Informatics on Drug Repurposing for Breast Cancer

References

• Pushpakom S, Iorio F, Eyers PA, et al. Drug repurposing: progress, challenges and recommendations. Nat Rev Drug Discov. 2019;18:41–58. doi:10.1038/nrd.2018.168
   PubMed Web of Science ®Google Scholar
• Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68:394–424. doi:10.3322/caac.21492
   PubMed Web of Science ®Google Scholar
• Arora S, Narayan P, Osgood CL, et al. U.S. FDA drug approvals for breast cancer: a decade in review. Clin Cancer Res. 2022;28:1072–1086. doi:10.1158/1078-0432.CCR-21-2600
   PubMed Web of Science ®Google Scholar
• Yam C, Mani SA, Moulder SL. Targeting the molecular subtypes of triple negative breast cancer: understanding the diversity to progress the field. Oncologist. 2017;22:1086–1093. doi:10.1634/theoncologist.2017-0095
   PubMed Web of Science ®Google Scholar
• Aggarwal S, Verma SS, Aggarwal S, Gupta SC. Drug repurposing for breast cancer therapy: old weapon for new battle. Semin Cancer Biol. 2021;68:8–20. doi:10.1016/j.semcancer.2019.09.012
   PubMed Web of Science ®Google Scholar
• Malik JA, Ahmed S, Jan B, et al. Drugs repurposed: an advanced step towards the treatment of breast cancer and associated challenges. Biomed Pharmacother. 2022;145:112375. doi:10.1016/j.biopha.2021.112375
   PubMed Web of Science ®Google Scholar
• Mottini C, Napolitano F, Li Z, Gao X, Cardone L. Computer-aided drug repurposing for cancer therapy: approaches and opportunities to challenge anticancer targets. Semin Cancer Biol. 2021;68:59–74. doi:10.1016/j.semcancer.2019.09.023
   PubMed Web of Science ®Google Scholar
• Jeselsohn R, Buchwalter G, De Angelis C, Brown M, Schiff R. ESR1 mutations-a mechanism for acquired endocrine resistance in breast cancer. Nat Rev Clin Oncol. 2015;12:573–583. doi:10.1038/nrclinonc.2015.117
   PubMed Web of Science ®Google Scholar
• Busonero C, Leone S, Bianchi F, Acconcia F. In silico screening for ERalpha down modulators identifies thioridazine as an anti-proliferative agent in primary, 4OH-tamoxifen-resistant and Y537S ERalpha-expressing breast cancer cells. Cell Oncol. 2018;41:677–686.
   Web of Science ®Google Scholar
• Subramanian A, Narayan R, Corsello SM, et al. A next generation connectivity map: L1000 platform and the first 1,000,000 profiles. Cell. 2017;171:1437–52 e17. doi:10.1016/j.cell.2017.10.049
   PubMed Web of Science ®Google Scholar
• Vasquez-Bochm LX, Velazquez-Paniagua M, Castro-Vazquez SS, et al. Transcriptome-based identification of lovastatin as a breast cancer stem cell-targeting drug. Pharmacol Rep. 2019;71:535–544. doi:10.1016/j.pharep.2019.02.011
   PubMed Web of Science ®Google Scholar
• Nguyen TM, Muhammad SA, Ibrahim S, et al. DeCoST: a new approach in drug repurposing from control system theory. Front Pharmacol. 2018;9:583. doi:10.3389/fphar.2018.00583
   PubMed Web of Science ®Google Scholar
• Musa A, Ghoraie LS, Zhang SD, et al. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform. 2017;18:903. doi:10.1093/bib/bbx023
   PubMed Web of Science ®Google Scholar
• Chan J, Wang X, Turner JA, Baldwin NE, Gu J. Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. Bioinformatics. 2019;35:2818–2826. doi:10.1093/bioinformatics/btz006
   PubMed Web of Science ®Google Scholar
• Mejia-Pedroza RA, Espinal-Enriquez J, Hernandez-Lemus E. Pathway-based drug repositioning for breast cancer molecular subtypes. Front Pharmacol. 2018;9:905. doi:10.3389/fphar.2018.00905
   PubMed Web of Science ®Google Scholar
• Griffith M, Griffith OL, Coffman AC, et al. DGIdb: mining the druggable genome. Nat Methods. 2013;10:1209–1210. doi:10.1038/nmeth.2689
   PubMed Web of Science ®Google Scholar
• Ding S, Chen X, Shen K. Single-cell RNA sequencing in breast cancer: understanding tumor heterogeneity and paving roads to individualized therapy. Cancer Commun. 2020;40:329–344. doi:10.1002/cac2.12078
   Web of Science ®Google Scholar
• Yuan X, Wang J, Huang Y, Shangguan D, Zhang P. Single-cell profiling to explore immunological heterogeneity of tumor microenvironment in breast cancer. Front Immunol. 2021;12:643692. doi:10.3389/fimmu.2021.643692
   PubMed Web of Science ®Google Scholar
• He B, Xiao Y, Liang H, et al. ASGARD is a single-cell guided pipeline to aid repurposing of drugs. Nat Commun. 2023;14:993. doi:10.1038/s41467-023-36637-3
   PubMed Web of Science ®Google Scholar
• Greene CS, Voight BF. Pathway and network-based strategies to translate genetic discoveries into effective therapies. Hum Mol Genet. 2016;25:R94–R8. doi:10.1093/hmg/ddw160
   PubMed Web of Science ®Google Scholar
• Ma J, Wang J, Ghoraie LS, Men X, Haibe-Kains B, Dai P. A comparative study of cluster detection algorithms in protein-protein interaction for drug target discovery and drug repurposing. Front Pharmacol. 2019;10:109. doi:10.3389/fphar.2019.00109
   PubMed Web of Science ®Google Scholar
• Turanli B, Karagoz K, Bidkhori G, et al. Multi-omic data interpretation to repurpose subtype specific drug candidates for breast cancer. Front Genet. 2019;10:420. doi:10.3389/fgene.2019.00420
   PubMed Web of Science ®Google Scholar
• Duan Q, Reid SP, Clark NR, et al. L1000CDS(2): LINCS L1000 characteristic direction signatures search engine. NPJ Syst Biol Appl. 2016;2:16015. doi:10.1038/npjsba.2016.15
   PubMed Web of Science ®Google Scholar
• Peyvandipour A, Saberian N, Shafi A, Donato M, Draghici S. A novel computational approach for drug repurposing using systems biology. Bioinformatics. 2018;34:2817–2825. doi:10.1093/bioinformatics/bty133
   PubMed Web of Science ®Google Scholar
• Firoozbakht F, Rezaeian I, Rueda L, Ngom A. Computationally repurposing drugs for breast cancer subtypes using a network-based approach. BMC Bioinform. 2022;23:143. doi:10.1186/s12859-022-04662-6
   PubMed Web of Science ®Google Scholar
• Islam MM, Wang Y, Hu P. A maximum flow-based approach to prioritize drugs for drug repurposing of chronic diseases. Life. 2021;11:54.
   PubMedGoogle Scholar
• Saha Detroja T, Detroja R, Mukherjee S, Samson AO. Identifying hub genes associated with neoadjuvant chemotherapy resistance in breast cancer and potential drug repurposing for the development of precision medicine. Int J Mol Sci. 2022;23:12628. doi:10.3390/ijms232012628
   PubMed Web of Science ®Google Scholar
• Di J, Zheng B, Kong Q, et al. Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities. Mol Oncol. 2019;13:2259–2277. doi:10.1002/1878-0261.12564
   PubMed Web of Science ®Google Scholar
• Al-Taie Z, Hannink M, Mitchem J, Papageorgiou C, Shyu CR. Drug repositioning and subgroup discovery for precision medicine implementation in triple negative breast cancer. Cancers. 2021;13:6278. doi:10.3390/cancers13246278
   PubMed Web of Science ®Google Scholar
• Hsu JL, Hung MC. The role of HER2, EGFR, and other receptor tyrosine kinases in breast cancer. Cancer Metastasis Rev. 2016;35:575–588. doi:10.1007/s10555-016-9649-6
   PubMed Web of Science ®Google Scholar
• Balbuena-Rebolledo I, Padilla M, Rosales-Hernandez MC, Bello M. Repurposing FDA drug compounds against breast cancer by targeting EGFR/HER2. Pharmaceuticals. 2021;14:791. doi:10.3390/ph14080791
   Web of Science ®Google Scholar
• Kandasamy T, Sen P, Ghosh SS. Multi-targeted drug repurposing approach for breast cancer via integrated functional network analysis. Mol Inform. 2022;41:e2100300. doi:10.1002/minf.202100300
   PubMed Web of Science ®Google Scholar
• Olsauskas-Kuprys R, Zlobin A, Osipo C. Gamma secretase inhibitors of Notch signaling. Onco Targets Ther. 2013;6:943–955. doi:10.2147/OTT.S33766
   PubMed Web of Science ®Google Scholar
• Pathak Y, Camps I, Mishra A, Tripathi V. Targeting notch signaling pathway in breast cancer stem cells through drug repurposing approach. Mol Divers. 2022. doi:10.1007/s11030-022-10561-y
   Web of Science ®Google Scholar
• Rui M, Cai M, Zhou Y, et al. Identification of potential RBPJ-specific inhibitors for blocking notch signaling in breast cancer using a drug repurposing strategy. Pharmaceuticals. 2022;15:556. doi:10.3390/ph15050556
   Web of Science ®Google Scholar
• Maruca A, Rocca R, Catalano R, et al. Natural products extracted from fungal species as new potential anti-cancer drugs: a structure-based drug repurposing approach targeting HDAC7. Molecules. 2020;25:5524. doi:10.3390/molecules25235524
   PubMed Web of Science ®Google Scholar
• Issa NT, Stathias V, Schurer S, Dakshanamurthy S. Machine and deep learning approaches for cancer drug repurposing. Semin Cancer Biol. 2021;68:132–142. doi:10.1016/j.semcancer.2019.12.011
   PubMed Web of Science ®Google Scholar
• Song J, Xu Z, Cao L, Wang M, Hou Y, Li K. The discovery of new drug-target interactions for breast cancer treatment. Molecules. 2021;26:7474. doi:10.3390/molecules26247474
   PubMed Web of Science ®Google Scholar
• You J, McLeod RD, Hu P. Predicting drug-target interaction network using deep learning model. Comput Biol Chem. 2019;80:90–101. doi:10.1016/j.compbiolchem.2019.03.016
   PubMed Web of Science ®Google Scholar
• Cui C, Ding X, Wang D, et al. Drug repurposing against breast cancer by integrating drug-exposure expression profiles and drug-drug links based on graph neural network. Bioinformatics. 2021;37:2930–2937. doi:10.1093/bioinformatics/btab191
   PubMed Web of Science ®Google Scholar
• Wang A, Lim H, Cheng SY, Xie L. ANTENNA, a multi-rank, multi-layered recommender system for inferring reliable drug-gene-disease associations: repurposing diazoxide as a targeted anti-cancer therapy. IEEE/ACM Trans Comput Biol Bioinform. 2018;15:1960–1967. doi:10.1109/TCBB.2018.2812189
   PubMed Web of Science ®Google Scholar
• Ji X, Jin C, Dong X, Dixon MS, Williams KP, Zheng W. Literature-wide association studies (LWAS) for a rare disease: drug repurposing for inflammatory breast cancer. Molecules. 2020;25:3933. doi:10.3390/molecules25173933
   PubMed Web of Science ®Google Scholar
• Malik JA, Ahmed S, Momin SS, et al. Drug repurposing: a new hope in drug discovery for prostate cancer. ACS Omega. 2023;8:56–73. doi:10.1021/acsomega.2c05821
   PubMed Web of Science ®Google Scholar
• Luck K, Kim DK, Lambourne L, et al. A reference map of the human binary protein interactome. Nature. 2020;580:402–408. doi:10.1038/s41586-020-2188-x
   PubMed Web of Science ®Google Scholar
• Kairys V, Baranauskiene L, Kazlauskiene M, Matulis D, Kazlauskas E. Binding affinity in drug design: experimental and computational techniques. Expert Opin Drug Discov. 2019;14:755–768. doi:10.1080/17460441.2019.1623202
   PubMed Web of Science ®Google Scholar
• Melnekoff DT, Lagana A. Single-cell sequencing technologies in precision oncology. Adv Exp Med Biol. 2022;1361:269–282.
   PubMedGoogle Scholar
• Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Perin O, Droit A. Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context. Front Mol Biosci. 2022;9:962799.
   PubMed Web of Science ®Google Scholar