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Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer

Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen (+6 others)
2021 Briefings in Bioinformatics  
of safe and effective combinatorial treatments that selectively inhibit cancer-related dysfunctions or resistance mechanisms in individual patients.  ...  In this case study, we show how the platform enables prediction of cancer-selective drug combinations for patients with high-grade serous ovarian cancer using single-cell imaging cytometry drug response  ...  clinical success of combinatorial therapies [8] .  ... 
doi:10.1093/bib/bbab272 pmid:34343245 pmcid:PMC8574973 fatcat:nejdkbbqp5bwhjrahqnzb3tgf4

Mapping genetic interactions in cancer: a road to rational combination therapies

Beril Tutuncuoglu, Nevan J. Krogan
2019 Genome Medicine  
as a monotherapy for patients with BRCA1/2-mutated breast or ovarian cancer.  ...  An important part of this effort is the systematic screening of genetic interactions in a variety of cancer types.  ...  Acknowledgements We would like to thank Manon Eckhardt and Minkyu Kim for critical reading of the manuscript. We would also like to thank Mike Shales for assistance with graphics.  ... 
doi:10.1186/s13073-019-0680-4 pmid:31640753 pmcid:PMC6805649 fatcat:lf7kz7mpnrfg5bt5cax7b4atbi

CanSeer: A Method for Development and Clinical Translation of Personalized Cancer Therapeutics [article]

Rida Nasir Butt, Bibi Amina, Muhammad Umer Sultan, Zain Bin Tanveer, Risham Hussain, Rida Akbar, Salaar Khan, Mahnoor Naseer Gondal, Muhammad Farhan Khalid, Amir Faisal, Muhammad Shoaib, Safee Ullah Chaudhary
2022 bioRxiv   pre-print
Computational modeling and analysis of biomolecular network models annotated with cancer patient-specific multi-omics data can enable the development of personalized therapies.  ...  Lastly, the ovarian cancer case study revealed the combinatorial efficacy of APR-246+carmustine, and APR-246+dinaciclib for treating ovarian serous cystadenocarcinoma.  ...  These breakthrough drugs further stimulated efforts aimed at identification of molecular targets in wider varieties of cancer and onward employment in devising targeted therapies [20] - [24] .  ... 
doi:10.1101/2022.06.29.498138 fatcat:ubn6j6vwmfaddegnd7i2cjqd6m

Peptide Phage Display for Discovery of Novel Biomarkers for Imaging and Therapy of Cell Subpopulations in Ovarian Cancer

Mette Soendergaard, Jessica R Newton- Northup
2012 Journal of Molecular Biomarkers & Diagnosis  
Such biomarkers may be utilized in diagnosis and in identification and selection of ovarian cancer subpopulations.  ...  Chen X, Sievers E, Hou Y, Park R, Tohme M et al. (2005) Integrin alpha v beta in ovarian cancer: antigens for multi-targeted antibody-guided therapy. J 3-targeted imaging of lung cancer.  ... 
doi:10.4172/2155-9929.s2-004 fatcat:unoglep7k5a6fny4mn5skmcrdm

Targeting Endothelin-1 Receptor/β-Arrestin-1 Axis in Ovarian Cancer: From Basic Research to a Therapeutic Approach

Piera Tocci, Laura Rosanò, Anna Bagnato
2019 Frontiers in Endocrinology  
studies warranting the repurposing of ET-1R antagonists for the design of more effective clinical trials based on combinatorial therapies to overcome, or prevent, the onset of drug resistance.  ...  In ovarian cancer, ET-1R/β-arr1 axis enables cancer cells to engage several integrated signaling, and represents an actionable target for developing novel therapeutic approaches.  ...  ACKNOWLEDGMENTS We gratefully acknowledge all members of the laboratory for their constant support and enthusiasm, and Maria Vincenza Sarcone for secretarial assistance.  ... 
doi:10.3389/fendo.2019.00609 fatcat:uwj67gfjhfe6zj2vklx3qeq73a

Improved prediction of PARP inhibitor response and identification of synergizing agents through use of a novel gene expression signature generation algorithm

Daniel J. McGrail, Curtis Chun-Jen Lin, Jeannine Garnett, Qingxin Liu, Wei Mo, Hui Dai, Yiling Lu, Qinghua Yu, Zhenlin Ju, Jun Yin, Christopher P. Vellano, Bryan Hennessy (+2 others)
2017 npj Systems Biology and Applications  
Despite rapid advancement in generation of large-scale microarray gene expression datasets, robust multigene expression signatures that are capable of guiding the use of specific therapies have not been  ...  These signatures were also capable of predicting patient response, as shown by applying a cisplatin sensitivity signature to ovarian cancer patients.  ...  The networks represented in this study were generated through the use of QIAGEN's Ingenuity Pathway Analysis (IPA ® , QIAGEN Redwood City, www.qiagen.com/ingenuity).  ... 
doi:10.1038/s41540-017-0011-6 pmid:28649435 pmcid:PMC5445594 fatcat:a4so63sra5elpcrgny2j2wnory

Large-scale datasets uncovering cell signalling networks in cancer: context matters

Sumana Sharma, Evangelia Petsalaki
2019 Current Opinion in Genetics and Development  
Such rewiring also can lead to cancer development and progression or cause resistance to therapies. While there exist static maps of annotated pathways, they do not capture these rewired networks.  ...  In this review, we will highlight the most recent approaches to study context-specific signaling networks using large-scale omics and genetic perturbation datasets, with a focus on studies of cancer and  ...  in ovarian cancer [23] or triple negative breast cancer [24] .  ... 
doi:10.1016/j.gde.2019.05.001 pmid:31200172 fatcat:67zptj3r4ndldkfs4szf7dwhna

Copy number networks to guide combinatorial therapy for cancer and other disorders [article]

Andy Lin, Desmond James Smith
2014 bioRxiv   pre-print
We then highlight the potential of using correlated CNAs to guide combinatorial drug treatment in common medical conditions.  ...  The strategy of seeking correlated CNAs can also be used to map survival networks for cancer.  ...  Network guided combinatorial therapy can employ either repositioned drugs or drugs in their usual disease context.  ... 
doi:10.1101/005942 fatcat:rizp34opirdr3ljg5gurklwiwm

Recent Advances in Integrative Multi-Omics Research in Breast and Ovarian Cancer

Christen A. Khella, Gaurav A. Mehta, Rushabh N. Mehta, Michael L. Gatza
2021 Journal of Personalized Medicine  
Recent advances in high-throughput proteogenomic profiling of tumor samples have resulted in the identification of novel oncogenic drivers, tumor suppressors, and signaling networks; biomarkers for the  ...  In this review, we will focus on the impact of historical and recent advances in single platform and integrative proteogenomic studies in breast and ovarian cancer, which constitute two of the most lethal  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/jpm11020149 pmid:33669749 pmcid:PMC7922242 fatcat:zu3fbbx2wfe7jk2n3lt23to37y

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework

Gaurav Kumar, Edmond J Breen, Shoba Ranganathan
2013 BMC Systems Biology  
A systems approach is needed to integrate diverse biological information for the prognosis and therapy risk assessment using mechanistic approach to understand gene interactions in pathways and networks  ...  Here, we report that the overexpressed genes IRAK1, CHEK1 and BUB1 may play an important role in ovarian cancer.  ...  This research was supported by the Macquarie University Research Scholarship (MQRES) to GK and the ARC Centre of Excellence in Bioinformatics grant (CE0348221) to SR.  ... 
doi:10.1186/1752-0509-7-12 pmid:23383610 pmcid:PMC3605242 fatcat:dywhr7dq5ffc7e5nn3rj3oegpq

Leveraging immunotherapy for the treatment of gynecologic cancers in the era of precision medicine

Dmitriy Zamarin, Amir A. Jazaeri
2016 Gynecologic Oncology  
In this review we outline the current immunotherapy based approaches for the treatment of gynecological cancers, and focus on the emerging clinical data on immune checkpoint inhibitors, adoptive cell therapies  ...  It is anticipated that in the coming years biomarker-guided clinical trials, will provide for a better understanding of the mechanisms of response and resistance to immunotherapy, and guide combination  ...  Acknowledgments D.Z. received funding from Foundation for Women's Cancers (Judith Liebenthal Robinson Ovarian Cancer Foundation Award).  ... 
doi:10.1016/j.ygyno.2015.12.030 pmid:27016233 pmcid:PMC5007873 fatcat:dco26ktuljaw7oxcwmb3j37i3i

Network Insights into the Genes Regulated by Hepatocyte Nuclear Factor 4 in Response to Drug Induced Perturbations: A Review

Asfar S. Azmi, Ginny W. Bao, Jiankun Gao, Ramzi M. Mohammad, Fazlul H. Sarkar
2013 Current Drug Discovery Technologies  
This article reviews how network pharmacology can help in the identification of druggable avenues in TFs and also allow the selection of drugs and their synergistic pairs against HNFs for cancer therapy  ...  Network biology is an emerging field of research that is finding applications in cancer drug discovery.  ...  Advanced genomic screening studies have shown that the presence of HNF3 in ER + breast cancer patients serves as an indicator of resistant to endocrine therapy [22, 23] .  ... 
doi:10.2174/1570163811310020007 pmid:23237677 pmcid:PMC3820112 fatcat:qyj6r3mjm5dnvgriseziioqwgq

Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics

Graeme Benstead-Hume, Sarah K. Wooller, Frances M.G. Pearl
2017 Journal of Integrative Bioinformatics  
AbstractThe development of improved cancer therapies is frequently cited as an urgent unmet medical need.  ...  Finally we discuss some of the identified targets with licensed drugs, inhibitors in clinical trials or with compounds under development.  ...  Here we describe how the identification of these genetic interactions is being used to guide therapeutic strategies for the treatment of cancer.  ... 
doi:10.1515/jib-2017-0027 pmid:28941356 fatcat:2nalcenbdre7be7siheyi74bei

Biomarker-guided sequential targeted therapies to overcome therapy resistance in rapidly evolving highly aggressive mammary tumors

Ozgur Sahin, Qingfei Wang, Samuel W Brady, Kenneth Ellis, Hai Wang, Chia-Chi Chang, Qingling Zhang, Preety Priya, Rui Zhu, Stephen T Wong, Melissa D Landis, William J Muller (+3 others)
2014 Cell Research  
Combinatorial targeted therapies are more effective in treating cancer by blocking by-pass mechanisms or inducing synthetic lethality.  ...  This fundamentally novel approach of using targeted therapies in a sequential order can effectively target and reprogram the signaling networks in cancers evolving resistance during treatment.  ...  We also thank Dr Mark Greene (University of Pennsylvania) for generously providing the hybridoma for 7.  ... 
doi:10.1038/cr.2014.37 pmid:24675532 pmcid:PMC4011340 fatcat:ho4or26cyrcsdcnl3k7r2jntam

Better Therapeutic Trials in Ovarian Cancer

M. A. Bookman, C. B. Gilks, E. C. Kohn, K. O. Kaplan, D. Huntsman, C. Aghajanian, M. J. Birrer, J. A. Ledermann, A. M. Oza, K. D. Swenerton
2014 Journal of the National Cancer Institute  
The Ovarian Task Force of the Gynecologic Cancer Steering Committee convened a clinical trials planning meeting on October 28-29, 2011, with the goals to identify key tumor types, associated molecular  ...  in response to an evolving landscape of scientific, regulatory, and funding priorities.  ...  Recent years have witnessed important changes in our understanding of epithelial ovarian cancer (EOC), from that of one disease toward an appreciation of a set of unique diseases of diverse origin and  ... 
doi:10.1093/jnci/dju029 pmid:24627272 pmcid:PMC3982885 fatcat:tuv4lyejxja4dben6srz2vnupa
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