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Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid, Ioannis Xenarios
2015 PLoS Computational Biology  
Discovery of Drug Synergies by Logical Modeling PLOS Computational Biology |  ...  We developed a dynamical model representing a cell fate decision network in the AGS gastric cancer cell line, relying on background knowledge extracted from literature and databases.  ...  Bjarte Bergstrøm (NTNU) for providing us with two of the inhibitors (BIRB0796 and CT99021) used in our experiments. Author Contributions  ... 
doi:10.1371/journal.pcbi.1004426 pmid:26317215 pmcid:PMC4567168 fatcat:yqrvd3busvfrrcjjmo7cgo5qmm

Logical modeling: Combining manual curation and automated parameterization to predict drug synergies [article]

Åsmund Flobak, John Zobolas, Miguel Vazquez, Tonje S. Steigedal, Liv Thommesen, Asle Grislingås, Barbara Niederdorfer, Evelina Folkesson, Martin Kuiper
2021 bioRxiv   pre-print
With our framework we predict the synergy of joint inhibition of PI3K and TAK1, and further substantiate this prediction with observation in cancer cell cultures and in xenograft experiments.  ...  We have previously shown that drug synergies targeting cancer can manually be identified based on a logical framework.  ...  Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.  ... 
doi:10.1101/2021.06.28.450165 fatcat:irbrsph2rjazzh54jygatwpkbe

Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction

Barbara Niederdorfer, Vasundra Touré, Miguel Vazquez, Liv Thommesen, Martin Kuiper, Astrid Lægreid, Åsmund Flobak
2020 Frontiers in Physiology  
Discrete dynamical modeling shows promise in prioritizing drug combinations for screening efforts by reducing the experimental workload inherent to the vast numbers of possible drug combinations.  ...  We demonstrate the possible enhancement of predictive capability of models by curation of literature knowledge further detailing subtle biologically founded signaling mechanisms in the model topology.  ...  Parts of this work has been included in a Ph.D. thesis.  ... 
doi:10.3389/fphys.2020.00862 pmid:32848834 pmcid:PMC7399174 fatcat:hwcvvtwusfbk7oxxd7btmevlpu

A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines

Eirini Tsirvouli, Vasundra Touré, Barbara Niederdorfer, Miguel Vázquez, Åsmund Flobak, Martin Kuiper
2020 Frontiers in Molecular Biosciences  
We tested this model for its ability to correctly predict drug combination synergies, against a dataset of experimentally determined cell growth responses with 18 drugs in all combinations, on eight cancer  ...  The results indicate that the extended model had an improved accuracy for drug synergy prediction for the majority of the experimentally tested cancer cell lines, although significant improvements of the  ...  The evaluation of the performance of the model in predicting experimentally validated synergies of combinations of 18 established cancer drugs in a panel of eight cancer cell lines revealed that the model  ... 
doi:10.3389/fmolb.2020.502573 pmid:33195403 pmcid:PMC7581946 fatcat:brkszn2xyvc6dk6ph63phxgjgq

Combinatorial benefit without synergy in recent clinical trials of immune checkpoint inhibitors [article]

Adam C Palmer, Benjamin Izar, Peter K Sorger, Haeun Hwangbo
2020 medRxiv   pre-print
Realizing the promise of drug additivity or synergy is likely to require better response biomarkers that identify patients in whom multiple constituents of a combination therapy are active.  ...  Hundreds of clinical trials are testing combinations of Immune Checkpoint Inhibitors (ICIs) with other cancer therapies in the hope that they will have additive or synergistic efficacy involving mechanisms  ...  false discoveries of synergy.  ... 
doi:10.1101/2020.01.31.20019604 fatcat:upti5zy26nfbrjognsqdz4sksi

Targeting MicroRNAs With Small Molecules: From Dream to Reality

S Zhang, L Chen, E J Jung, G A Calin
2010 Clinical Pharmacology and Therapeutics  
The causes of the widespread differential expression of miRNA genes in malignancy compared with normal cells can be explained by the location of these genes in cancer-associated genomic regions, by epigenetic  ...  A logic approach for better cure of cancer patients is to exploit the huge advances in understanding the genetic nature of cancer and the molecular pathways involved in malignant transformation.  ... 
doi:10.1038/clpt.2010.46 pmid:20428111 pmcid:PMC3902962 fatcat:3uwmm3b255e43hka4ecopkt5si

Modelling approaches in tumor microenvironment

Isaac Crespo, George Coukos, Marie-Agnes Doucey, Ioannis Xenarios
2018 Journal of Cancer Immunology & Therapy  
Mathematical and computational models may help on describing, explaining and predicting cancer in a new generation of experimental design assisted by computer simulations.  ...  Cancerous cells and stromal cells, including different types of infiltrating immune cells and resident tissue cells, interact with each other and with extracellular matrix components in a very convoluted  ...  [86] reported a computational approach to discover drug synergies in gastric cancer by logical modeling based on baseline (unperturbed) proliferative state of tumor cells derived from literature and  ... 
doi:10.35841/cancer-immunology.1.1.26-40 fatcat:zfg6wvz5fjgsno4fcn7wgzlbke

Ontologies and Knowledge Graphs in Oncology Research

Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria, Catia Pesquita
2022 Cancers  
Our review highlights the growing traction of ontologies in biomedical research in general, and cancer research in particular.  ...  This study reviews the application of ontologies and knowledge graphs in cancer research.  ...  The immense potential of ontologies and the knowledge graph paradigm to support cancer research data management and analysis is increasingly recognized by the oncology research community as an essential  ... 
doi:10.3390/cancers14081906 pmid:35454813 pmcid:PMC9029532 fatcat:t6erzohmvnextkix4infnk7kza

D1.1 Life Sciences Use Case: Initial Requirements and Scenario Definitions

Project Consortium Members
2019 Zenodo  
of cancer cells treated with different drug regimes.  ...  By using a Boolean model of carcinoma cell lines (AGS) and a lattice-free physics-based cell simulator for 3D multicellular modelling, PhysiBoSS, we aim to replicate experimental data of growth profiles  ...  simulations CSV files MB Model analysis / Mutant simulations / Drug effect predictions Logical modeling (GINsim, MaBoSS, PhysiBoSS) Manual historical In lab and public data on cancer  ... 
doi:10.5281/zenodo.4034013 fatcat:milq75kbjzeqtocterjowkl5iy

Cancer immunotherapy via combining oncolytic virotherapy with chemotherapy: recent advances

Hardev Pandha, Guy Simpson, Kate Relph, Alan Melcher, Kevin Harrington
2016 Oncolytic Virotherapy  
Similarly to oncolytic viruses, the benefits of chemotherapeutic agents may be that they induce systemic antitumor immunity through the induction of immunogenic cell death of cancer cells.  ...  Combining these two treatment modalities has to date resulted in significant potential in vitro and in vivo synergies through various mechanisms without any apparent additional toxicities.  ...  antitumor activity by antigen-specific CD8 + and CD4 + T cells. 59, 63, 64 Both in murine models 76, 77 and in human patients with cancer, 146 antitumor immune responses induced by cancer cells undergoing  ... 
doi:10.2147/ov.s66083 pmid:27579292 pmcid:PMC4996257 fatcat:e7ulxkrwizatjg2xhpn5ripnvu

Oncolytic herpes viruses, chemotherapeutics, and other cancer drugs

Lynne Braidwood, Sheila Graham, Alex Graham, Joe Conner
2013 Oncolytic Virotherapy  
They are selectively replication-competent viruses that propagate only in actively dividing tumor cells but not in normal cells and, as a result, destroy the tumor cells by consequence of lytic infection  ...  When synergistic interactions in cancer cell killing are observed, chemotherapy dose reductions that achieve the same overall efficacy may be possible, resulting in a valuable reduction of adverse side  ...  Thus, the damage, in terms of number of cancer cells killed by a specific amount of drug, is greater in the presence of oHSV. 37 Cellular kinases play a key role in the regulation of signaling events  ... 
doi:10.2147/ov.s52601 pmid:27512658 pmcid:PMC4918355 fatcat:4dmvk5yejbgy7elpc4javmhjta

Sorafenib and Mek inhibition is synergistic in medullary thyroid carcinoma in vitro

Yoon Woo Koh, Manisha H Shah, Kitty Agarwal, Samantha K McCarty, Bon Seok Koo, Victoria J Brendel, Chaojie Wang, Kyle Porter, David Jarjoura, Motoyasu Saji, Matthew D Ringel
2011 Endocrine-Related Cancer  
Everolimus was neither additive nor syngergistic in combination with sorafenib or AZD6244. In conclusion, sorafenib combined with a Mek inhibitor demonstrated synergy in MTC cells in vitro.  ...  Western blots were performed to confirm activity of the compounds and to determine possible mechanisms of resistance and predictors of synergy.  ...  Acknowledgments Funding This work was supported by a grant from NIH (CA P0124570) to M D Ringel.  ... 
doi:10.1530/erc-11-0155 pmid:22109971 pmcid:PMC3717592 fatcat:fmg62wkp3fex7lv6yr27rhztla

A novel strategy for combination of clofarabine and pictilisib is synergistic in gastric cancer

Shayan Khalafi, Shoumin Zhu, Rimpi Khurana, Ines Lohse, Silvia Giordano, Simona Corso, Hassan Al-Ali, Shaun P. Brothers, Claes Wahlestedt, Stephan Schürer, Wael El-Rifai
2022 Translational Oncology  
Gastric cancer (GC) is frequently characterized by resistance to standard chemotherapeutic regimens and poor clinical outcomes.  ...  DST of GC cell lines was performed with a library of 215 Federal Drug Administration (FDA) approved compounds and identified clofarabine as a potential therapeutic agent.  ...  Despite these results, the SynergySeq pipeline remains a powerful tool to predict drug efficacy in animal or human models of GC.  ... 
doi:10.1016/j.tranon.2021.101260 pmid:34735897 pmcid:PMC8571525 fatcat:ymxxvysatbchxbzpm6qozfsps4

Network Pharmacology [chapter]

Uma Chandran, Neelay Mehendale, Saniya Patil, Rathnam Chaguturu, Bhushan Patwardhan
2017 Innovative Approaches in Drug Discovery  
Polypharmacology expands the space in drug discovery approach.  ...  It is essential to understand how these molecules and the interactions among them determine the function of this immensely complex machinery, both in isolation and when surrounded by other cells.  ...  The types of cancers which are networked by Triphala include pancreatic, prostate, breast, lung, colorectal and gastric cancers, tumors, and more.  ... 
doi:10.1016/b978-0-12-801814-9.00005-2 fatcat:zhprs4augbcffnnh3iljlkth7i

D1.3 Life Sciences Use Case: Requirements, Scenario Definitions and Initial Evaluation Report

Project Consortium Members
2020 Zenodo  
the second is a study of drug combinations using the AGS gastric cancer cell line.  ...  These simulations are being scaled up by several orders of magnitude by parallelising the code in a hybrid OpenMP-MPI implementation, aiming to scale up simulations of cancer cell 3D spheroids up to a  ...  simulations MB Model analysis / Mutant simulations / Drug effect predictions Logical modelling (GINsim, MaBoSS, PhysiBoSS) Manual historical In lab and public data on cancer cell  ... 
doi:10.5281/zenodo.4034037 fatcat:kmcmrsgeerfzhmwzv2ogqylmbq
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