RNA Seq Analysis Of Triple Negative Breast Cancer Cells Lines For The Identification of Common Therapeutic Targets

Abstract

Triple Negative Breast cancer (TNBC) is a heterogeneous disease that is oestrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 negative based on immunohistochemistry. TNBC is distinguished by a specific molecular profile, aggressiveness, and a lack of targeted treatment. Some of the patients that have undergone treatment tend to relapse after a certain time period due to distant metastasis. Therapies already being used to treat TNBC include chemotherapy, targeted therapy, surgery, and radiation therapy. However, TNBC develops resistance to certain therapies over time and results in ineffective treatment. Therefore, no proper treatment is available and research needs to be done on finding new targets for drug manufacturing. In this study, we have performed RNA Sequencing analysis through Galaxy and Ballgown on two data sets of TNBC in order to determine differentially expressed genes that could be used as targets for the cancer. Then, we performed a comparative analysis to determine the common DEGs among the data sets. After this we performed pathway analysis of these DEGs using reactome, to discover targetable pathways. We found seven differentially expressed genes and ten targettable pathways. The common genes that can be targetted to treat the TNBC cancer included DDIT4, DYRK3, ELF3, H2BC21, JUN, LEPROT,and RPL21P16. The most enriched and significant pathways include Pre- NOTCH Transcription, Translation, Expression and Processing, Signaling by NOTCH, programmed cell death, Senescence-Associated Secretory Phenotype (SASP), Oxidative Stress Induced Senescence,HOX gene activation in Hindbrain development and differentiation, transcription and estrogen dependant gene expression.