Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

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Menden , M P , Wang , D , Mason , M J , Szalai , B , Bulusu , K C , Guan , Y , Yu , T , Kang , J , Jeon , M , Wolfinger , R , Nguyen , T , Zaslavskiy , M , Abante , J , Abecassis , B S , Aben , N , Aghamirzaie , D , Aittokallio , T , Akhtari , F S , Al-lazikani , B , Alam , T , Allam , A , Allen , C , de Almeida , M P , Altarawy , D , Alves , V , Amadoz , A , Anchang , B , Antolin , A A , Ash , J R , Aznar , V R , Ba-alawi , W , Bagheri , M , Bajic , V , Ball , G , Ballester , P J , Baptista , D , Bare , C , Bateson , M , Bender , A , Bertrand , D , Wijayawardena , B , Boroevich , K A , Bosdriesz , E , Bougouffa , S , Bounova , G , Brouwer , T , Bryant , B , Calaza , M , Calderone , A , Calza , S , Capuzzi , S , Carbonell-Caballero , J , Carlin , D , Carter , H , Castagnoli , L , Celebi , R , Cesareni , G , Chang , H , Chen , G , Chen , H , Chen , H , Cheng , L , Chernomoretz , A , Chicco , D , Cho , K-H , Cho , S , Choi , D , Choi , J , Choi , K , Choi , M , Cock , M D , Coker , E , Cortes-Ciriano , I , Cserzö , M , Cubuk , C , Curtis , C , Daele , D V , Dang , C C , Dijkstra , T , Dopazo , J , Draghici , S , Drosou , A , Dumontier , M , Ehrhart , F , Eid , F-E , ElHefnawi , M , Elmarakeby , H , van Engelen , B , Engin , H B , de Esch , I , Evelo , C , Falcao , A O , Farag , S , Fernandez-Lozano , C , Fisch , K , Flobak , A , Fornari , C , Foroushani , A B K , Fotso , D C , Fourches , D , Friend , S , Frigessi , A , Gao , F , Gao , X , Gerold , J M , Gestraud , P , Ghosh , S , Gillberg , J , Godoy-Lorite , A , Godynyuk , L , Godzik , A , Goldenberg , A , Gomez-Cabrero , D , Gonen , M , de Graaf , C , Gray , H , Grechkin , M , Guimera , R , Guney , E , Haibe-Kains , B , Han , Y , Hase , T , He , D , He , L , Heath , L S , Hellton , K H , Helmer-Citterich , M , Hidalgo , M R , Hidru , D , Hill , S M , Hochreiter , S , Hong , S , Hovig , E , Hsueh , Y-C , Hu , Z , Huang , J K , Huang , R S , Hunyady , L , Hwang , J , Hwang , T H , Hwang , W , Hwang , Y , Isayev , O , Don’t Walk , O B , Jack , J , Jahandideh , S , Ji , J , Jo , Y , Kamola , P J , Kanev , G K , Karacosta , L , Karimi , M , Kaski , S , Kazanov , M , Khamis , A M , Khan , S A , Kiani , N A , Kim , A , Kim , J , Kim , J , Kim , K , Kim , K , Kim , S , Kim , Y , Kim , Y , Kirk , P D W , Kitano , H , Klambauer , G , Knowles , D , Ko , M , Kohn-Luque , A , Kooistra , A J , Kuenemann , M A , Kuiper , M , Kurz , C , Kwon , M , van Laarhoven , T , Laegreid , A , Lederer , S , Lee , H , Lee , J , Lee , Y W , Lepp_aho , E , Lewis , R , Li , J , Li , L , Liley , J , Lim , W K , Lin , C , Liu , Y , Lopez , Y , Low , J , Lysenko , A , Machado , D , Madhukar , N , Maeyer , D D , Malpartida , A B , Mamitsuka , H , Marabita , F , Marchal , K , Marttinen , P , Mason , D , Mazaheri , A , Mehmood , A , Mehreen , A , Michaut , M , Miller , R A , Mitsopoulos , C , Modos , D , Moerbeke , M V , Moo , K , Motsinger-Reif , A , Movva , R , Muraru , S , Muratov , E , Mushthofa , M , Nagarajan , N , Nakken , S , Nath , A , Neuvial , P , Newton , R , Ning , Z , Niz , C D , Oliva , B , Olsen , C , Palmeri , A , Panesar , B , Papadopoulos , S , Park , J , Park , S , Park , S , Pawitan , Y , Peluso , D , Pendyala , S , Peng , J , Perfetto , L , Pirro , S , Plevritis , S , Politi , R , Poon , H , Porta , E , Prellner , I , Preuer , K , Pujana , M A , Ramnarine , R , Reid , J E , Reyal , F , Richardson , S , Ricketts , C , Rieswijk , L , Rocha , M , Rodriguez-Gonzalvez , C , Roell , K , Rotroff , D , de Ruiter , J R , Rukawa , P , Sadacca , B , Safikhani , Z , Safitri , F , Sales-Pardo , M , Sauer , S , Schlichting , M , Seoane , J A , Serra , J , Shang , M-M , Sharma , A , Sharma , H , Shen , Y , Shiga , M , Shin , M , Shkedy , Z , Shopsowitz , K , Sinai , S , Skola , D , Smirnov , P , Soerensen , I F , Soerensen , P , Song , J-H , Song , S O , Soufan , O , Spitzmueller , A , Steipe , B , Suphavilai , C , Tamayo , S P , Tamborero , D , Tang , J , Tanoli , Z-R , Tarres-Deulofeu , M , Tegner , J , Thommesen , L , Tonekaboni , S A M , Tran , H , Troyer , E D , Truong , A , Tsunoda , T , Turu , G , Tzeng , G-Y , Verbeke , L , Videla , S & Consortium , A-S D C DREAM 2019 , ' Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen ' , Nature Communications , vol. 10 , no. 1 , 2674 . https://doi.org/10.1038/s41467-019-09799-2

Title: Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Author: Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; Kang, Jaewoo; Jeon, Minji; Wolfinger, Russ; Nguyen, Tin; Zaslavskiy, Mikhail; Abante, Jordi; Abecassis, Barbara Schmitz; Aben, Nanne; Aghamirzaie, Delasa; Aittokallio, Tero; Akhtari, Farida S.; Al-lazikani, Bissan; Alam, Tanvir; Allam, Amin; Allen, Chad; de Almeida, Mariana Pelicano; Altarawy, Doaa; Alves, Vinicius; Amadoz, Alicia; Anchang, Benedict; Antolin, Albert A.; Ash, Jeremy R.; Aznar, Victoria Romeo; Ba-alawi, Wail; Bagheri, Moeen; Bajic, Vladimir; Ball, Gordon; Ballester, Pedro J.; Baptista, Delora; Bare, Christopher; Bateson, Mathilde; Bender, Andreas; Bertrand, Denis; Wijayawardena, Bhagya; Boroevich, Keith A.; Bosdriesz, Evert; Bougouffa, Salim; Bounova, Gergana; Brouwer, Thomas; Bryant, Barbara; Calaza, Manuel; Calderone, Alberto; Calza, Stefano; Capuzzi, Stephen; Carbonell-Caballero, Jose; Carlin, Daniel; Carter, Hannah; Castagnoli, Luisa; Celebi, Remzi; Cesareni, Gianni; Chang, Hyeokyoon; Chen, Guocai; Chen, Haoran; Chen, Huiyuan; Cheng, Lijun; Chernomoretz, Ariel; Chicco, Davide; Cho, Kwang-Hyun; Cho, Sunghwan; Choi, Daeseon; Choi, Jaejoon; Choi, Kwanghun; Choi, Minsoo; Cock, Martine De; Coker, Elizabeth; Cortes-Ciriano, Isidro; Cserzö, Miklós; Cubuk, Cankut; Curtis, Christina; Daele, Dries Van; Dang, Cuong C.; Dijkstra, Tjeerd; Dopazo, Joaquin; Draghici, Sorin; Drosou, Anastasios; Dumontier, Michel; Ehrhart, Friederike; Eid, Fatma-Elzahraa; ElHefnawi, Mahmoud; Elmarakeby, Haitham; van Engelen, Bo; Engin, Hatice Billur; de Esch, Iwan; Evelo, Chris; Falcao, Andre O.; Farag, Sherif; Fernandez-Lozano, Carlos; Fisch, Kathleen; Flobak, Asmund; Fornari, Chiara; Foroushani, Amir B. K.; Fotso, Donatien Chedom; Fourches, Denis; Friend, Stephen; Frigessi, Arnoldo; Gao, Feng; Gao, Xiaoting; Gerold, Jeffrey M.; Gestraud, Pierre; Ghosh, Samik; Gillberg, Jussi; Godoy-Lorite, Antonia; Godynyuk, Lizzy; Godzik, Adam; Goldenberg, Anna; Gomez-Cabrero, David; Gonen, Mehmet; de Graaf, Chris; Gray, Harry; Grechkin, Maxim; Guimera, Roger; Guney, Emre; Haibe-Kains, Benjamin; Han, Younghyun; Hase, Takeshi; He, Di; He, Liye; Heath, Lenwood S.; Hellton, Kristoffer H.; Helmer-Citterich, Manuela; Hidalgo, Marta R.; Hidru, Daniel; Hill, Steven M.; Hochreiter, Sepp; Hong, Seungpyo; Hovig, Eivind; Hsueh, Ya-Chih; Hu, Zhiyuan; Huang, Justin K.; Huang, R. Stephanie; Hunyady, László; Hwang, Jinseub; Hwang, Tae Hyun; Hwang, Woochang; Hwang, Yongdeuk; Isayev, Olexandr; Don’t Walk, Oliver Bear; Jack, John; Jahandideh, Samad; Ji, Jiadong; Jo, Yousang; Kamola, Piotr J.; Kanev, Georgi K.; Karacosta, Loukia; Karimi, Mostafa; Kaski, Samuel; Kazanov, Marat; Khamis, Abdullah M.; Khan, Suleiman Ali; Kiani, Narsis A.; Kim, Allen; Kim, Jinhan; Kim, Juntae; Kim, Kiseong; Kim, Kyung; Kim, Sunkyu; Kim, Yongsoo; Kim, Yunseong; Kirk, Paul D. W.; Kitano, Hiroaki; Klambauer, Gunter; Knowles, David; Ko, Melissa; Kohn-Luque, Alvaro; Kooistra, Albert J.; Kuenemann, Melaine A.; Kuiper, Martin; Kurz, Christoph; Kwon, Mijin; van Laarhoven, Twan; Laegreid, Astrid; Lederer, Simone; Lee, Heewon; Lee, Jeon; Lee, Yun Woo; Lepp_aho, Eemeli; Lewis, Richard; Li, Jing; Li, Lang; Liley, James; Lim, Weng Khong; Lin, Chieh; Liu, Yiyi; Lopez, Yosvany; Low, Joshua; Lysenko, Artem; Machado, Daniel; Madhukar, Neel; Maeyer, Dries De; Malpartida, Ana Belen; Mamitsuka, Hiroshi; Marabita, Francesco; Marchal, Kathleen; Marttinen, Pekka; Mason, Daniel; Mazaheri, Alireza; Mehmood, Arfa; Mehreen, Ali; Michaut, Magali; Miller, Ryan A.; Mitsopoulos, Costas; Modos, Dezso; Moerbeke, Marijke Van; Moo, Keagan; Motsinger-Reif, Alison; Movva, Rajiv; Muraru, Sebastian; Muratov, Eugene; Mushthofa, Mushthofa; Nagarajan, Niranjan; Nakken, Sigve; Nath, Aritro; Neuvial, Pierre; Newton, Richard; Ning, Zheng; Niz, Carlos De; Oliva, Baldo; Olsen, Catharina; Palmeri, Antonio; Panesar, Bhawan; Papadopoulos, Stavros; Park, Jaesub; Park, Seonyeong; Park, Sungjoon; Pawitan, Yudi; Peluso, Daniele; Pendyala, Sriram; Peng, Jian; Perfetto, Livia; Pirro, Stefano; Plevritis, Sylvia; Politi, Regina; Poon, Hoifung; Porta, Eduard; Prellner, Isak; Preuer, Kristina; Pujana, Miguel Angel; Ramnarine, Ricardo; Reid, John E.; Reyal, Fabien; Richardson, Sylvia; Ricketts, Camir; Rieswijk, Linda; Rocha, Miguel; Rodriguez-Gonzalvez, Carmen; Roell, Kyle; Rotroff, Daniel; de Ruiter, Julian R.; Rukawa, Ploy; Sadacca, Benjamin; Safikhani, Zhaleh; Safitri, Fita; Sales-Pardo, Marta; Sauer, Sebastian; Schlichting, Moritz; Seoane, Jose A.; Serra, Jordi; Shang, Ming-Mei; Sharma, Alok; Sharma, Hari; Shen, Yang; Shiga, Motoki; Shin, Moonshik; Shkedy, Ziv; Shopsowitz, Kevin; Sinai, Sam; Skola, Dylan; Smirnov, Petr; Soerensen, Izel Fourie; Soerensen, Peter; Song, Je-Hoon; Song, Sang Ok; Soufan, Othman; Spitzmueller, Andreas; Steipe, Boris; Suphavilai, Chayaporn; Tamayo, Sergio Pulido; Tamborero, David; Tang, Jing; Tanoli, Zia-ur-Rehman; Tarres-Deulofeu, Marc; Tegner, Jesper; Thommesen, Liv; Tonekaboni, Seyed Ali Madani; Tran, Hong; Troyer, Ewoud De; Truong, Amy; Tsunoda, Tatsuhiko; Turu, Gábor; Tzeng, Guang-Yo; Verbeke, Lieven; Videla, Santiago; Consortium, AstraZeneca-Sanger Drug Combination DREAM
Contributor organization: Tero Aittokallio / Principal Investigator
Bioinformatics
Institute for Molecular Medicine Finland
Date: 2019-06-17
Language: eng
Number of pages: 17
Belongs to series: Nature Communications
ISSN: 2041-1723
DOI: https://doi.org/10.1038/s41467-019-09799-2
URI: http://hdl.handle.net/10138/308081
Abstract: The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca’s large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
Subject: ANDROGEN RECEPTOR
BREAST-CANCER
CELL
GENE
INHIBITION
LANDSCAPE
MUTATIONS
PATHWAY
RESISTANCE
RESOURCE
317 Pharmacy
3122 Cancers
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


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