Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor

A caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge is how to make an integrated use of omics profiles of cancer cell lines for reliable discoveries. Here, we...

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Main Authors Jaiswal, Alok, Prson Gautam, Pietila, Elina Amanda, Timonen, Sanna, Nordstrom, Nora, Tanoli, Ziaurrehman, Sipari, Nina, Lehti, Kaisa, Wennerberg, Krister, Aittokallio, Tero
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 02.02.2020
Cold Spring Harbor Laboratory
Edition1.1
Subjects
Breast cancer
Cancer
Cancer Biology
Cell culture
Laboratories
Molecular modelling
PTEN protein
Ribonucleic acid
RNA
Tumor cell lines
Tumor suppressor genes
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Abstract A caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge is how to make an integrated use of omics profiles of cancer cell lines for reliable discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics profiling studies across 12 research laboratories for 2018 cell lines. To account for relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. Extension of the approach identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient cells on RNA helicases.
AbstractList A caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge is how to make an integrated use of omics profiles of cancer cell lines for reliable discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics profiling studies across 12 research laboratories for 2018 cell lines. To account for relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. Extension of the approach identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient cells on RNA helicases.
A caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge is how to make an integrated use of omics profiles of cancer cell lines for reliable discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics profiling studies across 12 research laboratories for 2018 cell lines. To account for relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. Extension of the approach identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient cells on RNA helicases. A comprehensive meta-analysis of 53 multi-modal omics profiles of >2000 cancer cell lines from 12 research laboratories An unexpected lack of consistency between TMT-labelled and non-labelled global proteomic profiles A non-parametric approach to integrate omics profiles from multiple laboratories and to identify robust molecular patterns in individual cell lines The multi-modal data integration reveals novel drivers and potential therapeutic targets, including ECHDC1 in breast cancers and DDX27 in PTEN mutant cancers.
Author Wennerberg, Krister
Timonen, Sanna
Pietila, Elina Amanda
Prson Gautam
Nordstrom, Nora
Sipari, Nina
Aittokallio, Tero
Jaiswal, Alok
Lehti, Kaisa
Tanoli, Ziaurrehman
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Cites_doi 10.1016/j.celrep.2013.07.018
10.1038/nature12831
10.1038/ng.3984
10.1038/nature12634
10.1073/pnas.0800441105
10.1016/j.cell.2018.03.042
10.1007/s00216-010-4425-x
10.1038/35021093
10.1038/nature20171
10.1016/j.cell.2013.08.003
10.1016/j.cell.2019.12.023
10.1186/gb-2013-14-10-r110
10.1186/1471-2164-10-277
10.1016/j.cell.2016.06.017
10.1101/gr.251983.119
10.1038/nbt.2877
10.1007/978-1-4939-8891-4_12
10.1038/srep05193
10.1093/jnci/djt007
10.1093/biostatistics/kxh008
10.1016/j.cell.2017.07.005
10.1038/nature20580
10.1016/j.semcdb.2019.04.013
10.1038/nbt.3955
10.1093/bioinformatics/bts013
10.1038/s41573-019-0046-z
10.1038/nrc1691
10.1038/nm.4333
10.1074/jbc.RA118.002027
10.1093/bioinformatics/btx292
10.1101/cshperspect.a032813
10.1038/415530a
10.1016/j.chembiol.2019.03.011
10.1016/j.celrep.2015.03.050
10.1093/nar/gkr959
10.1074/jbc.M111.281527
10.1038/sj.onc.1205600
10.1186/1471-2105-12-S1-S36
10.1158/1535-7163.MCT-09-0743
10.1093/nar/gkf493
10.1038/nprot.2009.86
10.1093/biostatistics/kxp045
10.1038/sj.bjc.6601894
10.1038/nature19838
10.1038/nm.3480
10.1093/nar/gks1111
10.4161/rna.23312
10.1038/nature11412
10.1016/j.chembiol.2015.06.021
10.1016/j.cell.2017.01.013
10.1038/s41586-019-1103-9
10.1016/j.ccell.2017.01.005
10.1016/j.cell.2011.03.020
10.1091/mbc.E04-08-0658
10.1093/nar/gks461
10.1038/nature17987
10.1016/j.ajhg.2011.03.004
10.1016/j.cell.2011.02.014
10.1038/s41467-019-13805-y
10.1126/science.1244669
10.1038/nature19839
10.1016/j.celrep.2017.08.010
10.1158/2159-8290.CD-15-0235
10.1038/ncomms12645
10.1158/0008-5472.CAN-12-3342
10.1093/bioinformatics/btt182
10.1038/s41388-018-0196-1
10.1038/nbt.3080
10.1158/2159-8290.CD-16-0154
10.1016/j.cels.2019.06.005
10.1101/sqb.2016.81.030866
10.18632/oncotarget.17734
10.1186/s12943-016-0517-3
10.1093/nar/gkr407
10.1016/j.cell.2015.11.062
10.1038/s41586-018-0409-3
10.1158/0008-5472.CAN-07-3293
10.1038/nature11003
10.1038/s41586-019-1186-3
10.1093/nar/gkx911
10.1016/j.cell.2019.12.031
10.1038/onc.2008.248
10.7554/eLife.06907
10.1038/nature11005
10.6084/m9.figshare.9201770.v2
10.1016/j.cell.2017.06.010
10.1186/s13073-017-0440-2
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References Dempster, Pacini, Pantel, Behan, Green, Krill-Burger, Beaver, Younger, Zhivich, Najgebauer, Allen, Gonçalves, Shepherd, Doench, Yusa, Vazquez, Parts, Boehm, Golub, Hahn, Root, Garnett, Tsherniak, Iorio (2020.01.31.929372v1.15) 2019; 10
Shihab, Gough, Cooper, Day, Gaunt (2020.01.31.929372v1.68) 2013; 29
Perou, Sørile, Eisen, Van De Rijn, Jeffrey, Ress, Pollack, Ross, Johnsen, Akslen, Fluge, Pergammenschlkov, Williams, Zhu, Lønning, Børresen-Dale, Brown, Botstein (2020.01.31.929372v1.61) 2000; 406
Gautam, Karhinen, Szwajda, Jha, Yadav, Aittokallio, Wennerberg (2020.01.31.929372v1.22) 2016; 15
Smirnov, Kofia, Maru, Freeman, Ho, El-Hachem, Adam, Ba-alawi, Safikhani, Haibe-Kains (2020.01.31.929372v1.69) 2018; 46
Helming, Wang, Wilson, Vazquez, Haswell, Manchester, Kim, Kryukov G, Ghandi, Aguirre, Jagani, Wang, Garraway, Hahn, Roberts (2020.01.31.929372v1.32) 2014; 20
Klijn, Durinck, Stawiski, Haverty, Jiang, Liu, Degenhardt, Mayba, Gnad, Liu, Pau, Reeder, Cao, Mukhyala, Selvaraj, Yu, Zynda, Brauer, Wu, Gentleman, Manning, Yauch, Bourgon, Stokoe, Modrusan, Neve, De Sauvage, Settleman, Seshagiri, Zhang (2020.01.31.929372v1.43) 2015; 33
Yang, Soares, Greninger, Edelman, Lightfoot, Forbes, Bindal, Beare, Smith, Thompson, Ramaswamy, Futreal, Haber, Stratton, Benes, McDermott, Garnett (2020.01.31.929372v1.84) 2012; 41
Haverty, Lin, Tan, Yu, Lam, Lianoglou, Neve, Martin, Settleman, Yauch, Bourgon (2020.01.31.929372v1.31) 2016; 533
Shankavaram, Varma, Kane, Sunshine, Chary, Reinhold, Pommier, Weinstein (2020.01.31.929372v1.67) 2009; 10
Coscia, Watters, Curtis, Eckert, Chiang, Tyanova, Montag, Lastra, Lengyel, Mann (2020.01.31.929372v1.10) 2016; 7
Huang, Garraway, Ashworth, Weber (2020.01.31.929372v1.33) 2020
Kumar, Henikoff, Ng (2020.01.31.929372v1.46) 2009; 4
Dalla Pozza, Dando, Pacchiana, Liboi, Scupoli, Donadelli, Palmieri (2020.01.31.929372v1.13) 2020
Ghandi, Huang, Jané-Valbuena, Kryukov G, Lo, McDonald, Barretina, Gelfand, Bielski, Li, Hu, Andreev-Drakhlin, Kim, Hess, Haas, Aguet, Weir, Rothberg M, Paolella, Lawrence, Akbani, Lu, Tiv, Gokhale, de Weck, Mansour, Oh, Shih, Hadi, Rosen, Bistline, Venkatesan, Reddy, Sonkin, Liu, Lehar, Korn, Porter, Jones, Golji, Caponigro, Taylor, Dunning, Creech, Warren, McFarland, Zamanighomi, Kauffmann, Stransky, Imielinski, Maruvka, Cherniack, Tsherniak, Vazquez, Jaffe, Lane, Weinstock, Johannessen, Morrissey, Stegmeier, Schlegel, Hahn, Getz, Mills, Boehm, Golub, Garraway, Sellers (2020.01.31.929372v1.24) 2019; 569
Tang, Chen, Wong, Liu, Li, Wang, Ji, Sung, Fang, Yu (2020.01.31.929372v1.72) 2018; 37
Daemen, Griffith, Heiser, Wang, Enache, Sanborn, Pepin, Durinck, Korkola, Griffith, Hur, Huh, Chung, Cope, Fackler, Umbricht, Sukumar, Seth, Sukhatme, Jakkula, Lu, Mills, Cho, Collisson, van’t Veer, Spellman, Gray (2020.01.31.929372v1.12) 2013; 14
Wang, Yan, Hu, Sucheston, Higgins, Ambrosone, Johnson, Smiraglia, Liu (2020.01.31.929372v1.79) 2012; 28
Costello, Heiser, Georgii, Gönen, Menden, Wang, Bansal, Ammad-Ud-Din, Hintsanen, Khan, Mpindi, Kallioniemi, Honkela, Aittokallio, Wennerberg, Collins, Gallahan, Singer, Saez-Rodriguez, Kaski, Gray, Stolovitzky, Abbuehl, Allen, Altman, Balcome, Battle, Bender, Berger, Bernard, Bhattacharjee, Bhuvaneshwar, Bieberich, Boehm, Califano, Chan, Chen, Chen, Choi, Coelho, Cokelaer, Collins, Creighton, Cui, Dampier, Davisson, De Baets, Deshpande, DiCamillo, Dundar, Duren, Ertel, Fan, Fang, Gauba, Gottlieb, Grau, Gusev, Ha, Han, Harris, Henderson, Hejase, Homicsko, Hou, Hwang, IJzerman, Karacali, Keles, Kendziorski, Kim, Kim, Kim, Knowles, Koller, Lee, Lee, Lenselink, Biao, Bin, Li, Liang, Ma, Madhavan, Mooney, Myers, Newton, Overington, Pal, Peng, Pestell, Prill, Qiu, Rajwa, Sadanandam, Sambo, Shin, Song, Song, Sridhar, Stock, Sun, Ta, Tadesse, Tan, Tang, Theodorescu, Toffolo, Tozeren, Trepicchio, Varoquaux, Vert, Waegeman, Walter, Wan, Wang, Wang, Wang, Wang, Wegner, Wu, Xia, Xiao, Xie, Xu, Yang, Yuan, Zhang, Zhang, Zhao, Zuo, Van Vlijmen, Van Westen (2020.01.31.929372v1.11) 2014; 32
Greenman, Bignell, Butler, Edkins, Hinton, Beare, Swamy, Santarius, Chen, Widaa, Futreal, Stratton (2020.01.31.929372v1.29) 2010; 11
Garnett, Edelman, Heidorn, Greenman, Dastur, Lau, Greninger, Thompson, Luo, Soares, Liu, Iorio, Surdez, Chen, Milano, Bignell, Tam, Davies, Stevenson, Barthorpe, Lutz, Kogera, Lawrence, McLaren-Douglas, Mitropoulos, Mironenko, Thi, Richardson, Zhou, Jewitt, Zhang, O’Brien, Boisvert, Price, Hur, Yang, Deng, Butler, Choi, Chang, Baselga, Stamenkovic, Engelman, Sharma S, Delattre, Saez-Rodriguez, Gray, Settleman, Futreal, Haber, Stratton, Ramaswamy, McDermott, Benes (2020.01.31.929372v1.20) 2012; 483
Seashore-Ludlow, Rees, Cheah, Coko, Price E, Coletti, Jones, Bodycombe, Soule, Gould, Alexander, Li, Montgomery, Wawer, Kuru, Kotz, Suk-Yee Hon, Munoz, Liefeld, Dančik, Bittker, Palmer, Bradner, Shamji, Clemons, Schreiber (2020.01.31.929372v1.66) 2015; 5
Nijman, Friend (2020.01.31.929372v1.57) 2013
Aguirre, Meyers, Weir, Vazquez, Zhang, Ben-David, Cook, Ha, Harrington, Doshi, Kost-Alimova, Gill, Xu, Ali, Jiang, Pantel, Lee, Goodale, Cherniack, Oh, Kryukov, Cowley, Garraway, Stegmaier, Roberts, Golub, Meyerson, Root, Tsherniak, Hahn (2020.01.31.929372v1.2) 2016; 6
Lawrence, Perez, Hernández, Miller, Haas, Irie, Lee, Blau, Villén (2020.01.31.929372v1.48) 2015; 11
Zinzalla, Stracka, Oppliger, Hall (2020.01.31.929372v1.87) 2011; 144
Keniry, Parsons (2020.01.31.929372v1.42) 2008
Van’t Veer, Dai, Van de Vijver, He, Hart, Mao, Peterse, Van Der Kooy, Marton, Witteveen, Schreiber, Kerkhoven, Roberts, Linsley, Bernards, Friend (2020.01.31.929372v1.77) 2002; 415
Kandoth, McLellan, Vandin, Ye, Niu, Lu, Xie, Zhang, McMichael, Wyczalkowski, Leiserson, Miller, Welch, Walter, Wendl, Ley, Wilson, Raphael, Ding (2020.01.31.929372v1.40) 2013; 502
Koh, Brown, Sayad, Kasimer, Ketela, Moffat (2020.01.31.929372v1.45) 2012; 40
Szwajda, Gautam, Karhinen, Jha, Saarela, Shakyawar, Turunen, Yadav, Tang, Wennerberg, Aittokallio (2020.01.31.929372v1.71) 2015; 22
Bamford, Dawson, Forbes, Clements, Pettett, Dogan, Flanagan, Teague, Futreal, Stratton, Wooster (2020.01.31.929372v1.4) 2004; 91
Behan, Iorio, Picco, Gonçalves, Beaver, Migliardi, Santos, Rao, Sassi, Pinnelli, Ansari, Harper, Jackson, McRae, Pooley, Wilkinson, van der Meer, Dow, Buser-Doepner, Bertotti, Trusolino, Stronach, Saez-Rodriguez, Yusa, Garnett (2020.01.31.929372v1.7) 2019; 568
Del Carratore, Jankevics, Eisinga, Heskes, Hong, Breitling (2020.01.31.929372v1.14) 2017; 33
Weinstein, Joe (2020.01.31.929372v1.81) 2008
Esteller (2020.01.31.929372v1.18) 2002
Wang, Yu, Hughes, Liu, Kendirli, Klein, Chen, Lander, Sabatini (2020.01.31.929372v1.80) 2017; 168
Safikhani, El-Hachem, Smirnov, Freeman, Goldenberg, Birkbak, Beck, Aerts, Quackenbush, Haibe-Kains (2020.01.31.929372v1.65) 2016; 540
McDonald, de Weck, Schlabach, Billy, Mavrakis, Hoffman, Belur, Castelletti, Frias, Gampa, Golji, Kao, Li, Megel, Perkins, Ramadan, Ruddy, Silver, Sovath, Stump, Weber, Widmer, Yu, Yu, Yue, Abramowski, Ackley, Barrett, Berger, Bernard, Billig, Brachmann, Buxton, Caothien, Caushi, Chung, Cortés-Cros, deBeaumont, Delaunay, Desplat, Duong, Dwoske, Eldridge, Farsidjani, Feng, Feng, Flemming, Forrester, Galli, Gao, Gauter, Gibaja, Haas, Hattenberger, Hood, Hurov, Jagani, Jenal, Johnson, Jones, Kapoor, Korn, Liu, Liu, Liu, Liu, Loo, Macchi, Martin, McAllister, Meyer, Mollé, Pagliarini, Phadke, Repko, Schouwey, Shanahan, Shen, Stamm, Stephan, Stucke, Tiedt, Varadarajan, Venkatesan, Vitari, Wallroth, Weiler, Zhang, Mickanin, Myer, Porter, Lai, Bitter, Lees, Keen, Kauffmann, Stegmeier, Hofmann, Schmelzle, Sellers (2020.01.31.929372v1.53) 2017; 170
Barretina, Caponigro, Stransky, Venkatesan, Margolin, Kim, Wilson, Lehár, Kryukov G, Sonkin, Reddy, Liu, Murray, Berger, Monahan, Morais, Meltzer, Korejwa, Jané-Valbuena, Mapa, Thibault, Bric-Furlong, Raman, Shipway, Engels, Cheng, Yu, Yu, Aspesi, De Silva, Jagtap, Jones, Wang, Hatton, Palescandolo, Gupta, Mahan, Sougnez, Onofrio, Liefeld, MacConaill, Winckler, Reich, Li, Mesirov, Gabriel, Getz, Ardlie, Chan, Myer, Weber, Porter, Warmuth, Finan, Harris, Meyerson, Golub, Morrissey, Sellers, Schlegel, Garraway (2020.01.31.929372v1.5) 2012; 483
Tauber, Tauber, Khong, Van Treeck, Pelletier, Parker (2020.01.31.929372v1.73) 2020
Mpindi, Yadav, Östling, Gautam, Malani, Murumägi, Hirasawa, Kangaspeska, Wennerberg, Kallioniemi, Aittokallio (2020.01.31.929372v1.55) 2016
Park, Rabinovsky, Carey, Hennessy, Agarwal, Liu, Ju, Deng, Lu, Woo, Kim, Cheong, Garraway, Weinstein, Mills, Lee, Davies (2020.01.31.929372v1.60) 2010; 9
Niepel, Hafner, Mills, Subramanian, Williams, Chung, Gaudio, Barrette, Stern, Hu, Korkola, Shamu, Jayaraman, Azeloglu, Iyengar, Sobie, Mills, Liby, Jaffe, Alimova, Davison, Lu, Golub, Subramanian, Shelley, Svendsen, Ma’ayan, Medvedovic, Gray, Birtwistle, Heiser, Sorger (2020.01.31.929372v1.56) 2019; 9
Roumeliotis, Williams, Gonçalves, Alsinet, Del Castillo Velasco-Herrera, Aben, Ghavidel, Michaut, Schubert, Price, Wright, Yu, Yang, Dienstmann, Guinney, Beltrao, Brazma, Pardo, Stegle, Adams, Wessels, Saez-Rodriguez, McDermott, Choudhary (2020.01.31.929372v1.64) 2017; 20
Yadav, Pemovska, Szwajda, Kulesskiy, Kontro, Karjalainen, Majumder, Malani, Murumägi, Knowles, Porkka, Heckman, Kallioniemi, Wennerberg, Aittokallio (2020.01.31.929372v1.83) 2014; 4
Gholami, Hahne, Wu, Auer, Meng, Wilhelm, Kuster (2020.01.31.929372v1.25) 2013; 4
Basu, Bodycombe, Cheah, Price E, Liu, Schaefer, Ebright, Stewart, Ito, Wang, Bracha, Liefeld, Wawer, Gilbert, Wilson, Stransky, Kryukov G, Dancik, Barretina, Garraway, Hon, Munoz, Bittker, Stockwell, Khabele, Stern, Clemons, Shamji, Schreiber (2020.01.31.929372v1.6) 2013; 154
Bouhaddou, Distefano, Riesel, Carrasco, Holzapfel, Jones, Smith, Stern, Somani, Thompson, Birtwistle (2020.01.31.929372v1.9) 2016
Ashworth, Lord, Reis-Filho (2020.01.31.929372v1.3) 2011
Haibe-Kains, El-Hachem, Birkbak, Jin, Beck, Aerts, Quackenbush (2020.01.31.929372v1.30) 2013; 504
Zehir, Benayed, Shah, Syed, Middha, Kim, Srinivasan, Gao, Chakravarty
References_xml – volume: 4
  start-page: 609
  year: 2013
  end-page: 620
  ident: 2020.01.31.929372v1.25
  article-title: Global proteome analysis of the NCI-60 cell line panel
  publication-title: Cell Rep
  doi: 10.1016/j.celrep.2013.07.018
– volume: 504
  start-page: 389
  year: 2013
  end-page: 393
  ident: 2020.01.31.929372v1.30
  article-title: Inconsistency in large pharmacogenomic studies
  publication-title: Nature
  doi: 10.1038/nature12831
– volume: 49
  start-page: 1779
  year: 2017
  end-page: 1784
  ident: 2020.01.31.929372v1.54
  article-title: Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells
  publication-title: Nat Genet
  doi: 10.1038/ng.3984
– volume: 502
  start-page: 333
  year: 2013
  end-page: 339
  ident: 2020.01.31.929372v1.40
  article-title: Mutational landscape and significance across 12 major cancer types
  publication-title: Nature
  doi: 10.1038/nature12634
– volume: 105
  start-page: 4340
  year: 2008
  end-page: 4345
  ident: 2020.01.31.929372v1.27
  article-title: Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
  publication-title: Proc Natl Acad Sci U S A
  doi: 10.1073/pnas.0800441105
– year: 2018
  ident: 2020.01.31.929372v1.34
  article-title: The Cancer Genome Atlas: Creating Lasting Value beyond Its Data
  publication-title: Cell
  doi: 10.1016/j.cell.2018.03.042
– volume: 399
  start-page: 1127
  year: 2011
  end-page: 1139
  ident: 2020.01.31.929372v1.17
  article-title: Metabolite extraction from adherently growing mammalian cells for metabolomics studies: Optimization of harvesting and extraction protocols
  publication-title: Anal Bioanal Chem
  doi: 10.1007/s00216-010-4425-x
– volume: 406
  start-page: 747
  year: 2000
  end-page: 752
  ident: 2020.01.31.929372v1.61
  article-title: Molecular portraits of human breast tumours
  publication-title: Nature
  doi: 10.1038/35021093
– year: 2016
  ident: 2020.01.31.929372v1.55
  article-title: Consistency in drug response profiling
  publication-title: Nature
  doi: 10.1038/nature20171
– volume: 154
  start-page: 1151
  year: 2013
  end-page: 1161
  ident: 2020.01.31.929372v1.6
  article-title: An interactive resource to identify cancer genetic and lineage dependencies targeted by small molecules
  publication-title: Cell
  doi: 10.1016/j.cell.2013.08.003
– volume: 180
  start-page: 387
  year: 2020
  end-page: 402.e16
  ident: 2020.01.31.929372v1.58
  article-title: Quantitative Proteomics of the Cancer Cell Line Encyclopedia
  publication-title: Cell
  doi: 10.1016/j.cell.2019.12.023
– volume: 14
  year: 2013
  ident: 2020.01.31.929372v1.12
  article-title: Modeling precision treatment of breast cancer
  publication-title: Genome Biol
  doi: 10.1186/gb-2013-14-10-r110
– volume: 10
  year: 2009
  ident: 2020.01.31.929372v1.67
  article-title: CellMiner: A relational database and query tool for the NCI-60 cancer cell lines
  publication-title: BMC Genomics
  doi: 10.1186/1471-2164-10-277
– volume: 166
  start-page: 740
  year: 2016
  end-page: 754
  ident: 2020.01.31.929372v1.35
  article-title: A Landscape of Pharmacogenomic Interactions in Cancer
  publication-title: Cell
  doi: 10.1016/j.cell.2016.06.017
– volume: 29
  start-page: 2034
  year: 2019
  end-page: 2045
  ident: 2020.01.31.929372v1.49
  article-title: Identifying gene function and module connections by the integration of multispecies expression compendia
  publication-title: Genome Res
  doi: 10.1101/gr.251983.119
– volume: 32
  start-page: 1202
  year: 2014
  end-page: 1212
  ident: 2020.01.31.929372v1.11
  article-title: A community effort to assess and improve drug sensitivity prediction algorithms
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt.2877
– start-page: 205
  year: 2019
  end-page: 217
  ident: 2020.01.31.929372v1.38
  publication-title: Molecular Biology
  doi: 10.1007/978-1-4939-8891-4_12
– volume: 4
  year: 2014
  ident: 2020.01.31.929372v1.83
  article-title: Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies
  publication-title: Sci Rep
  doi: 10.1038/srep05193
– volume: 105
  start-page: 452
  year: 2013
  end-page: 458
  ident: 2020.01.31.929372v1.26
  article-title: The Clinical Relevance of Cancer Cell Lines
  publication-title: JNCI J Natl Cancer Inst
  doi: 10.1093/jnci/djt007
– volume: 5
  start-page: 557
  year: 2004
  end-page: 572
  ident: 2020.01.31.929372v1.59
  article-title: Circular binary segmentation for the analysis of array-based DNA copy number data
  publication-title: Biostatistics
  doi: 10.1093/biostatistics/kxh008
– volume: 170
  start-page: 577
  year: 2017
  end-page: 592.e10
  ident: 2020.01.31.929372v1.53
  article-title: Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening
  publication-title: Cell
  doi: 10.1016/j.cell.2017.07.005
– year: 2016
  ident: 2020.01.31.929372v1.9
  article-title: Drug response consistency in CCLE and CGP
  publication-title: Nature
  doi: 10.1038/nature20580
– year: 2020
  ident: 2020.01.31.929372v1.13
  article-title: Regulation of succinate dehydrogenase and role of succinate in cancer
  publication-title: Semin Cell Dev Biol
  doi: 10.1016/j.semcdb.2019.04.013
– volume: 35
  start-page: 983
  year: 2017
  end-page: 989
  ident: 2020.01.31.929372v1.47
  article-title: Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt.3955
– volume: 28
  start-page: 729
  year: 2012
  end-page: 730
  ident: 2020.01.31.929372v1.79
  article-title: IMA: An R package for high-throughput analysis of Illumina’s 450K Infinium methylation data
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts013
– year: 2020
  ident: 2020.01.31.929372v1.33
  article-title: Synthetic lethality as an engine for cancer drug target discovery
  publication-title: Nat Rev Drug Discov
  doi: 10.1038/s41573-019-0046-z
– year: 2005
  ident: 2020.01.31.929372v1.39
  article-title: The concept of synthetic lethality in the context of anticancer therapy
  publication-title: Nat Rev Cancer
  doi: 10.1038/nrc1691
– volume: 23
  start-page: 703
  year: 2017
  end-page: 713
  ident: 2020.01.31.929372v1.85
  article-title: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
  publication-title: Nat Med
  doi: 10.1038/nm.4333
– volume: 293
  start-page: 13059
  year: 2018
  end-page: 137072
  ident: 2020.01.31.929372v1.41
  article-title: Arginine methylation of SMAD7 by PRMT1 in TGF-–induced epithelial–mesenchymal transition and epithelial stem-cell generation
  publication-title: J Biol Chem
  doi: 10.1074/jbc.RA118.002027
– volume: 33
  start-page: 2774
  year: 2017
  end-page: 2775
  ident: 2020.01.31.929372v1.14
  article-title: RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btx292
– volume: 11
  year: 2019
  ident: 2020.01.31.929372v1.36
  article-title: Stress granules and processing bodies in translational control
  publication-title: Cold Spring Harb Perspect Biol
  doi: 10.1101/cshperspect.a032813
– volume: 415
  start-page: 530
  year: 2002
  end-page: 536
  ident: 2020.01.31.929372v1.77
  article-title: Gene expression profiling predicts clinical outcome of breast cancer
  publication-title: Nature
  doi: 10.1038/415530a
– volume: 26
  start-page: 970
  year: 2019
  end-page: 979.e4
  ident: 2020.01.31.929372v1.21
  article-title: Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets
  publication-title: Cell Chem Biol
  doi: 10.1016/j.chembiol.2019.03.011
– volume: 11
  start-page: 630
  year: 2015
  end-page: 644
  ident: 2020.01.31.929372v1.48
  article-title: The Proteomic Landscape of Triple-Negative Breast Cancer
  publication-title: Cell Rep
  doi: 10.1016/j.celrep.2015.03.050
– volume: 40
  year: 2012
  ident: 2020.01.31.929372v1.45
  article-title: COLT-Cancer: Functional genetic screening resource for essential genes in human cancer cell lines
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkr959
– volume: 286
  start-page: 42992
  year: 2011
  end-page: 43003
  ident: 2020.01.31.929372v1.51
  article-title: Ethylmalonyl-CoA decarboxylase, a new enzyme involved in metabolite proofreading
  publication-title: J Biol Chem
  doi: 10.1074/jbc.M111.281527
– year: 2002
  ident: 2020.01.31.929372v1.18
  article-title: CpG island hypermethylation and tumor suppressor genes: A booming present, a brighter future
  publication-title: Oncogene
  doi: 10.1038/sj.onc.1205600
– volume: 12
  year: 2011
  ident: 2020.01.31.929372v1.70
  article-title: Integrated metabolome and transcriptome analysis of the NCI60 dataset
  publication-title: BMC Bioinformatics
  doi: 10.1186/1471-2105-12-S1-S36
– volume: 9
  start-page: 257
  year: 2010
  end-page: 267
  ident: 2020.01.31.929372v1.60
  article-title: Integrative analysis of proteomic signatures, mutations, and drug responsiveness in the NCI 60 cancer cell line set
  publication-title: Mol Cancer Ther
  doi: 10.1158/1535-7163.MCT-09-0743
– volume: 30
  start-page: 3894
  year: 2002
  end-page: 3900
  ident: 2020.01.31.929372v1.62
  article-title: Human non-synonymous SNPs: server and survey
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkf493
– volume: 4
  start-page: 1073
  year: 2009
  end-page: 1082
  ident: 2020.01.31.929372v1.46
  article-title: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
  publication-title: Nat Protoc
  doi: 10.1038/nprot.2009.86
– volume: 11
  start-page: 164
  year: 2010
  end-page: 175
  ident: 2020.01.31.929372v1.29
  article-title: PICNIC: An algorithm to predict absolute allelic copy number variation with microarray cancer data
  publication-title: Biostatistics
  doi: 10.1093/biostatistics/kxp045
– volume: 91
  start-page: 355
  year: 2004
  end-page: 358
  ident: 2020.01.31.929372v1.4
  article-title: The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website
  publication-title: Br J Cancer
  doi: 10.1038/sj.bjc.6601894
– year: 2016
  ident: 2020.01.31.929372v1.23
  article-title: Consistency in large pharmacogenomic studies
  publication-title: Nature
  doi: 10.1038/nature19838
– volume: 20
  start-page: 251
  year: 2014
  end-page: 254
  ident: 2020.01.31.929372v1.32
  article-title: ARID1B is a specific vulnerability in ARID1A-mutant cancers
  publication-title: Nat Med
  doi: 10.1038/nm.3480
– volume: 41
  start-page: D955
  year: 2012
  end-page: D961
  ident: 2020.01.31.929372v1.84
  article-title: Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gks1111
– year: 2013
  ident: 2020.01.31.929372v1.19
  article-title: DEAD box RNA helicase functions in cancer
  publication-title: RNA Biol
  doi: 10.4161/rna.23312
– volume: 490
  start-page: 61
  year: 2012
  end-page: 70
  ident: 2020.01.31.929372v1.44
  article-title: Comprehensive molecular portraits of human breast tumours
  publication-title: Nature
  doi: 10.1038/nature11412
– volume: 22
  start-page: 1144
  year: 2015
  end-page: 1155
  ident: 2020.01.31.929372v1.71
  article-title: Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles
  publication-title: Chem Biol
  doi: 10.1016/j.chembiol.2015.06.021
– volume: 168
  start-page: 890
  year: 2017
  end-page: 903.e15
  ident: 2020.01.31.929372v1.80
  article-title: Gene Essentiality Profiling Reveals Gene Networks and Synthetic Lethal Interactions with Oncogenic Ras
  publication-title: Cell
  doi: 10.1016/j.cell.2017.01.013
– volume: 568
  start-page: 511
  year: 2019
  end-page: 516
  ident: 2020.01.31.929372v1.7
  article-title: Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens
  publication-title: Nature
  doi: 10.1038/s41586-019-1103-9
– volume: 31
  start-page: 225
  year: 2017
  end-page: 239
  ident: 2020.01.31.929372v1.50
  article-title: Characterization of Human Cancer Cell Lines by Reverse-phase Protein Arrays
  publication-title: Cancer Cell
  doi: 10.1016/j.ccell.2017.01.005
– year: 2011
  ident: 2020.01.31.929372v1.3
  article-title: Genetic interactions in cancer progression and treatment
  publication-title: Cell
  doi: 10.1016/j.cell.2011.03.020
– volume: 16
  start-page: 1987
  year: 2005
  end-page: 2002
  ident: 2020.01.31.929372v1.76
  article-title: TGF-β and the Smad signaling pathway support transcriptomic reprogramming during epithelial-mesenchymal cell transition
  publication-title: Mol Biol Cell
  doi: 10.1091/mbc.E04-08-0658
– volume: 40
  start-page: e133
  year: 2012
  end-page: e133
  ident: 2020.01.31.929372v1.82
  article-title: Camera: a competitive gene set test accounting for inter-gene correlation
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gks461
– volume: 533
  start-page: 333
  year: 2016
  end-page: 337
  ident: 2020.01.31.929372v1.31
  article-title: Reproducible pharmacogenomic profiling of cancer cell line panels
  publication-title: Nature
  doi: 10.1038/nature17987
– volume: 88
  start-page: 440
  year: 2011
  end-page: 449
  ident: 2020.01.31.929372v1.28
  article-title: Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel
  publication-title: Am J Hum Genet
  doi: 10.1016/j.ajhg.2011.03.004
– volume: 144
  start-page: 757
  year: 2011
  end-page: 768
  ident: 2020.01.31.929372v1.87
  article-title: Activation of mTORC2 by association with the ribosome
  publication-title: Cell
  doi: 10.1016/j.cell.2011.02.014
– volume: 10
  start-page: 5817
  year: 2019
  ident: 2020.01.31.929372v1.15
  article-title: Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets
  publication-title: Nat Commun
  doi: 10.1038/s41467-019-13805-y
– year: 2013
  ident: 2020.01.31.929372v1.57
  article-title: Potential of the synthetic lethality principle
  publication-title: Science (80-)
  doi: 10.1126/science.1244669
– volume: 540
  start-page: E2
  year: 2016
  end-page: E4
  ident: 2020.01.31.929372v1.65
  article-title: Safikhani et al. reply
  publication-title: Nature
  doi: 10.1038/nature19839
– volume: 20
  start-page: 2201
  year: 2017
  end-page: 2214
  ident: 2020.01.31.929372v1.64
  article-title: Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells
  publication-title: Cell Rep
  doi: 10.1016/j.celrep.2017.08.010
– volume: 5
  start-page: 1210
  year: 2015
  end-page: 1223
  ident: 2020.01.31.929372v1.66
  article-title: Harnessing connectivity in a large-scale small-molecule sensitivity dataset
  publication-title: Cancer Discov
  doi: 10.1158/2159-8290.CD-15-0235
– volume: 7
  year: 2016
  ident: 2020.01.31.929372v1.10
  article-title: Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status
  publication-title: Nat Commun
  doi: 10.1038/ncomms12645
– volume: 73
  start-page: 4372
  year: 2013
  end-page: 4382
  ident: 2020.01.31.929372v1.1
  article-title: The exomes of the NCI-60 panel: A genomic resource for cancer biology and systems pharmacology
  publication-title: Cancer Res
  doi: 10.1158/0008-5472.CAN-12-3342
– volume: 29
  start-page: 1504
  year: 2013
  end-page: 1510
  ident: 2020.01.31.929372v1.68
  article-title: Predicting the functional consequences of cancer-associated amino acid substitutions
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btt182
– volume: 37
  start-page: 3006
  year: 2018
  end-page: 3021
  ident: 2020.01.31.929372v1.72
  article-title: DEAD-box helicase 27 promotes colorectal cancer growth and metastasis and predicts poor survival in CRC patients
  publication-title: Oncogene
  doi: 10.1038/s41388-018-0196-1
– volume: 33
  start-page: 306
  year: 2015
  end-page: 312
  ident: 2020.01.31.929372v1.43
  article-title: A comprehensive transcriptional portrait of human cancer cell lines
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt.3080
– volume: 6
  start-page: 914
  year: 2016
  end-page: 929
  ident: 2020.01.31.929372v1.2
  article-title: Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting
  publication-title: Cancer Discov
  doi: 10.1158/2159-8290.CD-16-0154
– volume: 9
  start-page: 35
  year: 2019
  end-page: 48.e5
  ident: 2020.01.31.929372v1.56
  article-title: A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines
  publication-title: Cell Syst
  doi: 10.1016/j.cels.2019.06.005
– volume: 81
  start-page: 247
  year: 2016
  end-page: 255
  ident: 2020.01.31.929372v1.78
  article-title: How Cancer Genomics Drives Cancer Biology: Does Synthetic Lethality Explain Mutually Exclusive Oncogenic Mutations?
  publication-title: Cold Spring Harb Symp Quant Biol
  doi: 10.1101/sqb.2016.81.030866
– volume: 8
  year: 2017
  ident: 2020.01.31.929372v1.86
  article-title: Succinate: An initiator in tumorigenesis and progression
  publication-title: Oncotarget
  doi: 10.18632/oncotarget.17734
– volume: 15
  year: 2016
  ident: 2020.01.31.929372v1.22
  article-title: Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells
  publication-title: Mol Cancer
  doi: 10.1186/s12943-016-0517-3
– volume: 39
  start-page: e118
  year: 2011
  end-page: e118
  ident: 2020.01.31.929372v1.63
  article-title: Predicting the functional impact of protein mutations: application to cancer genomics
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkr407
– volume: 164
  start-page: 293
  year: 2016
  end-page: 309
  ident: 2020.01.31.929372v1.52
  article-title: Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance
  publication-title: Cell
  doi: 10.1016/j.cell.2015.11.062
– volume: 560
  start-page: 325
  year: 2018
  end-page: 330
  ident: 2020.01.31.929372v1.8
  article-title: Genetic and transcriptional evolution alters cancer cell line drug response
  publication-title: Nature
  doi: 10.1038/s41586-018-0409-3
– year: 2008
  ident: 2020.01.31.929372v1.81
  article-title: Oncogene addiction
  publication-title: Cancer Res
  doi: 10.1158/0008-5472.CAN-07-3293
– volume: 483
  start-page: 603
  year: 2012
  end-page: 607
  ident: 2020.01.31.929372v1.5
  article-title: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
  publication-title: Nature
  doi: 10.1038/nature11003
– volume: 569
  start-page: 503
  year: 2019
  end-page: 508
  ident: 2020.01.31.929372v1.24
  article-title: Next-generation characterization of the Cancer Cell Line Encyclopedia
  publication-title: Nature
  doi: 10.1038/s41586-019-1186-3
– volume: 46
  start-page: D994
  year: 2018
  end-page: D1002
  ident: 2020.01.31.929372v1.69
  article-title: PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkx911
– year: 2020
  ident: 2020.01.31.929372v1.73
  article-title: Modulation of RNA Condensation by the DEAD-Box Protein eIF4A
  publication-title: Cell
  doi: 10.1016/j.cell.2019.12.031
– year: 2008
  ident: 2020.01.31.929372v1.42
  article-title: The role of PTEN signaling perturbations in cancer and in targeted therapy
  publication-title: Oncogene
  doi: 10.1038/onc.2008.248
– volume: 4
  start-page: 1
  year: 2015
  end-page: 23
  ident: 2020.01.31.929372v1.75
  article-title: Evidence that synthetic lethality underlies the mutual exclusivity of oncogenic KRAS and EGFR mutations in lung adenocarcinoma
  publication-title: Elife
  doi: 10.7554/eLife.06907
– volume: 483
  start-page: 570
  year: 2012
  end-page: 575
  ident: 2020.01.31.929372v1.20
  article-title: Systematic identification of genomic markers of drug sensitivity in cancer cells
  publication-title: Nature
  doi: 10.1038/nature11005
– year: 2019
  ident: 2020.01.31.929372v1.16
  article-title: DepMap 19Q3 Public
  doi: 10.6084/m9.figshare.9201770.v2
– volume: 170
  start-page: 564
  year: 2017
  end-page: 576.e16
  ident: 2020.01.31.929372v1.74
  article-title: Defining a Cancer Dependency Map
  publication-title: Cell
  doi: 10.1016/j.cell.2017.06.010
– volume: 9
  start-page: 51
  year: 2017
  ident: 2020.01.31.929372v1.37
  article-title: Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells
  publication-title: Genome Med
  doi: 10.1186/s13073-017-0440-2
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Snippet A caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis...
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SubjectTerms Breast cancer
Cancer
Cancer Biology
Cell culture
Laboratories
Molecular modelling
PTEN protein
Ribonucleic acid
RNA
Tumor cell lines
Tumor suppressor genes
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Title Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
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