KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-AKT | Cell Signaling Technology | Cat#9272, RRID:AB_329827 |
| Rabbit monoclonal anti-AMPKα (D63G4) | Cell Signaling Technology | Cat#5832, RRID:AB_10624867 |
| Rabbit monoclonal anti-ATF4 (D4B8) | Cell Signaling Technology | Cat#11815 RRID:AB_2616025 |
| Rabbit monoclonal anti-Atg7 (D12B11) | Cell Signaling Technology | Cat#8558, RRID:AB_10831194 |
| Mouse monoclonal anti-beta-Actin (clone AC-74) | Sigma-Aldrich | Cat#A2228, RRID:AB_476697 |
| Mouse monoclonal anti-BAF47 | BD Bioscience | Cat#612111, RRID:AB_2191717 |
| Rabbit monoclonal anti-BIP (C50B12) | Cell Signaling Technology | Cat#3177, RRID:AB_2119845 |
| Rabbit monoclonal anti-c-Jun (60A8) | Cell Signaling Technology | Cat#9165, RRID:AB_2130165 |
| Mouse monoclonal anti-c-Myc (9E10) | Santa Cruz Biotechnology | Cat#sc-40, RRID:AB_627268 |
| Rabbit polyclonal anti-c-Myc | Proteintech Group | Cat#10828–1-AP, RRID:AB_2148585 |
| Mouse monoclonal anti-CHOP (L63F7) | Cell Signaling Technology | Cat#2895, RRID:AB_2089254 |
| Mouse monoclonal anti-Cip1 | BD Biosciences | Cat#610233, RRID:AB_397628 |
| Rabbit monoclonal anti-Cleaved Caspase-3 (Asp175) (5A1E) | Cell Signaling Technology | Cat#9664, RRID:AB_2070042 |
| Rabbit monoclonal anti-Cleaved PARP (Asp214) (D64E10) XP | Cell Signaling Technology | Cat#5625, RRID:AB_10699459 |
| Rabbit polyclonal anti-DRAM1 | LifeSpan | Cat#LS-B2726–50, RRID:AB_1932638 |
| Rabbit monoclonal anti-eIF2alpha (D7D3) XP | Cell Signaling Technology | Cat#5324, RRID:AB_10692650 |
| Rabbit polyclonal anti-EIF2AK2 | Proteintech Group | Cat#18244–1-AP, RRID:AB_2246451 |
| Rabbit polyclonal anti-EIF2AK2/PKR | LifeSpan | Cat#LS-B563, RRID:AB_2095733 |
| Goat polyclonal anti-Firefly Luciferase | LifeSpan | Cat#LS-C147186–500, RRID:AB_11134935 |
| Chicken polyclonal anti-GFP | Abcam | Cat#ab13970, RRID:AB_300798 |
| Rabbit monoclonal anti-GFP (D5.1) | Cell Signaling Technology | Cat#2956, RRID:AB_1196615 |
| Rabbit monoclonal anti-HSP90 (C45G5) | Cell Signaling Technology | Cat#4877, RRID:AB_2233307 |
| Mouse monoclonal anti-IGFBP3 (B-5) | Santa Cruz Biotechnology | Cat#sc-365936, RRID:AB_10917037 |
| Rabbit monoclonal anti-IRE1α (14C10) | Cell Signaling Technology | Cat#3294, RRID:AB_823545 |
| Rabbit monoclonal anti-Ki-67 (SP6) | Thermo Fisher Scientific | Cat#MA5–14520, RRID:AB_10979488 |
| Rabbit monoclonal anti-LC3A/B (D3U4C) XP | Cell Signaling Technology | Cat#12741, RRID:AB_2617131 |
| Mouse monoclonal anti-MDM2 (SMP14) | Santa Cruz Biotechnology | Cat#sc-965, RRID:AB_627920 |
| Rat monoclonal anti-p19 ARF (5-C3–1) | Santa Cruz Biotechnology | Cat#sc-32748, RRID:AB_628071 |
| Mouse monoclonal anti-p53 (1C12) | Cell Signaling Technology | Cat#2524, RRID:AB_331743 |
| Mouse monoclonal anti-p53 (DO-7) | Cell Signaling Technology | Cat#48818, RRID:AB_2713958 |
| Rabbit monoclonal anti-p53 (7F5) | Cell Signaling Technology | Cat#2527, RRID:AB_331211 |
| Rabbit monoclonal anti-p70 S6 Kinase (49D7) | Cell Signaling Technology | Cat#2708, RRID:AB_390722 |
| Rabbit polyclonal anti-PDIA6 | Proteintech Group | Cat#18233–1-AP, RRID:AB_10805765 |
| Rabbit monoclonal anti-PERK (D11A8) | Cell Signaling Technology | Cat#5683, RRID:AB_10831515 |
| Rabbit monoclonal anti-phospho-AKT (Ser473) (D9E) XP | Cell Signaling Technology | Cat#4060, RRID:AB_2315049 |
| Rabbit monoclonal anti-phpspho-AMPKα (Thr172) (40H9) | Cell Signaling Technology | Cat#2535, RRID:AB_331250 |
| Rabbit monoclonal anti-phospho-eIF2alpha (Ser51) (D9G8) XP | Cell Signaling Technology | Cat#3398, RRID:AB_2096481 |
| Rabbit monoclonal anti-phospho-S6 Ribosomal Protein (Ser235/236) (D57.2.2E) XP | Cell Signaling Technology | Cat#4858, RRID:AB_916156 |
| Mouse monoclonal anti-phospho-p70 S6 Kinase (Thr389) (1A5) | Cell Signaling Technology | Cat#9206, RRID:AB_331790 |
| Rabbit monoclonal anti-phospho-SAPK/JNK (Thr183/Tyr185) (81E11) | Cell Signaling Technology | Cat#4668, RRID:AB_2307320 |
| Rabbit polyclonal anti-phospho-SAPK/JNK (Thr183/Tyr185) | Cell Signaling Technology | Cat#9251, RRID:AB_331659 |
| Rabbit monoclonal anti-phospho-4E-BP1 (Thr37/Thr46) (236B4) | Cell Signaling Technology | Cat#2855, RRID:AB_560835 |
| Mouse monoclonal anti-S6 Ribosomal Protein (54D2) | Cell Signaling Technology | Cat#2317, RRID:AB_2238583 |
| Rabbit polyclonal anti-SAPK/JNK | Cell Signaling Technology | Cat#9252, RRID:AB_2250373 |
| Rabbit monoclonal anti-SESN2 (EPR18907) | Abcam | Cat#ab178518, RRID:AB_2716805 |
| Rabbit polyclonal anti-SESN2 | Proteintech Group | Cat#21346–1-AP, RRID:AB_10733238 |
| Rabbit polyclonal anti-SMARCB1 | Sigma-Aldrich | Cat#HPA018248, RRID: AB_1851162 |
| Rabbit monoclonal anti-Survivin (71G4B7) | Cell Signaling Technology | Cat#2808, RRID:AB_2063948 |
| Rabbit polyclonal anti-TP53 | Proteintech Group | Cat#21891–1-AP, RRID:AB_10896826 |
| Mouse monoclonal anti-Ubiquitin (P4D1) | Cell Signaling Technology | Cat#3936, RRID:AB_10839120 |
| Rabbit monoclonal anti-Vimentin (D21H3) XP | Cell Signaling Technology | Cat#5741, RRID:AB_10695459 |
| Mouse monoclonal anti-Vimentin (RV202) | Abcam | Cat#ab8978, RRID:AB_306907 |
| Rabbit monoclonal anti-Vinculin (E1E9V) XP | Cell Signaling Technology | Cat#13901, RRID:AB_2728768 |
| Rabbit monoclonal anti-XBP-1s (D2C1F) | Cell Signaling Technology | Cat#12782, RRID:AB_2687943 |
| Rabbit monoclonal anti-4E-BP1 (53H11) | Cell Signaling Technology | Cat#9644, RRID:AB_2097841 |
| Bacterial and Virus Strains | ||
| psPAX2 packaging vector | Didier Trono | Addgene Cat#12260 |
| pMD2.G packaging vector | Didier Trono | Addgene Cat#12259 |
| Biological Samples | ||
| Copy number and mRNA expression values of SMARCB1 in human cell lines | Cancer Cell Lines Encyclopedia | https://portals.broadinstitute.org/ccle |
| Human MRT and normal samples | TARGET database | http://ocg.cancer.gov/programs/target |
| Mutation Signatures | PeCan database | https://pecan.stjude.cloud |
| Mutation Signatures for MRT and ATRT | Chun, H. J. E. et al., 2016; Johann, P. D. et al., 2016 | N/A |
| Rhabdoid FFPE | Dinesh Rakheja (dinesh.rakheja@utsouthwestern.edu) | N/A |
| Rhabdoid FFPE | Dolores Lopez-Terrada (dhterrad@texaschildrenshospital.org) | N/A |
| Rhabdoid FFPE | Liren Li (lilr@sysucc.org.cn) | N/A |
| RMC FFPE | George J. Netto (gnetto1@jhmi.edu) | N/A |
| RMC FFPE | Priya Rao (prao@mdanderson.org) | N/A |
| RMC2C cell line | Jose A. Karam (JAKaram@mdanderson.org) and Nizar M. Tannir (ntannir@mdanderson.org) | N/A |
| Sensitivity to the ER stress in human cell lines | Genomics of Drug Sensitivity in Cancer | https://www.cancerrxgene.org/translation/Drug |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Bortezomib | LC Laboratories | Cat#B-1408 |
| Chloroquine diphosphate salt | Sigma-Aldrich | Cat#C6628 |
| Cycloheximide solution | Sigma-Aldrich | Cat#C4859 |
| Doxycycline hyclate | Sigma-Aldrich | Cat#D9891 |
| Etoposide | Sigma-Aldrich | Cat#E1383 |
| Idasanutlin (RG-7388) | Selleckchem | Cat#S7205 |
| Ifosfamide | Sigma-Aldrich | Cat#I4909 |
| Ixazomib Citrate (MLN9708) | Selleckchem | Cat#S2181 |
| MG-132 | EMD Millipore | Cat#474787 |
| NVP-AUY922 | LC Laboratories | Cat#N-5300 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
| YM-155 | Proactive Molecular Research | Chemical Number P06–10194 CAS_RN 781661–94-7 |
| (Z)-4-Hydroxytamoxifen | Sigma-Aldrich | Cat#H7904 |
| Critical Commercial Assays | ||
| Adeno-X™ Maxi Purification Kit | Takara Bio Inc | Cat#631533 |
| Adeno-X™ Rapid Titer Kit | Takara Bio Inc | Cat#632250 |
| CellTiter-Glo® 2.0 Assay | Promega | Cat#G9243 |
| Click-iT™ Plus OPP Alexa Fluor™ 488 Protein Synthesis Assay Kit | Thermo Fisher Scientific | Cat#C10456 |
| Click-iT™ Plus OPP Alexa Fluor™ 594 Protein Synthesis Assay Kit | Thermo Fisher Scientific | Cat#C10457 |
| Dead Cell Apoptosis Kit with Annexin V FITC and PI, for flow cytometry | Thermo Fisher Scientific | Cat#V13242 |
| DNeasy Blood & Tissue Kit (250) | Qiagen | Cat#69506 |
| GeneChip™ Mouse Genome 430 2.0 Array | Thermo Fisher Scientific | Cat#900496 |
| Mouse on Mouse (M.O.M.™) Elite Peroxidase Kit | Vector Laboratories | Cat#PK-2200 |
| RNeasy Mini Kit (250) | Qiagen | Cat#74106 |
| Venor™ GeM Mycoplasma Detection Kit, PCR-based | Sigma Aldrich | Cat#MP0025 |
| XenoLight D-Luciferin-K+ Salt Bioluminescent Substrate | PerkinElmer | Cat#122799 |
| Deposited Data | ||
| Microarray data | EMBL-EBI | E-MTAB-7497 |
| Experimental Models: Cell Lines | ||
| A204 | ATCC | Cat#HTB-82, RRID:CVCL_1058 |
| HEK293T | ATCC | Cat#CRL-3216, RRID:CVCL_0063 |
| G401 | ATCC | Cat#CRL-1441, RRID:CVCL_0270 |
| G-402 | ATCC | Cat#CRL-1440, RRID:CVCL_1221 |
| RMC2C | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: Rosa26LSL-Luc: B6.129S4-Gt(ROSA)26Sortm3(CAG-luc)Tyj/J | The Jackson Laboratory | JAX:009044; RRID:IMSR_JAX:009044 |
| Mouse: KRASLSL/G12D: B6.129S4-Krastm4Tyj/J | The Jackson Laboratory | JAX:008179; RRID:IMSR_JAX:008179 |
| Mouse: Trp53LSL-R172H: 129S-Trp53tm2Tyj/J | The Jackson Laboratory | JAX:008652; RRID:IMSR_JAX:008652 |
| Mouse: Rosa26LSL-TdT: B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J | The Jackson Laboratory | JAX:007909; RRID:IMSR_JAX:007909 |
| Mouse: Rosa26LSL-Cas9-Gfp | Platt et al., 2014 | N/A |
| Mouse: Smarcb1LoxP | Roberts et al., 2002 | N/A |
| Mouse: Pax8Cre: B6.129P2(Cg)-Pax8tm1.1(cre)Mbu/J | The Jackson Laboratory | JAX:028196; RRID:IMSR_JAX:028196 |
| Mouse: Trp53LoxP | Marino et al., 2000 | N/A |
| Mouse: Rosa26FlpoERT2: STOCK Gt(ROSA)26Sortm3(CAG-flpo/ERT2)Alj/J | The Jackson Laboratory | JAX:018906; RRID:IMSR_JAX:018906 |
| Mouse: Trp53Frt | Lee et al., 2012a | N/A |
| Mouse: Rag2−/−: B6(Cg)-Rag2tm1.1Cgn/J | The Jackson Laboratory | JAX:008449; RRID:IMSR_JAX:008449 |
| Mouse: NSG: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ | The Jackson Laboratory | JAX:005557; RRID:IMSR_JAX:005557 |
| Oligonucleotides | ||
| shRNA Atg7 seed sequence: 5’-GCCAACATCCCTGGATACAAG-3’ |
This paper | N/A |
| shRNA Birc5–1 seed sequence: 5’-CAAAGACTACCCGTCAGTCAA-3’ |
This paper | N/A |
| shRNA Birc5–2 seed sequence: 5’-GAAGAACTAACCGTCAGTGAA-3’ |
This paper | N/A |
| shRNA CDKN2A seed sequences: 5’-GCTGGGTGGTCTTTGTGTA-3’ |
This paper | N/A |
| shRNA DRAM1–1 | Sigma Aldrich | Cat#SHCLNG-NM_027878, TRCN0000329081 |
| shRNA DRAM1–2 | Sigma Aldrich | Cat#SHCLNG-NM_027878, TRCN0000329023 |
| shRNA Myc seed sequence: 5’-TGGAGATGATGACCGAGTTAC-3’ |
This paper | N/A |
| shRNA TP53–1 | Sigma Aldrich | Cat#SHCLNG-NM_000546, TRCN0000003753 |
| shRNA TP53–2 | Sigma Aldrich | Cat#SHCLNG-NM_000546, TRCN0000003755 |
| Recombinant DNA | ||
| Adx | Oka Kazuhiro | N/A |
| Adx-A-Cre | This paper | N/A |
| Adx-LacZ | Oka Kazuhiro | N/A |
| ICPI-CS-iCreP2A-tdTomato | Oka Kazuhiro | N/A |
| pALB-GFP | Snorri Thorgeirsson (Heo et al., 2006) | Addgene Cat#55759 |
| pBABEpuro GFP-LC3 | Jayanta Debnath (Fung et al., 2008) | Addgene Cat#22405 |
| pGF-p53-mCMV-EF1α-Puro Lentivector | SBI | Cat#TR200pa-p |
| pLenti6/UbC/V5-DEST™ Gateway™ Vector | Thermo Fisher Scientific | Cat#V49910 |
| pLIX-iLacZ | This paper | N/A |
| pLIX-iSMARCB1 | This paper | N/A |
| pLIX_403 | David Root | Addgene Cat#41395 |
| pMSCV-loxP-dsRed-loxp-eGFP-Puro-WPRE | Hans Clevers (Koo et al., 2012) | Addgene Cat#32702 |
| pLSM4 | This paper | N/A |
| pLSM5 | Genovese et al., 2017 | N/A |
| pUb-GFP | This paper | N/A |
| pLV-p53R-Cre | This paper | N/A |
| Ub-M-GFP | Nico Dantuma (Dantuma et al., 2000) | Addgene Cat#11938 |
| Software and Algorithms | ||
| FlowJo_V10 | FlowJo LLC | www.flowjo.com |
| Gene Set Enrichment Analysis (GSEA) | Subramanian et al., 2005; Mootha et al., 2003 | http://software.broadinstitute.org/gsea/index.jsp |
| GraphPad Prism 7 | GraphPad Software | www.graphpad.com |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Linear Models for Microarray Data (limma package) | Bioconductor | https://bioconductor.org/packages/release/bioc/html/limma.html |
| Living Image 4.3 software | PerkinElmer | http://www.perkinelmer.com |
| Methods for Affymetrix Oligonucleotide Arrays (R/Bioconductor’s affy package (12925520)) | Bioconductor | http://bioconductor.org/packages/affy/ |
| RStudio version 1.0.143 with R version 3.4.3 | R-project | www.r-project.org/ |
| Other | ||