Chemotherapy resistance remains the main challenge facing breast cancer patients today. Understanding the underlying mechanisms and molecules involved is crucial to help overcome this obstacle. In this study, we screened the transcriptome of MCF7 parental cell lines and two variant resistant cell lines MCF7 4xAC and MCF7 4xAC+4xPAC, using NGS Illumina NovaSeq6000 and compared their gene expression profiles. Twelve significant differentially expressed RT-PCR verified genes (DEGs) out of 84 DEGs selected, including DAB2IP, ICAM1, MAP2K4, MYD88, OLFM2, EFNA3, PRKD1, ABCG2, ARHGEF19, BAG3, MYEOV and ITGA5. The DEGs were annotated in the Gene Ontology and KEGG databases. The annotation of the function of the DEGs in the KEGG database revealed pathways involved in resistance, including the MAPK and PI3K-AKT signaling pathways. Protein-protein interaction network was applied to analyze the association of the 12 DEGs with chemotherapy resistance and revealed significant pathways such as MAPK and TNF signaling pathways. These DEGs are involved in many biological activities such as cell proliferation, survival, migration and invasion, and apoptosis. The interactions between these DEGs and the chemotherapy resistance phenomenon need to be further studied at a functional level. We believe they could be promising therapeutic targets to be explored to develop new treatment options.