A Landscape of Pharmacogenomic Interactions in Cancer
Francesco Iorio,Francesco Iorio,Theo A. Knijnenburg,Theo A. Knijnenburg,Daniel J. Vis,Graham R. Bignell,Michael P. Menden,Michael P. Menden,Michael Schubert,Nanne Aben,Nanne Aben,Emanuel Gonçalves,Syd Barthorpe,Howard Lightfoot,Thomas Cokelaer,Thomas Cokelaer,Patricia Greninger,Ewald van Dyk,Han Chang,Heshani de Silva,Holger Heyn,Xianming Deng,Regina K. Egan,Qingsong Liu,Tatiana Mironenko,Xeni Mitropoulos,Laura Richardson,Jinhua Wang,Tinghu Zhang,Sebastian Moran,Sergi Sayols,Maryam Soleimani,David Tamborero,Nuria Lopez-Bigas,Nuria Lopez-Bigas,Petra Ross-Macdonald,Manel Esteller,Manel Esteller,Nathanael S. Gray,Daniel A. Haber,Daniel A. Haber,Michael R. Stratton,Cyril H. Benes,Lodewyk F. A. Wessels,Lodewyk F. A. Wessels,Julio Saez-Rodriguez,Julio Saez-Rodriguez,Ultan McDermott,Mathew J. Garnett +48 more
TLDR
It is reported how cancer-driven alterations identified in 11,289 tumors from 29 tissues can be mapped onto 1,001 molecularly annotated human cancer cell lines and correlated with sensitivity to 265 drugs.About:
This article is published in Cell.The article was published on 2016-07-28 and is currently open access. It has received 1414 citations till now. The article focuses on the topics: Cancer & Pharmacogenomics.read more
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Drug repurposing: progress, challenges and recommendations
Sudeep Pushpakom,Francesco Iorio,Patrick A. Eyers,K. Jane Escott,Shirley Hopper,Andrew D. Wells,Andrew J. Doig,Tim Guilliams,Joanna Latimer,Christine J. McNamee,Alan Norris,Philippe Sanseau,David Cavalla,Munir Pirmohamed +13 more
TL;DR: Approaches used for drug repurposing (also known as drug repositioning) are presented, the challenges faced by the repurpose community are discussed, and innovative ways by which these challenges could be addressed are recommended to help realize the full potential of drugRepurposing.
Journal ArticleDOI
Next-generation characterization of the Cancer Cell Line Encyclopedia
Mahmoud Ghandi,Franklin W. Huang,Franklin W. Huang,Franklin W. Huang,Judit Jané-Valbuena,Judit Jané-Valbuena,Gregory V. Kryukov,Christopher Lo,E. Robert McDonald,Jordi Barretina,Ellen Gelfand,Craig M. Bielski,Haoxin Li,Haoxin Li,Kevin Hu,Alexander Y. Andreev-Drakhlin,Jaegil Kim,Julian M. Hess,Brian J. Haas,François Aguet,Barbara A. Weir,Michael V. Rothberg,Brenton R. Paolella,Michael S. Lawrence,Rehan Akbani,Yiling Lu,Hong L. Tiv,Prafulla C. Gokhale,Antoine de Weck,Ali Amin Mansour,Coyin Oh,Juliann Shih,Kevin Hadi,Yanay Rosen,Jonathan Bistline,Kavitha Venkatesan,Anupama Reddy,Dmitriy Sonkin,Dmitriy Sonkin,Manway Liu,Joseph Lehar,Joshua M. Korn,Dale Porter,Michael D. Jones,Javad Golji,Giordano Caponigro,Jordan E. Taylor,Caitlin M. Dunning,Amanda L. Creech,Allison Warren,James M. McFarland,Mahdi Zamanighomi,Audrey Kauffmann,Nicolas Stransky,Marcin Imielinski,Yosef E. Maruvka,Yosef E. Maruvka,Andrew D. Cherniack,Andrew D. Cherniack,Aviad Tsherniak,Francisca Vazquez,Jacob D. Jaffe,Andrew A. Lane,David M. Weinstock,Cory M. Johannessen,Michael Morrissey,Frank Stegmeier,Robert Schlegel,William C. Hahn,William C. Hahn,Gad Getz,Gordon B. Mills,Jesse S. Boehm,Todd R. Golub,Todd R. Golub,Todd R. Golub,Levi A. Garraway,Levi A. Garraway,William R. Sellers,William R. Sellers +79 more
TL;DR: The original Cancer Cell Line Encyclopedia is expanded with deeper characterization of over 1,000 cell lines, including genomic, transcriptomic, and proteomic data, and integration with drug-sensitivity and gene-dependency data, which reveals potential targets for cancer drugs and associated biomarkers.
Journal ArticleDOI
COSMIC: somatic cancer genetics at high-resolution.
Simon A. Forbes,David Beare,Harry Boutselakis,Sally Bamford,Nidhi Bindal,John Tate,Charlotte G. Cole,Sari Ward,Elisabeth Dawson,Laura Ponting,Raymund Stefancsik,Bhavana Harsha,Chai Yin Kok,Mingming Jia,Harry Jubb,Zbyslaw Sondka,Sam Thompson,Tisham De,Peter J. Campbell +18 more
TL;DR: COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours.
Journal ArticleDOI
Applications of machine learning in drug discovery and development.
Jessica Vamathevan,Dominic Clark,Paul Czodrowski,Ian Dunham,Edgardo Ferran,George Lee,Bin Li,Anant Madabhushi,Anant Madabhushi,Parantu K. Shah,Michaela Spitzer,Shanrong Zhao +11 more
TL;DR: The most useful techniques and how machine learning can promote data-driven decision making in drug discovery and development are discussed and major hurdles in the field are highlighted.
Journal ArticleDOI
Human primary liver cancer–derived organoid cultures for disease modeling and drug screening
Laura Broutier,Gianmarco Mastrogiovanni,Monique M A Verstegen,Hayley E. Francies,Lena Morrill Gavarró,Charles R. Bradshaw,George E. Allen,Robert Arnes-Benito,Olga Sidorova,Marcia P. Gaspersz,Nikitas Georgakopoulos,Bon-Kyoung Koo,Sabine Dietmann,Susan E. Davies,Raaj K. Praseedom,Ruby Lieshout,Jan N. M. IJzermans,Stephen J. Wigmore,Kourosh Saeb-Parsy,Mathew J. Garnett,Luc J. W. van der Laan,Meritxell Huch +21 more
TL;DR: The wide-ranging biomedical utilities of PLC-derived organoid models in furthering the understanding of liver cancer biology and in developing personalized-medicine approaches for the disease are demonstrated.
References
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TL;DR: This work has been supported by the Department of the Army and the National Institutes of Health, and the author acknowledges the support and encouragement of the National Cancer Institute.
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Gefitinib or Carboplatin–Paclitaxel in Pulmonary Adenocarcinoma
Tony Mok,Yi-Long Wu,Sumitra Thongprasert,Chih-Hsin Yang,Da Tong Chu,Nagahiro Saijo,Patrapim Sunpaweravong,Baohui Han,Benjamin Margono,Benjamin Margono,Yukito Ichinose,Yutaka Nishiwaki,Yuichiro Ohe,Jin Ji Yang,Busyamas Chewaskulyong,Haiyi Jiang,Emma Duffield,Claire Watkins,Alison Armour,Masahiro Fukuoka +19 more
TL;DR: Gefit inib is superior to carboplatin-paclitaxel as an initial treatment for pulmonary adenocarcinoma among nonsmokers or former light smokers in East Asia and the presence in the tumor of a mutation of the EGFR gene is a strong predictor of a better outcome with gefitinib.
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Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation
Paul B. Chapman,Axel Hauschild,Caroline Robert,John B. A. G. Haanen,Paolo A. Ascierto,James Larkin,Reinhard Dummer,Claus Garbe,Alessandro Testori,Michele Maio,David W. Hogg,Paul Lorigan,Céleste Lebbé,Thomas Jouary,Dirk Schadendorf,Antoni Ribas,Jeffrey A. Sosman,John M. Kirkwood,Brigitte Dréno,K. B. Nolop,Jiang Li,B. Nelson,Jeannie Hou,Richard J. Lee,Keith T. Flaherty,Grant A. McArthur +25 more
TL;DR: Vemurafenib produced improved rates of overall and progression-free survival in patients with previously untreated melanoma with the BRAF V600E mutation in a phase 3 randomized clinical trial.
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Cancer Genome Landscapes
Bert Vogelstein,Nickolas Papadopoulos,Victor E. Velculescu,Shibin Zhou,Luis A. Diaz,Kenneth W. Kinzler +5 more
TL;DR: This work has revealed the genomic landscapes of common forms of human cancer, which consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of "hills" (Genes altered infrequently).
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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,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 +65 more
TL;DR: The results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents and the generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of ‘personalized’ therapeutic regimens.
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