Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity

被引：29

作者：

Amadoz, Alicia ^{[1
]}

Sebastian-Leon, Patricia ^{[1
]}

Vidal, Enrique ^{[1
,2
]}

Salavert, Francisco ^{[1
,2
]}

Dopazo, Joaquin ^{[1
,2
,3
]}

机构：

[1] CIPF, Computat Genom Dept, Valencia, Spain

[2] CIBERER, Bioinformat Rare Dis BIER, Valencia, Spain

[3] INB CIPF, Funct Genom Node, Valencia, Spain

来源：

SCIENTIFIC REPORTS | 2015年 / 5卷

关键词：

SQUAMOUS-CELL CARCINOMA; GENE-EXPRESSION; BREAST-CANCER; HEPATOCELLULAR-CARCINOMA; AZD6244; ARRY-142886; ANTITUMOR-ACTIVITY; CONNECTIVITY MAP; DOWN-REGULATION; LUNG-CANCER; RNA-SEQ;

D O I：

10.1038/srep18494

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Many complex traits, as drug response, are associated with changes in biological pathways rather than being caused by single gene alterations. Here, a predictive framework is presented in which gene expression data are recoded into activity statuses of signal transduction circuits (sub-pathways within signaling pathways that connect receptor proteins to final effector proteins that trigger cell actions). Such activity values are used as features by a prediction algorithm which can efficiently predict a continuous variable such as the IC50 value. The main advantage of this prediction method is that the features selected by the predictor, the signaling circuits, are themselves rich-informative, mechanism-based biomarkers which provide insight into or drug molecular mechanisms of action (MoA).

引用

页数：13

共 97 条

[1]

Inhibition of Hedgehog signaling sensitizes NSCLC cells to standard therapies through modulation of EMT-regulating miRNAs [J].

Ahmad, Aamir ;

Maitah, Ma'in Y. ;

Ginnebaugh, Kevin R. ;

Li, Yiwei ;

Bao, Bin ;

Gadgeel, Shirish M. ;

Sarkar, Fazlul H. .

JOURNAL OF HEMATOLOGY & ONCOLOGY, 2013, 6

[2]

Babelomics 5.0: functional interpretation for new generations of genomic data [J].

Alonso, Roberto ;

Salavert, Francisco ;

Garcia-Garcia, Francisco ;

Carbonell-Caballero, Jose ;

Bleda, Marta ;

Garcia-Alonso, Luz ;

Sanchis-Juan, Alba ;

Perez-Gil, Daniel ;

Marin-Garcia, Pablo ;

Sanchez, Ruben ;

Cubuk, Cankut ;

Hidalgo, Marta R. ;

Amadoz, Alicia ;

Hernansaiz-Ballesteros, Rosa D. ;

Aleman, Alejandro ;

Tarraga, Joaquin ;

Montaner, David ;

Medina, Ignacio ;

Dopazo, Joaquin .

NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W117-W121

[3]

Synergistic Growth Inhibition of Squamous Cell Carcinoma of the Head and Neck by Erlotinib and Epigallocatechin-3-Gallate: The Role of p53-Dependent Inhibition of Nuclear Factor-κB [J].

Amin, A. R. M. Ruhul ;

Khuri, Fadlo R. ;

Chen, Zhuo ;

Shin, Dong M. .

CANCER PREVENTION RESEARCH, 2009, 2 (06) :538-545

[4]

[Anonymous], 2013, Package 'FSelector

[5]

Network medicine: a network-based approach to human disease [J].

Barabasi, Albert-Laszlo ;

Gulbahce, Natali ;

Loscalzo, Joseph .

NATURE REVIEWS GENETICS, 2011, 12 (01) :56-68

[6]

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity [J].

Barretina, Jordi ;

Caponigro, Giordano ;

Stransky, Nicolas ;

Venkatesan, Kavitha ;

Margolin, Adam A. ;

Kim, Sungjoon ;

Wilson, Christopher J. ;

Lehar, Joseph ;

Kryukov, Gregory V. ;

Sonkin, Dmitriy ;

Reddy, Anupama ;

Liu, Manway ;

Murray, Lauren ;

Berger, Michael F. ;

Monahan, John E. ;

Morais, Paula ;

Meltzer, Jodi ;

Korejwa, Adam ;

Jane-Valbuena, Judit ;

Mapa, Felipa A. ;

Thibault, Joseph ;

Bric-Furlong, Eva ;

Raman, Pichai ;

Shipway, Aaron ;

Engels, Ingo H. ;

Cheng, Jill ;

Yu, Guoying K. ;

Yu, Jianjun ;

Aspesi, Peter, Jr. ;

de Silva, Melanie ;

Jagtap, Kalpana ;

Jones, Michael D. ;

Wang, Li ;

Hatton, Charles ;

Palescandolo, Emanuele ;

Gupta, Supriya ;

Mahan, Scott ;

Sougnez, Carrie ;

Onofrio, Robert C. ;

Liefeld, Ted ;

MacConaill, Laura ;

Winckler, Wendy ;

Reich, Michael ;

Li, Nanxin ;

Mesirov, Jill P. ;

Gabriel, Stacey B. ;

Getz, Gad ;

Ardlie, Kristin ;

Chan, Vivien ;

Myer, Vic E. .

NATURE, 2012, 483 (7391) :603-607

[7]

Wnt/β-Catenin Signaling and AXIN1 Regulate Apoptosis Triggered by Inhibition of the Mutant Kinase BRAFV600E in Human Melanoma [J].

Biechele, Travis L. ;

Kulikauskas, Rima M. ;

Toroni, Rachel A. ;

Lucero, Olivia M. ;

Swift, Reyna D. ;

James, Richard G. ;

Robin, Nick C. ;

Dawson, David W. ;

Moon, Randall T. ;

Chien, Andy J. .

SCIENCE SIGNALING, 2012, 5 (206)

[8]

Combined inhibition of EGFR and CK2 augments the attenuation of PI3K-Akt-mTOR signaling and the killing of cancer cells [J].

Bliesath, Joshua ;

Huser, Nanni ;

Omori, Mayuko ;

Bunag, Daniel ;

Proffitt, Chris ;

Streiner, Nicole ;

Ho, Caroline ;

Siddiqui-Jain, Adam ;

O'Brien, Sean E. ;

Lim, John K. C. ;

Ryckman, David M. ;

Anderes, Kenna ;

Rice, William G. ;

Drygin, Denis .

CANCER LETTERS, 2012, 322 (01) :113-118

[9]

Paclitaxel induces calcium oscillations via an inositol 1,4,5-trisphosphate receptor and neuronal calcium sensor 1-dependent mechanism [J].

Boehmerle, Wolfgang ;

Splittgerber, Ute ;

Lazarus, Michael B. ;

McKenzie, Kathleen M. ;

Johnston, David G. ;

Austin, David J. ;

Ehrlich, Barbara E. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (48) :18356-18361

[10]

Signaling pathways activation profiles make better markers of cancer than expression of individual genes [J].

Borisov, Nikolay M. ;

Terekhanova, Nadezhda V. ;

Aliper, Alexander M. ;

Venkova, Larisa S. ;

Smirnov, Philip Yu ;

Roumiantsev, Sergey ;

Korzinkin, Mikhail B. ;

Zhavoronkov, Alex A. ;

Buzdin, Anton A. .

ONCOTARGET, 2014, 5 (20) :10198-10205

← 1 2 3 4 5 6 7 8 9 10 →