Comprehensive analysis of MicroRNA (miRNA) targets in breast cancer cells

Meiyun Fan, Raisa Krutilina, Jing Sun, Aarti Sethuraman, Chuan Yang, Zhaohui Wu, Junming Yue, Lawrence Pfeffer

Research output: Contribution to journalArticle

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Abstract

MicroRNAs (miRNAs) regulate mRNA stability and translation through the action of the RNAi-induced silencing complex. In this study, we systematically identified endogenous miRNA target genes by using AGO2 immunoprecipitation (AGO2-IP) and microarray analyses in two breast cancer cell lines, MCF7 and MDA-MB-231, representing luminal and basal-like breast cancer, respectively. The expression levels of ∼70% of the AGO2-IP mRNAs were increased by DROSHA or DICER1 knockdown. In addition, integrated analysis of miRNA expression profiles, mRNA-AGO2 interaction, and the 3'-UTR of mRNAs revealed that > 60% of the AGO2-IP mRNAs were putative targets of the 50 most abundantly expressed miRNAs. Together, these results suggested that the majority of the AGO2-associated mRNAs were bona fide miRNA targets. Functional enrichment analysis uncovered that the AGO2-IP mRNAs were involved in regulation of cell cycle, apoptosis, adhesion/migration/invasion, stress responses (e.g. DNA damage and endoplasmic reticulum stress and hypoxia), and cell-cell communication (e.g. Notch and Ephrin signaling pathways). A role of miRNAs in regulating cell migration/invasion and stress responsewasfurther defined by examining the impact of DROSHA knockdown on cell behaviors. We demonstrated that DROSHA knockdown enhanced cell migration and invasion, whereas it sensitized cells to cell death induced by suspension culture, glucose depletion, and unfolding protein stress. Data from an orthotopic xenograft model showed that DROSHA knockdown resulted in reduced growth of primary tumors but enhanced lung metastasis. Taken together, these results suggest that miRNAs collectively function to promote survival of tumor cells under stress but suppress cell migration/invasion in breast cancer cells.

Original languageEnglish (US)
Pages (from-to)27480-27493
Number of pages14
JournalJournal of Biological Chemistry
Volume288
Issue number38
DOIs
StatePublished - Sep 20 2013

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MicroRNAs
Cells
Breast Neoplasms
Messenger RNA
Immunoprecipitation
Cell Movement
Tumors
Ephrins
Cell Hypoxia
Protein Unfolding
Endoplasmic Reticulum Stress
RNA Stability
Protein Biosynthesis
3' Untranslated Regions
Cell death
Microarray Analysis
Microarrays
Heat-Shock Proteins
RNA Interference
Cell culture

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Comprehensive analysis of MicroRNA (miRNA) targets in breast cancer cells. / Fan, Meiyun; Krutilina, Raisa; Sun, Jing; Sethuraman, Aarti; Yang, Chuan; Wu, Zhaohui; Yue, Junming; Pfeffer, Lawrence.

In: Journal of Biological Chemistry, Vol. 288, No. 38, 20.09.2013, p. 27480-27493.

Research output: Contribution to journalArticle

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