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Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data

Karen A. Ryall, Jimin Shin, Minjae Yoo, Trista K. Hinz, Jihye Kim, Jaewoo Kang, Lynn E. Heasley, Aik Choon Tan
2015 Bioinformatics  
Results: We developed Kinase Addiction Ranker (KAR), an algorithm that integrates high-throughput drug screening data, comprehensive kinase inhibition data and gene expression profiles to identify kinase  ...  High-throughput drug screens are powerful tools for determining kinase dependency, but drug polypharmacology can make results difficult to interpret.  ...  .), the National Institutes of Health P50CA058187, P30CA046934, Cancer League of Colorado, and the David F. and Margaret T. Grohne Family Foundation.  ... 
doi:10.1093/bioinformatics/btv427 pmid:26206305 pmcid:PMC4675831 fatcat:kqos6aqyrrf2vozx7gfechrhz4

An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer

Karen A Ryall, Jihye Kim, Peter J Klauck, Jimin Shin, Minjae Yoo, Anastasia Ionkina, Todd M Pitts, John J Tentler, Jennifer R Diamond, S Eckhardt, Lynn E Heasley, Jaewoo Kang (+1 others)
2015 BMC Genomics  
Results: We integrated publicly available gene expression data, high-throughput pharmacological profiling data, and quantitative in vitro kinase binding data to determine the kinase dependency in 12 TNBC  ...  The goal of this study was to determine the kinase dependency in TNBC cell lines and to predict compounds that could inhibit these kinases using integrative bioinformatics analysis.  ...  The Kinase Addiction Ranker (KAR) algorithm integrates gene expression, drug screen, and quantitative kinase-drug binding data to predict kinase dependence in TNBC cell lines.  ... 
doi:10.1186/1471-2164-16-s12-s2 pmid:26681397 pmcid:PMC4682411 fatcat:fnvr37whf5dl7lpp43z5vdhqra

Systems biology approaches for advancing the discovery of effective drug combinations

Karen A Ryall, Aik Tan
2015 Journal of Cheminformatics  
, functional genomics, and high-throughput combination screens.  ...  Complex diseases like cancer are regulated by large, interconnected networks with many pathways affecting cell proliferation, invasion, and drug resistance.  ...  .), the National Institutes of Health P50CA058187, Cancer League of Colorado, the Department of Defense Award W81XWH-11-1-0527 and the David F. and Margaret T. Grohne Family Foundation.  ... 
doi:10.1186/s13321-015-0055-9 pmid:25741385 pmcid:PMC4348553 fatcat:wu2dx5zzmjcdnkz3jiawehblnm

Phosphoproteomics: Unraveling the Signaling Web

Paul H. Huang, Forest M. White
2008 Molecular Cell  
The DNA-Damage-Response Network Cells maintain their genome integrity via a surveillance network known as the DNA damage response (DDR).  ...  The importance of the DDR is revealed by physiological abnormalities that manifest as a result of genetic defects in specific signaling components (nodes) in the DDR  ...  Introduction Progress in cancer therapeutic development has historically relied on the high-throughput screening of small molecule libraries to identify compounds that exert a phenotypic effect on cancer  ... 
doi:10.1016/j.molcel.2008.09.001 pmid:18922462 pmcid:PMC2754874 fatcat:w6qduigvxbarffqoldisdbnh6m

Exploiting receptor tyrosine kinase co-activation for cancer therapy

Aik-Choon Tan, Simon Vyse, Paul H. Huang
2017 Drug Discovery Today  
We discuss direct and indirect approaches to exploit RTK co-activation for cancer therapy and describe recent developments in computational approaches to predict kinase codependencies by integrating drug  ...  screening data and kinase inhibitor selectivity profiles.  ...  Acknowledgments This work was supported by grants from the Institute of Cancer Research (ICR) and Cancer Research UK (C36478/ A19281) to PHH and Margaret T. Grohne Family Foundation to ACT.  ... 
doi:10.1016/j.drudis.2016.07.010 pmid:27452454 pmcid:PMC5346155 fatcat:lv2owxvdofanfc6p2la5wpa4yy

A Gene Expression High-Throughput Screen (GE-HTS) for Coordinated Detection of Functionally Similar Effectors in Cancer

Chaitra Rao, Dianna H. Huisman, Heidi M. Vieira, Danielle E. Frodyma, Beth K. Neilsen, Binita Chakraborty, Suzie K. Hight, Michael A. White, Kurt W. Fisher, Robert E. Lewis
2020 Cancers  
FUSION uses cell-based high-throughput screening and computational analysis to match gene expression signatures produced by natural products to those produced by small interfering RNA (siRNA) and synthetic  ...  Genome-wide, loss-of-function screening can be used to identify novel vulnerabilities upon which specific tumor cells depend for survival.  ...  The funders had no role in the decision to publish or preparation of the manuscript.  ... 
doi:10.3390/cancers12113143 pmid:33120942 pmcid:PMC7692652 fatcat:bhezewhslzeh7kjvr67vsnzubi

Developing a Novel Multiplexed Immune Assay Platform to Screen Kinase Modulators of T Cell Activation [chapter]

Zhaoping Liu, Andrea Gomez-Donart, Caroline Weldon, Nina Senutovitch, John O'Rourke
2021 High-Throughput Screening for Drug Discovery [Working Title]  
T cell activation plays a central role in inflammation, autoimmune diseases and cancer.  ...  The assay screened a kinase chemogenomic library and identified 25 kinase inhibitors with distinct inhibition profiles on early (CD69) and late (CD25) activation markers and the cytokines IFNγ and TNFα  ...  The authors received no financial support for the research, authorship, and/or publication of this article.  ... 
doi:10.5772/intechopen.97304 fatcat:22zwxubdsbgz7c6cr6iyb6wo7a

STK33 Kinase Activity Is Nonessential in KRAS-Dependent Cancer Cells

C. Babij, Y. Zhang, R. J. Kurzeja, A. Munzli, A. Shehabeldin, M. Fernando, K. Quon, P. D. Kassner, A. A. Ruefli-Brasse, V. J. Watson, F. Fajardo, A. Jackson (+11 others)
2011 Cancer Research  
We also obtained similar negative results using small molecule inhibitors of the STK33 kinase identified by high-throughput screening.  ...  In this study, we investigated the role of STK33 in mutant KRAS human cancer cells using RNA interference, dominant mutant overexpression, and small molecule inhibitors.  ...  The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C.  ... 
doi:10.1158/0008-5472.can-11-0778 pmid:21742770 fatcat:cxxdbqzm2nan7eymx4zycmr2wy

High-Throughput Molecular Imaging for the Identification of FADD Kinase Inhibitors

Amjad P. Khan, Katrina A. Schinske, Shyam Nyati, Mahaveer S. Bhojani, Brian D. Ross, Alnawaz Rehemtulla
2010 Journal of Biomolecular Screening  
The reporter assay, optimized for a high throughput screen (HTS), measures bioluminescence in response to modulation of FADD kinase activity in live cells.  ...  In an effort to delineate signaling events that lead to FADD phosphorylation and to identify novel compounds that impinge on this pathway, we developed a cell based reporter for FADD kinase activity.  ...  MSB by the National Institutes of Health through the University of Michigan's Head and Neck SPORE Grant (5 P50 CADE97248).  ... 
doi:10.1177/1087057110380570 pmid:20855560 pmcid:PMC3108567 fatcat:jzpftehgejbcnjhgztr6dnqyty

High-throughput Chemical Screening Identifies Focal Adhesion Kinase and Aurora Kinase B Inhibition as a Synergistic Treatment Combination in Ewing Sarcoma

Sarah Wang, Elizabeth E Hwang, Rajarshi Guha, Allison F O'Neill, Nicole Melong, Chansey J. Veinotte, Amy Saur Conway, Kellsey Wuerthele, Min Shen, Crystal McKnight, Gabriela Alexe, Madeleine E Lemieux (+10 others)
2019 Clinical Cancer Research  
Results High-throughput screen identifies synergistic drug combinations with FAK inhibitors in Ewing sarcoma To identify new candidate combination treatment approaches with FAK inhibitors in Ewing sarcoma  ...  Materials and Methods Small-molecule library drug combination screening A high-throughput screen was conducted in 1536-well white flat bottom plates (Corning) on a Kalypsys robotic system .  ...  Conclusions: FAK and Aurora kinase B inhibitors synergistically impair Ewing sarcoma cell viability and significantly inhibit tumor progression.  ... 
doi:10.1158/1078-0432.ccr-17-0375 pmid:30979745 pmcid:PMC6634997 fatcat:sq35djmwgrbzjgshkq5spvkabu


2012 Biocomputing 2013  
Briefly, a pharmacophore modeling method was employed to guide the selection of docked poses resulting from our high-throughput virtual screening.  ...  The approaches were applied to the repurposing of existing drugs against ACK1, a novel cancer target significantly overexpressed in breast and prostate cancers during their progression.  ...  This work was also supported by the MDACC IRG program and the Prostate SPORE Career Award (P50CA140388 SPORE).  ... 
doi:10.1142/9789814447973_0004 fatcat:aqc2sz37mjf4rhuuf7ifnkbzoi

Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression

Trish P Tran, Edison Ong, Andrew P Hodges, Giovanni Paternostro, Carlo Piermarocchi
2014 BMC Systems Biology  
We have developed the Kinase Inhibitors Elastic Net (KIEN) method, which integrates information contained in drug-kinase networks with in vitro screening.  ...  Data from two-drug combinations leads to predictive models, and predictivity can be improved by applying logarithmic transformation to the data.  ...  We would like to acknowledge the NSF grant (CCF0829891) and the DOD/CDMRP Lung Cancer Research Program (grant W81XWH-12-1-0233) for support.  ... 
doi:10.1186/1752-0509-8-74 pmid:24961498 pmcid:PMC4094402 fatcat:6djdbjedozhkdknlyihvo2uaea

A novel multi-modal drug repurposing approach for identification of potent ACK1 inhibitors

Sharangdhar S Phatak, Shuxing Zhang
2013 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Briefly, a pharmacophore modeling method was employed to guide the selection of docked poses resulting from our high-throughput virtual screening.  ...  The approaches were applied to the repurposing of existing drugs against ACK1, a novel cancer target significantly overexpressed in breast and prostate cancers during their progression.  ...  This work was also supported by the MDACC IRG program and the Prostate SPORE Career Award (P50CA140388 SPORE).  ... 
pmid:23424109 pmcid:PMC3864554 fatcat:rwbkpihvvvautaq36ascofgnni

From Integrative Genomics to Therapeutic Targets

R. Natrajan, P. Wilkerson
2013 Cancer Research  
By focusing efforts on homogenous subgroups of breast cancer and integrating orthogonal data-types combined with functional approaches, we can begin to unravel the heterogeneity and identify aberrations  ...  These methods have identified key genotypic-phenotypic correlations in different breast cancer subtypes that have led to the discovery of genetic dependencies that drive their behavior.  ...  , with si/shRNA screens of druggable genes and high-throughput small-molecule drug screens.  ... 
doi:10.1158/0008-5472.can-12-4717 pmid:23740772 pmcid:PMC3736308 fatcat:zsebq3wadncodkgh2w7nlqmofq

Application of High Throughput Technologies in the Development of Acute Myeloid Leukemia Therapy: Challenges and Progress

Wei Xiang, Yi Hui Lam, Giridharan Periyasamy, Charles Chuah
2022 International Journal of Molecular Sciences  
Given the accessibility to hematologic malignancy patient samples and recent advances in high-throughput technologies, large amounts of biological data that are clinically relevant for diagnosis, risk  ...  medicine for AML, and recent clinical studies for evaluating the utility of integrating genomics-guided and drug sensitivity testing-guided treatment approaches for AML patients.  ...  Ryall et al. have integrated data from high-throughput drug screening, drug-kinase binding, and transcriptomics using an algorithm named Kinase Addiction Ranker (KAR) [53] .  ... 
doi:10.3390/ijms23052863 pmid:35270002 pmcid:PMC8910862 fatcat:w4b2rm2njvfahekxacrkjvsp6a
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