title: Identification and characterization of microRNAs expressed in human breast cancer chemo-resistant MCF-7/Adr cells by Solexa deep-sequencing technology.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Pengfei
authors: P
authors: Xu
authors: The Second Affiliated Hospital of Soochow University,1055 Sanxiang Road, Soochow 215004, China.
authors: Luyu
authors: L
authors: Wang
authors: Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029 Nanjing, China.
authors: Lei
authors: L
authors: Huang
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Wenqu
authors: W
authors: Li
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Shanshan
authors: S
authors: Lv
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Mingming
authors: M
authors: Lv
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Jingjing
authors: J
authors: Ma
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Qian
authors: Q
authors: Zhou
authors: Department of Pharmacology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 210029, China.
authors: Xiaowei
authors: X
authors: Wu
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Ziyi
authors: Z
authors: Fu
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China.
authors: Cheng
authors: C
authors: Lu
authors: Nanjing Maternity and Child Health Care Hospital, Affiliated Nanjing Medical University, Nanjing 210004, China. Electronic address: hongyinnjmu@163.com.
authors: Hong
authors: H
authors: Yin
mesh_terms: D000903:Antibiotics, Antineoplastic / Q000494:pharmacology*; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D004317:Doxorubicin / Q000494:pharmacology*; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010641:Phenotype; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results
chemical_list: D000903:Antibiotics, Antineoplastic; D035683:MicroRNAs; D004317:Doxorubicin
keywords: Breast cancer; Chemoresistance; Solexa deep-sequencing; microRNAs