Breast cancer is the most common type of tumor in female and chemoresistance has been a major clinical obstacle to the treatment in clinical patients. miRNA was one of the factors demonstrated to play certain roles in chemoesistance in breast cancer. In this study, we exploited Solexa deep sequencing technology to identify differentially expressed miRNA from samples in vitro, trying to find novel relationship between miRNA and chemoresistance in breast cancer.

The human breast cancer MCF-7 cell line was pulse-selected with doxorubicin (10 pulses, once a week for 4h, with 1μM doxorubicin) to generate MCF-7/Adr cells. Total RNA was extracted from the treated and untreated MCF-7 cells and subsequently subjected to real time PCR. Two small RNA libraries of MCF7NON and MCF7ADR were established to record the Solexa sequencing results of the PCR products above. All the sequencing results were verified by Stem-loop real-time PCR. GO annotation and KEGG analysis program were exploited to enrich the differentially expressed miRNAs.

The results showed that 214,822 and 378,597 reads were mapped in the MCF7ADR and MCF7NON libraries when aligned to hairpin structure respectively. Meanwhile, 1323 and 520 reads were mapped when aligned to mature sequences. In addition, 310 known mature miRNAs were coexpressed in both libraries. Comparing the MCF7ADR group to the MCF7NON group, 18 miRNAs were significantly differentially expressed. GO annotation and KEGG analysis showed that the target genes were enriched in regulation of transcription and development as well as Wnt signaling pathway, MAPK signaling pathway and TGF-ß signaling pathway.

The results proved that the Solexa deep sequencing was a powerful and reliable platform to analyze small RNAs. And further investigation should be conducted for the biological process and pathways that have been identified and more efforts should be made to research the mechanism of chemoresistance in breast cancer.