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Int. J. Mol. Sci. 2018, 19(6), 1810; https://doi.org/10.3390/ijms19061810

Differential Expression and Pathway Analysis in Drug-Resistant Triple-Negative Breast Cancer Cell Lines Using RNASeq Analysis

1
Genomics Central, Thrissur 680125, India
2
Weill Cornell Medicine, Qatar Foundation-Education City, P.O. Box 24144, Doha, Qatar
*
Author to whom correspondence should be addressed.
Received: 9 May 2018 / Revised: 5 June 2018 / Accepted: 13 June 2018 / Published: 19 June 2018
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Abstract

Triple-negative breast cancer (TNBC) is among the most notorious types of breast cancer, the treatment of which does not give consistent results due to the absence of the three receptors (estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) as well as high amount of molecular variability. Drug resistance also contributes to treatment unresponsiveness. We studied differentially expressed genes, their biological roles, as well as pathways from RNA-Seq datasets of two different TNBC drug-resistant cell lines of Basal B subtype SUM159 and MDA-MB-231 treated with drugs JQ1 and Dexamethasone, respectively, to elucidate the mechanism of drug resistance. RNA sequencing(RNA-Seq) data analysis was done using edgeR which is an efficient program for determining the most significant Differentially Expressed Genes (DEGs), Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. iPathway analysis was further used to obtain validated results using analysis that takes into consideration type, function, and interactions of genes in the pathway. The significant similarities and differences throw light into the molecular heterogeneity of TNBC, giving clues into the aspects that can be focused to overcome drug resistance. From this study, cytokine-cytokine receptor interaction pathway appeared to be a key factor in TNBC drug resistance. View Full-Text
Keywords: Triple-negative breast cancer; drug resistance; RNASeq; cytokine-cytokine receptor interaction; basal b Triple-negative breast cancer; drug resistance; RNASeq; cytokine-cytokine receptor interaction; basal b
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Shaheen, S.; Fawaz, F.; Shah, S.; Büsselberg, D. Differential Expression and Pathway Analysis in Drug-Resistant Triple-Negative Breast Cancer Cell Lines Using RNASeq Analysis. Int. J. Mol. Sci. 2018, 19, 1810.

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