Erratum: Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity (Nature (2012) 483 7391 (603-607))
Jordi Barretina,Jordi Barretina,Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,Sungjoon Kim,Christine D. Wilson,Joseph Lehar,Gregory V. Kryukov,Dmitriy Sonkin,Anupama Reddy,Manway Liu,Lauren Murray,Michael F. Berger,Michael F. Berger,John Monahan,Paula Morais,Jodi Meltzer,Adam Korejwa,Judit Jané-Valbuena,Judit Jané-Valbuena,Felipa A. Mapa,Joseph Thibault,Eva Bric-Furlong,Pichai Raman,Aaron Shipway,Ingo H. Engels,Jill Cheng,Guoying K. Yu,Jianjun Yu,Peter Aspesi,Melanie de Silva,Kalpana Jagtap,Michael D. Jones,Li Wang,Charlie Hatton,Emanuele Palescandolo,Supriya Gupta,Scott Mahan,Carrie Sougnez,Robert C. Onofrio,Ted Liefeld,Laura E. MacConaill,Wendy Winckler,Michael R. Reich,Nanxin Li,Jill P. Mesirov,Stacey Gabriel,Gad Getz,Kristin G. Ardlie,Vivien W. Chan,Vic E. Myer,Barbara L. Weber,Jeffrey A. Porter,Markus Warmuth,Peter Finan,Jennifer L. Harris,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Michael Morrissey,William R. Sellers,Robert Schlegel,Levi A. Garraway,Levi A. Garraway +66 more
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Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A. Golub, Michael P. Morais, Jodi Meltzer, Judit Jané-Valbuena, Felipa A. Mapa, Joseph Thibault, Eva Bric-Furlong, Pichai Raman, Aaron Shipway, Ingo H. Engels, Jill Cheng, Guoying K. YuAbstract:
Jordi Barretina, Giordano Caponigro, Nicolas Stransky, Kavitha Venkatesan, Adam A. Margolin, Sungjoon Kim, Christopher J. Wilson, Joseph Lehár, Gregory V. Kryukov, Dmitriy Sonkin, Anupama Reddy, Manway Liu, Lauren Murray, Michael F. Berger, John E. Monahan, Paula Morais, Jodi Meltzer, Adam Korejwa, Judit Jané-Valbuena, Felipa A. Mapa, Joseph Thibault, Eva Bric-Furlong, Pichai Raman, Aaron Shipway, Ingo H. Engels, Jill Cheng, Guoying K. Yu, Jianjun Yu, Peter Aspesi Jr, Melanie de Silva, Kalpana Jagtap, Michael D. Jones, Li Wang, Charles Hatton, Emanuele Palescandolo, Supriya Gupta, Scott Mahan, Carrie Sougnez, Robert C. Onofrio, Ted Liefeld, Laura MacConaill, Wendy Winckler, Michael Reich, Nanxin Li, Jill P. Mesirov, Stacey B. Gabriel, Gad Getz, Kristin Ardlie, Vivien Chan, Vic E. Myer, Barbara L. Weber, Jeff Porter, Markus Warmuth, Peter Finan, Jennifer L. Harris, Matthew Meyerson, Todd R. Golub, Michael P. Morrissey, William R. Sellers, Robert Schlegel & Levi A. Garrawayread more
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xCell: digitally portraying the tissue cellular heterogeneity landscape
TL;DR: This work presents xCell, a novel gene signature-based method, and uses it to infer 64 immune and stromal cell types and shows that xCell outperforms other methods.
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STK11/LKB1 deficiency promotes neutrophil recruitment and proinflammatory cytokine production to suppress T cell activity in the lung tumor microenvironment
Shohei Koyama,Esra A. Akbay,Yvonne Y. Li,Amir Reza Aref,Ferdinandos Skoulidis,Grit S. Herter-Sprie,Kevin A. Buczkowski,Yan Liu,Mark M. Awad,Warren Denning,Lixia Diao,Jing Wang,Edwin Parra-Cuentas,Ignacio I. Wistuba,Margaret Soucheray,Tran C. Thai,Hajime Asahina,Shunsuke Kitajima,Abigail Altabef,Jillian D. Cavanaugh,Kevin Rhee,Peng Gao,Haikuo Zhang,Peter E. Fecci,Takeshi Shimamura,Matthew D. Hellmann,John V. Heymach,F. Stephen Hodi,Gordon J. Freeman,David A. Barbie,Glenn Dranoff,Peter S. Hammerman,Peter S. Hammerman,Kwok-Kin Wong +33 more
TL;DR: The findings illustrate how tumor suppressor mutations can modulate the immune milieu of the tumor microenvironment, and they offer specific implications for addressing STK11/LKB1-mutated tumors with PD-1-targeting antibody therapies.
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MYC and MCL1 Cooperatively Promote Chemotherapy-Resistant Breast Cancer Stem Cells via Regulation of Mitochondrial Oxidative Phosphorylation
Kyungmin Lee,Jennifer M. Giltnane,Justin M. Balko,Luis J. Schwarz,Angel Guerrero-Zotano,Katherine E. Hutchinson,Mellissa J. Nixon,Monica V. Estrada,Violeta Sanchez,Melinda E. Sanders,Taekyu Lee,Henry L. Gomez,Ana Lluch,J. Alejandro Pérez-Fidalgo,Melissa M. Wolf,Gabriela Andrejeva,Jeffrey C. Rathmell,Stephen W. Fesik,Carlos L. Arteaga +18 more
TL;DR: The data suggest that MYC and MCL1 confer resistance to chemotherapy by expanding CSCs via mtOXPHOS and targeting mitochondrial respiration and HIF-1α may reverse chemotherapy resistance in TNBC.
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Chemosensitive Relapse in Small Cell Lung Cancer Proceeds through an EZH2-SLFN11 Axis
Eric E. Gardner,Eric E. Gardner,Benjamin H. Lok,Valentina E. Schneeberger,Patrice Desmeules,Linde A. Miles,Paige K. Arnold,Andy Ni,Inna Khodos,Elisa de Stanchina,Thuyen Nguyen,Julien Sage,John Campbell,Scott Ribich,Natasha Rekhtman,Afshin Dowlati,Pierre P. Massion,Charles M. Rudin,Charles M. Rudin,John T. Poirier +19 more
TL;DR: Inclusion of an EZH2 inhibitor with standard cytotoxic therapies prevented emergence of acquired resistance and augmented chemotherapeutic efficacy in both chemosensitive and chemoresistant models of small cell lung cancer.
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The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology
Artur Kadurin,Alexander Aliper,Andrey Kazennov,Polina Mamoshina,Quentin Vanhaelen,Kuzma Khrabrov,Alex Zhavoronkov +6 more
TL;DR: This paper presents the first application of generative adversarial autoencoders (AAE) for generating novel molecular fingerprints with a defined set of parameters, developed a 7-layer AAE architecture with the latent middle layer serving as a discriminator.
References
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Pharmacogenomic agreement between two cancer cell line data sets
Nicolas Stransky,Mahmoud Ghandi,Gregory V. Kryukov,Levi A. Garraway,Arnaud Amzallag,Iulian Pruteanu-Malinici,Daniel A. Haber,Sridhar Ramaswamy,Cyril H. Benes,Joseph Lehar,Manway Liu,Dmitriy Sonkin,Audrey Kauffmann,Kavitha Venkatesan,Elena J. Edelman,Markus Riester,Jordi Barretina,Giordano Caponigro,Robert Schlegel,William R. Sellers,Frank Stegmeier,Michael B. Morrissey,Michael P. Menden,Francesco Iorio,Michael R. Stratton,Ultan McDermott,Julio Saez-Rodriguez,Mathew J. Garnett +27 more
TL;DR: There is substantial agreement and biological consilience between drug sensitivity measurements and their associated genomic predictors from two publicly available large-scale pharmacogenomics resources: The Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer databases.
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