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  Publications:
• Fan, M., Xia, P., Clarke, R., Wang, Y. & Li, L. “Radiogenomic signatures reveal multiscale intratumour heterogeneity associated with biological functions and survival in breast cancer.” Nature Commun, 11:4861 doi 10.1038/s41467-020-18703-2, 2020.
• Remoli, A.L., Sgarbanti, M., Perrotti, E., Acchioni, M., Orsatti,
R., Acchioni, B., Clarke, R. & Marsili, G. “IĸB kinase-ε-mediated phosphorylation triggers IRF-1 degradation in breast cancer cells.” Neoplasia, 22: 459- 469, 2020.
• Chen, X., Neuwald, A.F., Hilakivi-Clarke, L.A., Clarke, R., Wang, T.-L. & Xuan, J. “ChIP-GSM: Inferring active transcription factor modules to predict functional regulatory elements.” PLoS Comput Biol, 2021 https://doi.org/10.1371/journal.pcbi.1009203.
• Chen, X., Gu, J., Neuwald, A.F., Hilakivi-Clarke, L.A., Clarke, R. & Xuan, J. “Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence.” Sci Rep. 11: 385. doi: 10.1038/s41598-020-79603-5, 2021.
• Chen, L., Lu, Y., Wu, C.-T., Clarke, R., Yu, G., Van Eyk, J.E., Herrington, D.E. & Wang, Y. “Data-driven detection of subtype-specific differentially expressed genes.” Sci Rep. 11: 332 doi: 10.1038/ s41598-020-79704-1, 2021.
  inhibiting PFKFB3 enzyme we have determined impaired TCA cycle in endocrine therapy resistant cells that may control the stability of hypoxia-inducible factor-1 alpha.
Role of Sirtuins in endocrine therapy resistance: The primary objective of this project is to determine the roles of sirtuins (SIRTs) as key sensors of, and responders to energy changes induced by endocrine therapies in endocrine sensitive and resistant ER+ breast cancer cells. To achieve the goals of this project we will first measure expression of SIRTS 1-7 in different cell lines under different treatment conditions and determine the mechanistic role of robustly regulated SIRT genes by depleting and overexpressing experiments. Further, we will identify other members of SIRT signaling module by using gene network modeling tools in our cell lines and patient transcriptome data sets.

























































































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