TY - JOUR ID - 51151 TI - A Systems Biology Approach Provides Deeper Insights into Differentially Expressed Genes in Taxane-Anthracycline Chemoresistant and Non-Resistant Breast Cancers JO - Asian Pacific Journal of Cancer Prevention JA - APJCP LA - en SN - 1513-7368 AU - Sarhadi, Shamim AU - Sadeghi, Somayeh AU - Nikmanesh, Fatemeh AU - Pilehvar-Soltanahmadi, Younes AU - Shahabi, Arman AU - Fekri Aval, Sedigheh AU - Zarghami, Nosratollah AD - Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran. AD - Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. AD - Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran. Y1 - 2017 PY - 2017 VL - 18 IS - 10 SP - 2629 EP - 2636 KW - breast cancer KW - Chemoresistance KW - DEG Analysis KW - Neoadjuvant KW - Protein-Protein Interaction Network DO - 10.22034/APJCP.2017.18.10.2629 N2 -   Objective: To date, numerous studies have been conducted to search for reasons for chemoresistance and differences in survival rates of patients receiving chemotherapy. We have sought to identify differentially expressed genes (DEGs) between predicted chemotherapy resistance and sensitive phenotypes by a network as well as gene enrichment approach. Methods: Functional modules were explored with network analysis of DEGs in predicted neoadjuvant taxane-anthracycline resistance versus sensitive cases in the GSE25066 dataset, including 508 samples. A linear model was created by limma package in R to establish DEGs. Results: A gene set related to phagocytic vesicle membrane was found to be up-regulated in chemoresistance samples. Also, we found GO_CYTOKINE_ACTIVITY and GO_GROWTH_FACTOR BINDING to be up-regulated gene sets with the chemoresistance phenotype. Growth factors and cytokines are two groups of agents that induce the immune system to recruit APCs and promote tolerogenic phagocytosis. Some hub nodes like S100A8 were found to be important in the chemoresistant tumor cell network with associated high rank genes in GSEA. Conclusions: Functional gene sets and hub nodes could be considered as potential treatment targets. Moreover, by screening and enrichment analysis of a chemoresistance network, ligands and chemical agents have been found that could modify significant gene sets like the phagocytic vesicle membrane functional gene set as a key to chemoresistance. They could also impact on down- or up-regulated hub nodes. UR - https://journal.waocp.org/article_51151.html L1 - https://journal.waocp.org/article_51151_d29b2ec76cbcbe65d820990c2c78a02d.pdf ER -