Comprehensive analysis of microRNAs in breast cancer

BackgroundMicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in breast cancer progression by downregulating gene expression. The detailed mechanisms and biological functions of miRNA molecules in breast carcinogenesis have yet to be fully elucidated. This study used bioinformatics and experimental approaches to conduct detailed analysis of the dysregulated miRNAs, arm selection preferences, 3' end modifications, and position shifts in isoforms of miRNAs (isomiRs) in breast cancer.MethodsNext-generation sequencing (NGS) data on breast cancer was obtained from the NCBI Sequence Read Archive (SRA). The miRNA expression profiles and isomiRs in normal breast and breast tumor tissues were determined by mapping the clean reads back to human miRNAs. Differences in miRNA expression and pre-miRNA 5p/3p arm usage between normal and breast tumor tissues were further investigated using stem-loop reverse transcription and real-time polymerase chain reaction.ResultsThe analysis identified and confirmed the aberrant expression of 22 miRNAs in breast cancer. Results from pathway enrichment analysis further indicated that the aberrantly expressed miRNAs play important roles in breast carcinogenesis by regulating the mitogen-activated protein kinase (MAPK) signaling pathway. Data also indicated that the position shifts in isomiRs and 3' end modifications were consistent in breast tumor and adjacent normal tissues, and that 5p/3p arm usage of some miRNAs displayed significant preferences in breast cancer.ConclusionsExpression pattern and arm selection of miRNAs are significantly varied in breast cancers through analyzing NGS data and experimental approach. These miRNA candidates have high potential to play critical roles in the progression of breast cancer and could potentially provide as targets for future therapy.

[1]  B. White,et al.  The Micro-Ribonucleic Acid (miRNA) miR-206 Targets the Human Estrogen Receptor-α (ERα) and Represses ERα Messenger RNA and Protein Expression in Breast Cancer Cell Lines , 2007 .

[2]  J. Rhim,et al.  MiRNA 26a expression in a novel panel of African American prostate cancer cell lines. , 2010, Ethnicity & disease.

[3]  C. Croce,et al.  MicroRNA gene expression deregulation in human breast cancer. , 2005, Cancer research.

[4]  Jennifer L. Clancy,et al.  Complexity of Murine Cardiomyocyte miRNA Biogenesis, Sequence Variant Expression and Function , 2012, PloS one.

[5]  B. White,et al.  The micro-ribonucleic acid (miRNA) miR-206 targets the human estrogen receptor-alpha (ERalpha) and represses ERalpha messenger RNA and protein expression in breast cancer cell lines. , 2007, Molecular endocrinology.

[6]  Ryan D. Morin,et al.  Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. , 2008, Genome research.

[7]  A. Keller,et al.  Whole blood-derived miRNA profiles as potential new tools for ovarian cancer screening , 2010, British Journal of Cancer.

[8]  Herbert H. Tsang,et al.  Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications , 2009, Nucleic acids research.

[9]  S. Hammond,et al.  Emerging paradigms of regulated microRNA processing. , 2010, Genes & development.

[10]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[11]  Bo Zhang,et al.  Transcriptional inhibiton of Hoxd4 expression by miRNA-10a in human breast cancer cells , 2009, BMC Molecular Biology.

[12]  Patricia P. Chan,et al.  GtRNAdb: a database of transfer RNA genes detected in genomic sequence , 2008, Nucleic Acids Res..

[13]  Chunquan Li,et al.  SubpathwayMiner: a software package for flexible identification of pathways , 2009, Nucleic acids research.

[14]  N. Rajewsky.  microRNA target predictions in animals , 2006, Nature Genetics.

[15]  Martti T. Tammi,et al.  MicroTar: predicting microRNA targets from RNA duplexes , 2006, BMC Bioinformatics.

[16]  Selene L. Fernandez-Valverde,et al.  Dynamic isomiR regulation in Drosophila development. , 2010, RNA.

[17]  Jiannis Ragoussis,et al.  Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization , 2011, Nature Medicine.

[18]  L. Kastl,et al.  miRNA-34a is associated with docetaxel resistance in human breast cancer cells , 2011, Breast Cancer Research and Treatment.

[19]  Qun Zhou,et al.  miR-200a Regulates SIRT1 Expression and Epithelial to Mesenchymal Transition (EMT)-like Transformation in Mammary Epithelial Cells* , 2011, The Journal of Biological Chemistry.

[20]  Volker Hovestadt,et al.  Molecular and Cellular Pathobiology MicroRNA Sequence and Expression Analysis in Breast Tumors by Deep Sequencing , 2011 .

[21]  W. McCombie,et al.  Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures , 2011, PloS one.

[22]  O. Rath,et al.  MAP kinase signalling pathways in cancer , 2007, Oncogene.

[23]  Jining Lu,et al.  Expression of microRNA and their gene targets are dysregulated in preinvasive breast cancer , 2011, Breast Cancer Research.

[24]  K. Gunsalus,et al.  Combinatorial microRNA target predictions , 2005, Nature Genetics.

[25]  R. Lyle,et al.  miR-511-3p modulates genetic programs of tumor-associated macrophages. , 2012, Cell reports.

[26]  Tingming Liang,et al.  Consistent isomiR expression patterns and 3′ addition events in miRNA gene clusters and families implicate functional and evolutionary relationships , 2012, Molecular Biology Reports.

[27]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

[28]  Zuhong Lu,et al.  Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data , 2010, Comput. Biol. Chem..

[29]  C. Croce,et al.  Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA , 2012, Proceedings of the National Academy of Sciences.

[30]  R. Giegerich,et al.  Fast and effective prediction of microRNA/target duplexes. , 2004, RNA.

[31]  Chun-Hung Lai,et al.  miRNA arm selection and isomiR distribution in gastric cancer , 2012, BMC Genomics.

[32]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.

[33]  Qiong Shao,et al.  MicroRNA miR-21 overexpression in human breast cancer is associated with advanced clinical stage, lymph node metastasis and patient poor prognosis. , 2008, RNA.

[34]  Chun-Hung Lai,et al.  UMARS: Un-MAppable Reads Solution , 2011, BMC Bioinformatics.

[35]  Li Lin,et al.  Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. , 2011, Cancer cell.

[36]  M. F. Shannon,et al.  An autocrine TGF-β/ZEB/miR-200 signaling network regulates establishment and maintenance of epithelial-mesenchymal transition , 2011, Molecular biology of the cell.

[37]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[38]  Chun-Nan Hsu,et al.  Interrogation of rabbit miRNAs and their isomiRs. , 2011, Genomics.

[39]  Paola Briata,et al.  How to control miRNA maturation? Co-activators and co-repressors take the stage , 2009 .

[40]  Chin-Wen Chi,et al.  miR-21 microRNA expression in human gastric carcinomas and its clinical association. , 2008, Anticancer research.

[41]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences: current status, policy and new initiatives , 2008, Nucleic Acids Res..

[42]  E. Morii,et al.  MicroRNA-mediated downregulation of mTOR/FGFR3 controls tumor growth induced by Src-related oncogenic pathways , 2011, Oncogene.

[43]  Kai-Ping Chang,et al.  Characterization of Epstein-Barr Virus miRNAome in Nasopharyngeal Carcinoma by Deep Sequencing , 2010, PloS one.

[44]  Ulrich Lehmann,et al.  MicroRNA profiles of healthy basal and luminal mammary epithelial cells are distinct and reflected in different breast cancer subtypes , 2011, Breast Cancer Research and Treatment.

[45]  Todd Wylie,et al.  Next-generation sequencing identifies the natural killer cell microRNA transcriptome. , 2010, Genome research.

[46]  Martin M Matzuk,et al.  Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes. , 2008, Genome research.

[47]  Jia Yu,et al.  miRNA-96 suppresses KRAS and functions as a tumor suppressor gene in pancreatic cancer. , 2010, Cancer research.

[48]  D. Warburton,et al.  MIR-99a and MIR-99b Modulate TGF-β Induced Epithelial to Mesenchymal Plasticity in Normal Murine Mammary Gland Cells , 2012, PloS one.

[49]  A. van den Berg,et al.  MicroRNAs, macrocontrol: regulation of miRNA processing. , 2010, RNA.

[50]  David L. A. Wood,et al.  MicroRNAs and their isomiRs function cooperatively to target common biological pathways , 2011, Genome Biology.

[51]  Li Guo,et al.  A Comprehensive Survey of miRNA Repertoire and 3′ Addition Events in the Placentas of Patients with Pre-Eclampsia from High-Throughput Sequencing , 2011, PloS one.

[52]  H. Ditzel,et al.  The miRNA-200 family and miRNA-9 exhibit differential expression in primary versus corresponding metastatic tissue in breast cancer , 2012, Breast Cancer Research and Treatment.

[53]  Huazong Zeng,et al.  miRNA-145 inhibits non-small cell lung cancer cell proliferation by targeting c-Myc , 2010, Journal of experimental & clinical cancer research : CR.

[54]  Paola Briata,et al.  How to control miRNA maturation? , 2009, RNA biology.

[55]  C. Sander,et al.  A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing , 2007, Cell.

[56]  Yi Zhao,et al.  NONCODE: an integrated knowledge database of non-coding RNAs , 2004, Nucleic Acids Res..

[57]  Carme Camps,et al.  microRNA-associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer. , 2011, Cancer research.

[58]  Lihong Ye,et al.  miRNA-520b and miR-520e sensitize breast cancer cells to complement attack via directly targeting 3′UTR of CD46 , 2010, Cancer biology & therapy.

[59]  Domenico Coppola,et al.  MicroRNA-155 Is Regulated by the Transforming Growth Factor β/Smad Pathway and Contributes to Epithelial Cell Plasticity by Targeting RhoA , 2008, Molecular and Cellular Biology.