal anti-GFP | Abcam | Cat# ab6673; RRID: AB_305643 |
| Chicken polyclonal anti-GFP | Abcam | Cat# ab13970; RRID: AB_300798 |
| Mouse monoclonal anti-Ki67 (clone B56) | BD Biosciences | Cat# 550609; RRID: AB_393778 |
| Rat monoclonal anti-Ki67 (clone SolA15) | ThermoFisher | Cat# 14–5698-82; RRID: AB_10854564 |
| Rabbit monoclonal anti-Human Ki67 (clone SP6) | ThermoFisher | Cat# RM-9106-S1; RRID: AB_149792 |
| Guinea pig polyclonal anti-Synaptophysin | Synaptic Systems | Cat# 101 004; RRID: AB_1210382 |
| Rabbit monoclonal anti-Synaptophysin (clone MRQ-40) | Origene | Cat# TA327740 |
| Rabbit monoclonal anti-Synaptophysin (clone D8F6H) | Cell Signaling Technology | Cat# 36406; RRID: AB_2799098 |
| Rabbit polyclonal anti-CGRP | Sigma-Aldrich | Cat# C8198; RRID: AB_259091 |
| Rabbit polyclonal anti-Androgen Receptor (AR) | Santa Cruz Biotechnology | Cat# sc-816; RRID: AB_1563391 |
| Rabbit polyclonal anti-CCSP (CC10) | Seven Hills Bioreagents | WRAB-3950 |
| Rabbit polyclonal anti-pro SPC | Abcam | Cat# ab40879; RRID: AB_777473 |
| Mouse monoclonal anti-PARP-1 (clone C2–10) | Santa Cruz Biotechnology | Cat# sc-53643; RRID: AB_785086 |
| Mouse monoclonal anti-a TUBULIN (clone DM1A) | Santa Cruz Biotechnology | Cat# sc-32293; RRID: AB_628412 |
| Mouse monoclonal anti-TEAD1 (clone 31/TEF-1) | BD Biosciences | Cat# 610923; RRID: AB_398238 |
| Rabbit monoclonal anti-pan TEAD (clone D3F7L) | Cell Signaling Technology | Cat# 13295; RRID: AB_2687902 |
| Mouse monoclonal anti-TEAD4 (clone N-G2) | Santa Cruz Biotechnology | Cat# sc-101184; RRID: AB_2203086 |
| Mouse monoclonal anti-ASCL1 (clone D-7) | Santa Cruz Biotechnology | Cat# sc-374104; RRID: AB_10918561 |
| Mouse monoclonal anti-NEUROD (clone A-10) | Santa Cruz Biotechnology | Cat# sc-46684; RRID: AB_671759 |
| Mouse monoclonal anti-MYCN (clone B8.4.B) | Santa Cruz Biotechnology | Cat# sc-53993, RRID:AB_831602 |
| Goat polyclonal anti-MYCL | Novus Biologicals | Cat# AF4050 |
| Mouse monoclonal anti-RB1 (clone G99–549) | BD Biosciences | Cat# 554164; RRID: AB_395279 |
| Mouse monoclonal anti-b-ACTIN (clone AC-15) | Sigma-Aldrich | Cat# A5441; RRID: AB_476744 |
| Mouse monoclonal anti-RXRg (clone A-2) | Santa Cruz Biotechnology | Cat# sc-365252; RRID: AB_10850062 |
| Goat polyclonal anti-MCM3 (N-19) | Santa Cruz Biotechnology | Cat# sc-9850; RRID: AB_2142269 |
| Mouse monoclonal anti-ITGB5 (clone F-5) | Santa Cruz Biotechnology | Cat# sc-398214 |
| Rabbit monoclonal anti-ITGB1 (clone D2E5) | Cell Signaling Technology | Cat# 9699; RRID: AB_11178800 |
| Rabbit monoclonal anti-ITGB4 (clone D8P6C) | Cell Signaling Technology | Cat# 14803; RRID: AB_2798620 |
| Rabbit monoclonal anti-ITGA4 (clone D2E1) | Cell Signaling Technology | Cat# 8440; RRID: AB_2797643 |
| Rabbit polyclonal anti-ITGAV (clone D2E5) | Cell Signaling Technology | Cat# 4711; RRID: AB_2128178 |
| Rabbit polyclonal anti-Histone H3 (trimethyl Lys4) | Abcam | Cat# ab8580; RRID: AB_306649 |
| Rabbit polyclonal anti-Histone H3, (trimethyl Lys27) | Millipore | Cat# 07–449; RRID: AB_310624 |
| Rabbit polyclonal anti-Histone H3 (trimethyl Lys9) | Abcam | Cat# ab8898; RRID: AB_306848 |
| Rabbit polyclonal anti-Histone H3 (acetyl Lys27) | Abcam | Cat# ab4729; RRID: AB_2118291 |
| Mouse monoclonal anti-RNA polymerase II CTD repeat YSPTSPS antibody [clone 4H8] | Abcam | Cat# ab5408; RRID: AB_304868 |
| Mouse monoclonal anti-Methylcytidine | Eurogentec | Cat# BI-MECY-0100; RRID: AB_2616058 |
| Mouse monoclonal anti-ITGAV/B5 (clone P1F6) | Santa Cruz Biotechnology | Cat# sc-81632; RRID: AB_1123634 |
| Mouse monoclonal anti-ITGB1 (clone P5D2) | Santa Cruz Biotechnology | Cat# sc-13590, RRID:AB_627008 |
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| Bacterial and virus strains | ||
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| Ad5CMVCre | University of Iowa Viral Vector Core Facility | VVC-U of Iowa-5 |
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| Biological samples | ||
|
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| Human fetal retinas | Morgentaler Clinic | N/A |
| SCLC patient derived xenografts | Dr. Charles Rudin | Gardner et al., 2017; Lok et al., 2017 |
| Paraffin-embedded SCLC TMA | Princess Margaret Cancer Centre | N/A |
| Paraffin-embedded NSCLC PDX TMA | Princess Margaret Cancer Centre | N/A |
| Paraffin-embedded NET TMA | Roswell Park Cancer Institute | N/A |
| Paraffin-embedded primary prostate cancer tissue samples | Roswell Park Cancer Institute | N/A |
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| Chemicals, peptides, and recombinant proteins | ||
|
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| Insulin, human recombinant, zinc solution | ThermoFisher | Cat# 12585014 |
| Transferrin, Bovine (Holo form) | ThermoFisher | Cat# 11107047 |
| Sodium selenite | Sigma-Aldrich | Cat# S5261 |
| Hydrocortisone | Sigma-Aldrich | Cat# H0888 |
| b-Estradiol | Sigma-Aldrich | Cat# E2758 |
| Somatostatin | Sigma-Aldrich | Cat# S1763 |
| Glycyl-L-histidyl-L-lysine | Sigma-Aldrich | Cat# G7387 |
| REDExtract-N-Amp PCR ReadyMix | Sigma-Aldrich | Cat# R4775 |
| 2-hydroxyethyl agarose | Sigma-Aldrich | Cat# A4018 |
| Crystal Violet | Sigma-Aldrich | Cat# C6158 |
| EdU (5-ethynyl-2’-deoxyuridine) | ThermoFisher | Cat# E10187 |
| Paraformaldehyde | Electron Microscopy Sciences | Cat# 15710 |
| Alexa Fluor 647 Azide, Triethylammonium Salt | ThermoFisher | Cat# A10277 |
| FxCycle Violet Stain | ThermoFisher | Cat# F10347 |
| AlamarBlue Cell Viability Reagent | ThermoFisher | Cat# DAL1100 |
| Alisertib | Selleck Chemicals | Cat# S1133 |
| KPT-330 (Selinexor) | Selleck Chemicals | Cat# S7252 |
| Navitoclax | Selleck Chemicals | Cat# S1001 |
| Daporinad | Selleck Chemicals | Cat# S2799 |
| SsoAdvanced Universal SYBR Green Supermix | Bio-Rad | Cat# 1725270 |
| Protease/Phosphatase Inhibitor Cocktail | Cell Signaling Technology | Cat# 5872S |
| Phenylmethanesulfonyl fluoride (PMSF) solution | Sigma-Aldrich | Cat# 93482 |
| Protein G Agarose Beads | Cell Signaling Technology | Cat# 37478S |
| Cyclic RGD (cRGD) peptide | Sigma-Aldrich | Cat# SCP0111 |
| Superscript II Reverse Transcriptase | ThermoFisher | Cat# 18064014 |
| Power SYBR Green PCR Master Mix | ThermoFisher | Cat# 4368708 |
| Dynabeads M-280 Sheep Anti-Mouse IgG | ThermoFisher | Cat# 11202D |
| Dynabeads M-280 Sheep Anti-Rabbit IgG | ThermoFisher | Cat# 11204D |
| Proteinase K, recombinant, PCR grade | ThermoFisher | Cat# EO0491 |
|
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| Critical commercial assays | ||
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| Papain Dissociation System | Worthington Biochemical | Cat# LK003150 |
| Alexa Fluor 488 Tyramide SuperBoost Kit, goat anti-rabbit IgG | ThermoFisher | Cat# B40943 |
| Alexa Fluor 594 Tyramide SuperBoost Kit, goat anti-mouse IgG | ThermoFisher | Cat# B40915 |
| TruSeq Stranded mRNA Library Prep Kit | Illumina | Cat# 20020594; Cat# RS-122–2101 |
| TruSeq ChIP Sample Prep Kit | Illumina | Cat# IP-202–101 |
|
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| Deposited data | ||
|
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| RNA-seq from YAP-transduced SCLC and retinoblastoma cell lines | This paper | GSE144972 |
| TEAD4 ChIP-seq in SCLC and retinoblastoma cell lines | This paper | GSE144973 |
| Microarray from YAP/TAZ knockdown SK-Hep1 cells | Park et al., 2016 | GSE54617 |
| Microarray from YAP/TAZ knockdown UM-SCC-2 cells | Hiemer et al., 2015 | GSE66949 |
| Microarray from YAP/TAZ knockdown MDA-MB-231 cells | Zanconato et al., 2015 | GSE66082 |
| Microarray from YAP/TAZ knockdown SKMEL28 cells | Kim et al., 2016 | GSE68599 |
| Microarray from YAP/TAZ knockdown Meso-33 cells | Li et al., 2014 | GSE56157 |
| TEAD4 ChIP-seq from A549, HCT116 and HepG2 cells | ENCODE project | http://genome.ucsc.edu/ENCODE/downloads.html |
| TEAD4 ChIP-seq from MDA-MB-231 cells | Zanconato et al., 2015 | GSE66081 |
| Cancer Cell Line Encyclopedia microarray gene expression data | Barretina et al., 2012 | https://portals.broadinstitute.org/ccle |
| TCGA and TARGET RNA-seq gene expression data from primary tumor samples | Cancer Genome Atlas Research Network et al., 2013; Ma et al., 2018 | https://xena.ucsc.edu/ |
| Gene expression data from primary human lung tumors | Clinical Lung Cancer Genome Project (CLCGP) and Network Genomic Medicine (NGM), 2013 | http://www.uni-koeln.de/med-fak/clcgp/ |
| RNA-seq from murine prostate cancer models | Ku et al., 2017 | GSE90891 |
| RNA-seq from normal epithelia and PARCB-transformed SCN tumors | Park et al., 2018 | GSE118206 |
| Cancer DepMap Public 20Q2 | Meyers et al., 2017 | https://depmap.org/portal/download/ |
| Cancer Therapeutics Response Portal (CTRPv2) drug sensitivity data | Seashore-Ludlow et al., 2015 | https://portals.broadinstitute.org/ctrp/ |
| Genomics of Drug Sensitivity in Cancer (GDSC1 & GDSC2) drug sensitivity data | Iorio et al., 2016 | https://www.cancerrxgene.org/ |
|
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| Experimental models: Cell lines | ||
|
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| RB1021 | Dr. Brenda Gallie (To et al., 2012) | RRID:CVCL_S624 |
| RB3823 | Dr. Brenda Gallie (To et al., 2012) | RRID:CVCL_ZF07 |
| RB247 | Dr. Brenda Gallie (To et al., 2012) | RRID:CVCL_2704 |
| Y79 | Rod Bremner lab | RRID: CVCL_1893 |
| WERI-RB1 | Rod Bremner lab | RRID: CVCL_1792 |
| NCI-H526 | ATCC | Cat# CRL-5811; RRID: CVCL_1569 |
| SHP77 | ATCC | Cat# CRL-2195; RRID: CVCL_1693 |
| NCI-H510A | ATCC | Cat# HTB-184; RRID: CVCL_1565 |
| NCI-H82 | ATCC | Cat# HTB-175; RRID: CVCL_1591 |
| NCI-H2171 | ATCC | Cat# CRL-5929; RRID: CVCL_1536 |
| NCI-H209 | Susan P.C. Cole lab | RRID: CVCL_1525 |
| NCI-H69 | Susan P.C. Cole lab | RRID: CVCL_1579 |
| NCI-N417 | Susan P.C. Cole lab | RRID: CVCL_1602 |
| NCI-H660 | ATCC | Cat# CRL-5813; RRID: CVCL_1576 |
| DU4475 | Dr. Eldad Zacksenhaus | RRID: CVCL_1183 |
| QGP-1 | Dr. Todd McMullen | RRID: CVCL_3143 |
| BON-1 | Dr. Todd McMullen | RRID:CVCL_3985 |
| SH-SY5Y | Dr. Meredith Irwin | RRID: CVCL_0019 |
| SK-N-SH | Dr. Meredith Irwin | RRID: CVCL_0531 |
| NCI-H661 | ATCC | Cat# HTB-183; RRID: CVCL_1577 |
| NCI-H1650 | ATCC | Cat# CRL-5883; RRID: CVCL_1483 |
| A549 | Rod Bremner lab | RRID: CVCL_0023 |
| SW-1573 | Susan P.C. Cole lab | RRID: CVCL_1720 |
| MCF7 | Rod Bremner lab | RRID: CVCL_0031 |
| MDA-MB-231 | Rod Bremner lab | RRID: CVCL_0062 |
| HCC1419 | Dr. Benjamin Neel | RRID: CVCL_1251 |
| DU145 | Dr. Jan Jongstra | RRID: CVCL_0105 |
| BPH-1 | Rod Bremner lab | RRID: CVCL_1091 |
| PANC-1 | Rod Bremner lab | RRID: CVCL_0480 |
| Hs 766T | Rod Bremner lab | RRID: CVCL_0334 |
| T24 | Jeff L. Wrana lab | RRID: CVCL_0554 |
| Karpas 299 | Dr. Rob Ingham | RRID: CVCL_1324 |
| SUP-M2 | Dr. Rob Ingham | RRID: CVCL_2209 |
| SU-DHL-1 | Dr. Rob Ingham | RRID: CVCL_0538 |
| SR-786 | Dr. Rob Ingham | RRID: CVCL_1711 |
| UCONN | Dr. Rob Ingham | RRID: CVCL_A693 |
| HDMY-Z | Dr. Rob Ingham | RRID: CVCL_1273 |
| KM-H2 | Dr. Rob Ingham | RRID: CVCL_1330 |
| L428 | Dr. Rob Ingham | RRID: CVCL_1361 |
| L540 | Dr. Rob Ingham | RRID: CVCL_1362 |
| HDLM-2 | Dr. Rob Ingham | RRID: CVCL_0009 |
| OCI-AML2 | Dr. Mark Minden | RRID: CVCL_1619 |
| OCI-AML3 | Dr. Mark Minden | RRID: CVCL_1844 |
| THP-1 | Dr. Aaron Schimmer | RRID: CVCL_0006 |
| HL-60 | Dr. Aaron Schimmer | RRID: CVCL_0002 |
| K562 | Dr. Aaron Schimmer | RRID: CVCL_0004 |
| Lenti-X 293T | Takara/Clontech | Cat# 632180 |
|
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| Experimental models: Organisms/strains | ||
|
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| Mouse: αCre: Tg(Pax6-cre,GFP)2Pgr | Dr. Peter Gruss | MGI:3052661 |
| Mouse: Rb1f/f: Rb1tm2Brn | Dr. Anton Berns | MGI:1931018 |
| Mouse: Rbl1−/−: Rbl1tm1Mru | Dr. Michael Rudnicki | MGI:1857798 |
| Mouse: Yapf/f: Yap1tm1Hmc | Reginensi et al., 2013 | MGI:5486298 |
| Mouse: Tazf/f: Wwtr1tm1Hmc | Reginensi et al., 2013 | MGI:5486299 |
| Mouse: p53f/f: Trp53tm1Brn | NCI Mouse Repository | Strain# 01XC2; MGI:1931011 |
| Mouse: CgrpCreER: Calcatm1.1(cre/ERT2)Ptch | Dr. Pao-Tien Chuang (Song et al., 2012) | MGI:5460801 |
| Mouse: TRE-Yap: TRE-HA-YapTg | Gregorieff et al., 2015 | N/A |
| Mouse: ROSA-rtTA: Gt(ROSA)26Sortm1(rtTA,EGFP)Nagy | Dr. Andras Nagy | MGI:3583817 |
| Mouse: Ccsp-rtTA: Tg(Scgb1a1-rtTA)1Jaw | Tichelaar et al., 2000 | MGI:2445707 |
| Mouse: tetO-EGFRL858R: Tg(tetO-EGFR*L858R)56Hev | Politi et al., 2006 | MGI:3690078 |
| Mouse: Ptenf/f: Ptentm1Hwu | Lesche et al., 2002 | MGI:2156086 |
| Mouse: SPC-rtTA: SFTPC-rtTA | Perl et al., 2002a | N/A |
| Mouse: tetO-Cre: Tg(tetO-cre)1Jaw | Perl et al., 2002b | MGI:2679524 |
| Mouse: PB-Cre4: Tg(Pbsn-cre)4Prb | Wu et al., 2001 | MGI:2385927 |
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| Oligonucleotides | ||
|
| ||
| See Table S8 for oligonucleotide sequences used | ||
| for CRISPR sgRNA vectors, the CRIPSR library, | ||
| RT-qPCR, ChIP-qPCR and mouse genotyping. | ||
|
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| Recombinant DNA | ||
|
| ||
| psPax2 | Didier Trono | Addgene plasmid #12260; RRID: Addgene_12260 |
| pMD2.G | Didier Trono | Addgene plasmid #12259; RRID: Addgene_12259 |
| LentiCRISPR v2 | Sanjana et al., 2014 | Addgene plasmid #52961; RRID: Addgene_52961 |
| pLKO.1-puro | Stewart et al., 2003 | Addgene plasmid #8453; RRID: Addgene_8453 |
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| Software and algorithms | ||
|
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| Kaluza, Flow Cytometry analysis software | Beckman Coulter | https://www.mybeckman.ca/flow-cytometry/software/kaluza |
| Prism | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| RSEM | Li and Dewey, 2011 | https://deweylab.github.io/RSEM/ |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| RRHO | Plaisier et al., 2010 | https://bioconductor.org/packages/release/bioc/html/RRHO.html |
| RRHO2 | Cahill et al., 2018 | https://github.com/RRHO2/RRHO2 |
| DeepTools | Ramírez et al., 2016 | https://github.com/deeptools/deeptools |
| Homer package | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| NMF | Gaujoux and Seoighe, 2010 | https://cran.r-project.org/web/packages/NMF/index.html |
| fastQC | N/A | https://www.bioinformatics.babraham.ac.uk/projects/fastqc |
| Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2 |
| SAMtools | Li et al., 2009 | http://samtools.sourceforge.net |
| MACS2 | Zhang et al., 2008 | https://github.com/macs3-project/MACS |
| Integrative Genomics Viewer (IGV) | Robinson et al., 2011 | https://software.broadinstitute.org/software/igv/ |
| UCSC tool bedGraphToBigWig | Kent WJ., 2010 | https://anaconda.org/bioconda/ucsc-bedgraphtobigwig |
| ReMap | Chèneby et al., 2018 | http://remap.univ-amu.fr/ |
| GSEA | Subramanian, et al., 2005 | https://www.gsea-msigdb.org/gsea/index.jsp |
| R package ‘‘ggplot2’’ | Wickham, 2016 | https://cran.r-project.org/web/packages/ggplot2 |
| R package ‘‘scales’’ | N/A | https://scales.r-lib.org |