CADDIE - An online knowledge base for network-based mechanism exploration and drug repurposing in oncolog
Autori
Hartung, MichaelAnastasi, Elisa
M. Mamdouh, Zeinab
Nogales, Cristian
HHW Schmidt, Harald
Baumbach, Jan
Zolotareva, Olga
List, Markus
Ostala autorstva
Morić, IvanaĐorđević, Valentina
Konferencijski prilog (Objavljena verzija)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
Drug repurposing is the use of previously developed and tested pharmaceutical agents in new
application cases and lately often used as a solution to the increasing drug development costs.
Cancers are extremely heterogeneous disorders demonstrating a wide variability of drug responses
due to diverse subtypes, quickly evolving and acquiring drug resistance. Therefore, the identification
of compounds that can effectively combat a specific tumor type is crucial. Drug candidates that are
potentially effective against a specific tumor can be chosen based on the set of driver mutations
acquired by this tumor. For optimal treatment, it is important to consider targeted anti-cancer
therapies and drugs initially developed to treat non-cancerous diseases.
To overcome this hurdle, we present CADDIE (Cancer Driver Drug Interaction Explorer), a web platform
to identify oncological drug repurposing candidates. CADDIE’s biomedical knowledge base integrates
a multitude of gene-gene and drug-g...ene interaction datasets, detailed anticancer drug information
and cancer biology data such as cancer driver genes, mutation frequencies and gene expressions. For
the purpose of locating drug targets and candidates for drug repurposing, CADDIE makes network
medicine algorithms available to the researchers. It guides the users from the choice of seed genes
through the discovery of therapeutic targets or drug candidates. Network medicine also provides
indirect strategies that take into account other functionally relevant targets in the gene interaction
network since potential cancer driver genes may be inaccessible for direct targeting. We demonstrate
the application of CADDIE in different cancer subtypes such as sarcoma and ovarian cancer with a
detailed analysis of the found drug targets and chemical compounds. CADDIE is available online at
https://exbio.wzw.tum.de/caddie/ and as a python package at https://pypi.org/project/caddiepy/.
Ključne reči:
drug repurposing / drug prioritization / network medicine / cancer / network analysis / network medicineIzvor:
4th Belgrade Bioinformatics Conference, 2023, 4, 36-36Izdavač:
- Belgrade : Institute of molecular genetics and genetic engineering
Finansiranje / projekti:
- This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 777111. This project reflects only the authors’ view and the European Commission is not responsible for any use that may be made of the information it contains. This work was supported by the German Federal Ministry of Education and Research (BMBF) within the framework of the *e:Med* research and funding concept (*grants 01ZX1910D and 01ZX2210D*). JB was partially funded by his VILLUM Young Investigator Grant nr.13154.; Z.M. is funded by a full scholarship [40463/2019] from the Ministry of Higher Education of the Arab Republic of Egypt.
Napomena:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Kolekcije
Institucija/grupa
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Hartung, Michael AU - Anastasi, Elisa AU - M. Mamdouh, Zeinab AU - Nogales, Cristian AU - HHW Schmidt, Harald AU - Baumbach, Jan AU - Zolotareva, Olga AU - List, Markus PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1974 AB - Drug repurposing is the use of previously developed and tested pharmaceutical agents in new application cases and lately often used as a solution to the increasing drug development costs. Cancers are extremely heterogeneous disorders demonstrating a wide variability of drug responses due to diverse subtypes, quickly evolving and acquiring drug resistance. Therefore, the identification of compounds that can effectively combat a specific tumor type is crucial. Drug candidates that are potentially effective against a specific tumor can be chosen based on the set of driver mutations acquired by this tumor. For optimal treatment, it is important to consider targeted anti-cancer therapies and drugs initially developed to treat non-cancerous diseases. To overcome this hurdle, we present CADDIE (Cancer Driver Drug Interaction Explorer), a web platform to identify oncological drug repurposing candidates. CADDIE’s biomedical knowledge base integrates a multitude of gene-gene and drug-gene interaction datasets, detailed anticancer drug information and cancer biology data such as cancer driver genes, mutation frequencies and gene expressions. For the purpose of locating drug targets and candidates for drug repurposing, CADDIE makes network medicine algorithms available to the researchers. It guides the users from the choice of seed genes through the discovery of therapeutic targets or drug candidates. Network medicine also provides indirect strategies that take into account other functionally relevant targets in the gene interaction network since potential cancer driver genes may be inaccessible for direct targeting. We demonstrate the application of CADDIE in different cancer subtypes such as sarcoma and ovarian cancer with a detailed analysis of the found drug targets and chemical compounds. CADDIE is available online at https://exbio.wzw.tum.de/caddie/ and as a python package at https://pypi.org/project/caddiepy/. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - CADDIE - An online knowledge base for network-based mechanism exploration and drug repurposing in oncolog EP - 36 SP - 36 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_1974 ER -
@conference{ author = "Hartung, Michael and Anastasi, Elisa and M. Mamdouh, Zeinab and Nogales, Cristian and HHW Schmidt, Harald and Baumbach, Jan and Zolotareva, Olga and List, Markus", year = "2023", abstract = "Drug repurposing is the use of previously developed and tested pharmaceutical agents in new application cases and lately often used as a solution to the increasing drug development costs. Cancers are extremely heterogeneous disorders demonstrating a wide variability of drug responses due to diverse subtypes, quickly evolving and acquiring drug resistance. Therefore, the identification of compounds that can effectively combat a specific tumor type is crucial. Drug candidates that are potentially effective against a specific tumor can be chosen based on the set of driver mutations acquired by this tumor. For optimal treatment, it is important to consider targeted anti-cancer therapies and drugs initially developed to treat non-cancerous diseases. To overcome this hurdle, we present CADDIE (Cancer Driver Drug Interaction Explorer), a web platform to identify oncological drug repurposing candidates. CADDIE’s biomedical knowledge base integrates a multitude of gene-gene and drug-gene interaction datasets, detailed anticancer drug information and cancer biology data such as cancer driver genes, mutation frequencies and gene expressions. For the purpose of locating drug targets and candidates for drug repurposing, CADDIE makes network medicine algorithms available to the researchers. It guides the users from the choice of seed genes through the discovery of therapeutic targets or drug candidates. Network medicine also provides indirect strategies that take into account other functionally relevant targets in the gene interaction network since potential cancer driver genes may be inaccessible for direct targeting. We demonstrate the application of CADDIE in different cancer subtypes such as sarcoma and ovarian cancer with a detailed analysis of the found drug targets and chemical compounds. CADDIE is available online at https://exbio.wzw.tum.de/caddie/ and as a python package at https://pypi.org/project/caddiepy/.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "CADDIE - An online knowledge base for network-based mechanism exploration and drug repurposing in oncolog", pages = "36-36", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_1974" }
Hartung, M., Anastasi, E., M. Mamdouh, Z., Nogales, C., HHW Schmidt, H., Baumbach, J., Zolotareva, O.,& List, M.. (2023). CADDIE - An online knowledge base for network-based mechanism exploration and drug repurposing in oncolog. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 36-36. https://hdl.handle.net/21.15107/rcub_imagine_1974
Hartung M, Anastasi E, M. Mamdouh Z, Nogales C, HHW Schmidt H, Baumbach J, Zolotareva O, List M. CADDIE - An online knowledge base for network-based mechanism exploration and drug repurposing in oncolog. in 4th Belgrade Bioinformatics Conference. 2023;4:36-36. https://hdl.handle.net/21.15107/rcub_imagine_1974 .
Hartung, Michael, Anastasi, Elisa, M. Mamdouh, Zeinab, Nogales, Cristian, HHW Schmidt, Harald, Baumbach, Jan, Zolotareva, Olga, List, Markus, "CADDIE - An online knowledge base for network-based mechanism exploration and drug repurposing in oncolog" in 4th Belgrade Bioinformatics Conference, 4 (2023):36-36, https://hdl.handle.net/21.15107/rcub_imagine_1974 .