Comprehensive analysis of microRNA (miRNA) targets in breast cancer cells.
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 response was further 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.
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163. Electronic address: mfan2@uthsc.edu.
Meiyun
M
Fan
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Raisa
R
Krutilina
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Jing
J
Sun
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Aarti
A
Sethuraman
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Chuan He
CH
Yang
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Zhao-Hui
ZH
Wu
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Junming
J
Yue
Departments of Pathology and Laboratory Medicine, Center for Adult Cancer Research, University of Tennessee Health Science Center, Memphis, Tennessee 38163.
Lawrence M
LM
Pfeffer
D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D060565:Argonaute Proteins / Q000096:biosynthesis / Q000235:genetics; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D045744:Cell Line, Tumor; D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism; D005260:Female; D055785:Gene Knockdown Techniques; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D009368:Neoplasm Transplantation; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism*; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism; D014183:Transplantation, Heterologous
D020413:3' Untranslated Regions; C466422:AGO2 protein, human; D060565:Argonaute Proteins; D035683:MicroRNAs; D009363:Neoplasm Proteins; D012334:RNA, Neoplasm; C408087:DICER1 protein, human; C517918:DROSHA protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases
Breast Cancer; Gene Regulation; Metastasis; MicroRNA; Stress Response