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Supplementary Tables Table S1. List of the 121 Lung Cancer Cell Lines

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Supplementary Tables Table S1. List of the 121 Lung Cancer Cell Lines Supplementary Tables Table S1. List of the 121 lung cancer cell lines screened for MAX alterations. Information about the histopathology of each cell line, and the presence of alterations at MYC and BRG1 is also included. Grey boxes indicate that no information is available. Table S2. List of genes that are up-regulated or down-regulated upon MAX reconstitution. The values represent the n-fold change in the level of gene expression of each of the lung cancer cell lines infected with the wild type MAX relative to the controls (Ø). Table S3. List of genes that are up-regulated or down-regulated upon depletion of BRG1. The values represent the n-fold change in the level of gene expression of each of the lung cancer cell lines infected with the shBRG1 relative to the controls Ø. Table S4. List of the cell lines included in Figure 5. The information about alterations at the indicated genes was obtained from different sources, as indicated. For data extracted from databases we applied the following criteria to define a mutation: i) mutations at tumor suppressor genes (BRG1, SMARCB1, MAX, ARID1A, PRBM1, and MGA) should be homozygous and predictive of truncated proteins, ii) for amplification at the MYC family of oncogenes, only very high levels of gene amplification have been considered to be positive. Other genes, related to MYC/MAX or to the SWI/SNF complex, have also been searched for alterations (i.e., ARID1B, ARID2, MXI, MXDs) but either no alterations were reported in the databases or the changes did not fulfill our selection criteria. CCLE, Cancer Cell Line Encyclopedia (Broad-Novartis Cancer Cell Line Encyclopedia; website, http://www.broadinstitute.org/ccle/). COSMIC, Catalogue of Somatic Mutations in Cancer (Trust Sanger Institute’s Cancer Cell Line Project; website, http://cancer.sanger.ac.uk/). Table S1: List of the 121 lung cancer cell lines screened for MAX alterations. Information about the histopathology of each cell line, and the presence of alterations at MYC and BRG1 is also included. Grey boxes indicate that no information is available. Cell line Histopathology MAX BRG1 MYC MYCL1 MYCN H1417 SCLC Mutant LU134 SCLC Mutant LU165 SCLC Mutant CORL95 SCLC Mutant A427 AC Mutant A549 AC Mutant DMS114 SCLC Mutant H1299 LCC/NSCLC Mutant H1573 AC Mutant H1703 AC Mutant H1819 AC Mutant H2126 AC Mutant H23 AC Mutant HCC366 AC Mutant H522 AC Mutant H661 LCC Mutant H841 SCLC Mutant HCC15 SCC Mutant Ma29 AC Mutant RERFLCMS AC Mutant DMS273 SCLC Ampl. Ampl. H1395 AC Ampl. H187 SCLC Ampl. H1975 AC Ampl. H2122 AC Ampl. H2170 SCC Ampl. H2171 SCLC Ampl. H446 SCLC Ampl. H460 AC Ampl. H524 SCLC Ampl. H82 SCLC Ampl. HCC44 AC Ampl. Lu135 SCLC Ampl. LU65 LCC/NSCLC Ampl. N417 SCLC Ampl. H1963 SCLC Ampl. H2029 SCLC Ampl. H2107 SCLC Ampl. H2141 SCLC Ampl. H510 SCLC Ampl. H889 SCLC Ampl. HCC33 SCLC Ampl. H1770 Neuroendocrine Ampl. H526 SCLC Ampl. H69 SCLC Ampl. H720 CARCINOID Ampl. ABC1 AC CALU1 SCC CALU3 AC DMS153 SCLC DMS53 SCLC EBC1 SCC H1048 AC H1155 LCC/NSCLC H1184 SCLC H128 SCLC H1339 SCLC H1385 NSCLC H1436 SCLC H1437 AC H1450 SCLC H1607 SCLC H1618 SCLC H1623 AC H1648 AC H1650 AC H1672 SCLC H1930 SCLC AC H1993 H2009 AC H2081 SCLC H2087 AC H209 SCLC H2195 SCLC H2196 SCLC H2227 SCLC H2291 AC H2347 AC H249 SCLC H322 AC H345 SCLC H441 AC H520 SCC H596 AC-SCC H711 SCLC H719 SCLC H727 LCC/NSCLC H774 SCLC H820 AC HCC193 AC HCC515 AC HCC78 AC HCC827 AC HCC95 SCC II-18 AC LC1SQSF SCC LK2 SCC Lu139 SCLC Lu24 SCLC LU99 LCC/NSCLC Ma1 AC Ma10 AC Ma12 AC Ma17 AC Ma2 LCC Ma24 AC Ma25 LCC Ma26 AC Ms18 SCLC PC10 SCC PC13 LCC PC14 AC PC3 AC PC7 AC PC9 AC RERF-LC-OK AC SBC5 SCLC SHP77 SCLC SKMES1 SCC MAX-signature Supplementary Table S2 OFFICIAL_GENGene Name Lu134_H1417_Lu165_MAX TNFSF12 TNFSF12-TNFSF13 readthrough transcript; tumor necrosis factor (ligand) superfamily, 1.123 1.424 5.376 KISS1R kinesin family member 20A 1.865 2.569 2.258 GDF15 growth differentiation factor 15 1.865 5.97 2.203 ADAD2 adenosine deaminase domain containing 2 1.156 1.477 2.058 MCTP2 multiple coagulation factor deficiency 2 1.282 1.354 2.056 NIM1 naked cuticle homolog 2 (Drosophila) 1.146 2.434 2.014 ADAMTS18 ADAM metallopeptidase with thrombospondin type 1 motif, 18 1.5 2.189 1.955 PRSS56 PRSS56 1.199 2.311 1.946 ENST000004404ENST00000440451 1.732 2.671 1.908 SSC5D hypothetical LOC284297 1.105 1.446 1.904 FAM162A family with sequence similarity 162, member A 1.63 2.047 1.856 APLN apelin 1.409 2.404 1.82 IER3 heparan sulfate proteoglycan 2 1.311 1.746 1.761 PRR7 proline rich 7 (synaptic) 1.081 1.123 1.75 HK2 histone cluster 1, H3j; histone cluster 1, H3i; histone cluster 1, H3h; histone cluster 1, H 3.783 7.459 1.746 SYCE3 synaptonemal complex central element protein 3 1.211 1.635 1.717 RCOR2 REST corepressor 2 1.119 1.685 1.716 BNIP3 BCL2/adenovirus E1B 19kDa interacting protein 3 2.105 2.326 1.714 C4orf47 chromosome 4 open reading frame 47 2.01 1.933 1.69 SV2B synaptic vesicle glycoprotein 2B; hypothetical protein LOC100128403 1.23 1.681 1.669 GMPR glutaminase 1.646 1.479 1.65 CXCR4 chemokine (C-X-C motif) receptor 4 1.357 2.051 1.646 SLC9B1 solute carrier family 9, subfamily B 1.095 1.232 1.644 C6orf57 chromosome 6 open reading frame 57 1.239 1.619 1.639 LOC728730 similar to hCG2031213 1.272 1.331 1.635 C7orf52 chromosome 7 open reading frame 52 1.36 2.152 1.633 NRTN neurotensin 1.133 1.715 1.626 VEGFA vascular endothelial growth factor A 7.84 4.103 1.61 KREMEN2 kallikrein-related peptidase 11 1.112 1.628 1.604 DDIT3 DNA-damage-inducible transcript 3 1.208 2.248 1.603 ADA adenosine deaminase 2.06 3.379 1.595 PFKFB3 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 1.503 2.912 1.583 F12 coagulation factor XII (Hageman factor) 1.235 1.426 1.583 LOC285141 hypothetical protein LOC283713 1.385 1.717 1.582 Page 1 MAX-signature P4HA1 prolyl 4-hydroxylase, alpha polypeptide I 1.989 2.651 1.581 STC2 stanniocalcin 2 1.938 1.506 1.58 COPZ2 coatomer protein complex, subunit zeta 2 1.148 2.314 1.578 MLKL MHC class I polypeptide-related sequence B 1.339 1.499 1.578 VWA5A von Willebrand factor A domain containing 5A 1.291 2.354 1.575 TMEM130 transmembrane protein 130 1.101 1.744 1.566 SNORD114-23 small nucleolar RNA, C/D box 114-14; small nucleolar RNA, C/D box 113-1; small nucle 1.134 1.376 1.564 WFDC2 WAP four-disulfide core domain 2 1.45 1.329 1.562 ABCG4 ATP-binding cassette, sub-family G (WHITE), member 4 1.116 1.714 1.561 MMP10 matrix metallopeptidase 1 (interstitial collagenase) 2.266 1.317 1.55 ADM adrenomedullin 1.893 2.329 1.537 FUT3 fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group) 1.171 3.059 1.534 GPR172B G protein-coupled receptor 171 1.126 1.566 1.525 LOC100289187 similar to Protein FAM27D1 1.376 1.743 1.524 GAL3ST1 galactose-3-O-sulfotransferase 1 1.07 1.537 1.519 TRIB3 tribbles homolog 3 (Drosophila) 2.903 4.329 1.511 BATF2 basic leucine zipper transcription factor, ATF-like 2 1.295 2.269 1.505 FBXO2 F-box protein 2 1.151 2.177 1.505 AHNAK AHNAK nucleoprotein 1.392 1.199 1.504 ESRP1 epithelial splicing regulatory protein 1 1.237 1.713 1.502 MMP1 MLX interacting protein-like 1.503 1.247 1.501 NGEF neuronal guanine nucleotide exchange factor 0.947 2.059 1.496 PARP14 poly (ADP-ribose) polymerase family, member 14 1.109 4.825 1.494 FHOD1 formin homology 2 domain containing 1 1.104 2.194 1.493 LOC155060 hypothetical protein LOC149351 1.236 1.431 1.489 SEC24D SEC24 family, member D (S. cerevisiae) 1.155 1.257 1.488 TMC4 transmembrane channel-like 4 1.456 1.923 1.486 SYNGR3 synaptogyrin 3 1.112 1.959 1.485 TXNIP thioredoxin interacting protein 1.51 1.839 1.485 NFATC4 nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4 1.383 2.132 1.483 RELB v-rel reticuloendotheliosis viral oncogene homolog B 1.249 1.412 1.48 PFKFB4 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4 1.494 3.673 1.48 C1orf213 chromosome 1 open reading frame 213 1.115 1.477 1.475 PLA2G4D phospholipase A2, group IVD (cytosolic) 1.106 2.561 1.472 FGF11 fibroblast growth factor 11 1.275 1.546 1.472 SLC16A3 solute carrier family 16, member 3 (monocarboxylic acid transporter 4) 5.221 4.071 1.468 Page 2 MAX-signature MYO15A v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian) 1.599 2.224 1.467 APOE hypothetical LOC100129500; apolipoprotein E 1.549 5.763 1.466 MSMB mannose-P-dolichol utilization defect 1 1.95 1.26 1.461 AATK apoptosis-associated tyrosine kinase 2.453 2.297 1.461 SMPDL3A sphingomyelin phosphodiesterase, acid-like 3A 1.916 1.336 1.46 PDK1 pyruvate dehydrogenase kinase, isozyme 1 1.904 4.317 1.458 GRTP1 gastrin-releasing peptide 1.245 1.876 1.453 ATF3 activating transcription factor 3 1.389 1.43 1.448 ROPN1 ropporin, rhophilin associated protein 1 2.063 1.728 1.446 LDHA leucine carboxyl methyltransferase 2 2.049 1.97 1.446 MOXD1 matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) 1.269 1.632 1.444 ZNF204P zinc finger protein 204 pseudogene 1.374 1.582 1.441 ATP1B2 ATPase, Na+/K+ transporting, beta 2 polypeptide 1.411 2.633 1.438 OBFC1 obscurin-like 1 1.12 1.401 1.436 SERPINA6 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6 1.194 1.802 1.436 RPRML reprimo-like 1.133 2.012 1.434 LOC100507401 LOC100507401 1.135 1.66 1.431 BIK BCL2-interacting killer (apoptosis-inducing) 1.866 1.478 1.431 FLJ37644 hypothetical gene supported by AK094963 1.17 1.365 1.428 EML2 echinoderm microtubule associated protein like 2 1.954 1.773 1.428 TMEM45B transmembrane protein 45B 2.067 1.403 1.425 PLOD2 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 1.513 1.727 1.424 CLDN1
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