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Genomic and Epigenomic Cross-Talks in the Regulatory Landscape of Mirnas in Breast Cancer

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Genomic and Epigenomic Cross-Talks in the Regulatory Landscape of Mirnas in Breast Cancer Published OnlineFirst January 29, 2013; DOI: 10.1158/1541-7786.MCR-12-0649 Molecular Cancer Review Research Genomic and Epigenomic Cross-talks in the Regulatory Landscape of miRNAs in Breast Cancer Devyani Samantarrai1, Subhra Dash2, Bini Chhetri1, and Bibekanand Mallick1 Abstract MicroRNAs (miRNA) are a class of endogenous, small noncoding RNAs found in animals, plants, and viruses that control their target gene expression posttranscriptionally. They are involved in a wide array of biological processes including cell differentiation, development, cell death and homeostasis, and fine-tune the regulation of these pathways. Their aberrant expressions have been associated with different diseases. These small RNAs are also known to function as oncogenes, oncosupressor genes, modulators of metastatic spread, and regulators of cancer stem cells. Their deregulation is a hallmark of different cancers types including breast cancer. Despite the growing evidence for their involvement in breast cancer, understanding the interplay between miRNAs and their targets leading to the disease remains largely unknown. Here, we provide a comprehensive story on miRNA signatures of breast cancer, miRNAs in breast cancer stem cells, metastamirs (i.e., metastasis regulatory miRNAs), circulating miRNAs as invasive blood-based biomarkers, and oncomiRs and oncosupressor miRNAs associated with breast cancer. Furthermore, we provide biological insights on their regulation by various mechanisms including genomic alterations and demonstration of a complicated feedback network between miRNAs and epigenetic regulators forming an epigenetics–miRNA regulatory circuit whose disruption may underlie the cause of breast cancer. Mol Cancer Res; 11(4); 315–28. Ó2013 AACR. Introduction (7, 8). Moreover, the binding regions have now been extended to any region of the target including the coding MicroRNAs (miRNA) are short, approximately 19 to 24 0 nucleotides (nts) long, single-stranded endogenous noncod- region (CDS) and 5 UTR (6). Seven years after the discovery of the first miRNA, another miRNA family member, let-7, ing RNAs (ncRNA) that posttranscriptionally modulate fi gene expression (1) and thereby regulate a wide array of was identi ed from the same species by Ruvkun and col- biological processes including cell differentiation, develop- leagues (9). Since then, there has been an explosion in the – fi number of miRNAs discovered every year. As of now, ment, cell death, and homeostasis (2 3). The rst miRNA fi gene, lin-4, was discovered in Caenorhabditis elegans in 1993 21,264 miRNAs have been identi ed in various organisms, (4) while studying the genes involved in regulating the out of which 1,600 precursor miRNAs encoding 2,042 timing of larval development in nematode. Lin-4 was found mature miRNAs are in humans [miRBase (http://www. to negatively regulate translation of lin-14 mRNA by bind- mirbase.org/), Release 19, August 2012]. ing to the complementary sites within the 30untranslated These small regulatory RNAs are also known to be 0 involved in various pathophysiological processes, including region (3 UTR) of mRNA through imperfect base pairing – during the first larval stage (L1) of the nematode (5). The cancer etiology, progression, and prognosis (10 11). The miRNAs generally bind to target mRNAs through Watson expression of miRNAs is altered in cancer cells and many and Crick complementary base pairing between 2 through seminal studies have unraveled the differences in expression 0 of miRNAs in tumor and normal tissues and between tumor 7/8 nts of miRNA (known as seed region) at 3 UTR (6). – These reduce levels of target transcripts and inhibit protein types (12 13). The aberrant expression of miRNAs in translation, sometimes via noncomplete complementation cancers can lead to the altered expression of target mRNAs. with one or more mismatches in sequence complementarity miRNAs themselves are also regulated, especially by genetic or epigenetic mechanisms or by aberrant expression of transcription factors. Furthermore, miRNAs can also mod- Authors' Affiliations: 1RNA Biology and Functional Genomics Laboratory, ulate multiple genes epigenetically by controlling the levels Department of Life Science, National Institute of Technology, Rourkela; and 2KIIT School of Biotechnology, KIIT University, Bhubaneswar, Orissa, India of primary epigenetic regulators, DNA methyltransferases (DNMT ), or histone deacetylases (HDAC; refs. 14, 15). Corresponding Author: Bibekanand Mallick, RNA Biology and Functional Genomics Laboratory, Department of Life Science, National Institute of There is interplay between miRNAs and target mRNAs that Technology, Rourkela 769008, India. Phone: 91-661-2462685; Fax: 91- determines the fate of the cell, either normal or diseased. 661-2472926; E-mail: [email protected], [email protected] Breast cancer is one of the leading causes of cancer-related doi: 10.1158/1541-7786.MCR-12-0649 death among women of all races. Aberrant miRNA expres- Ó2013 American Association for Cancer Research. sion in human breast cancer was first shown in 2005 (16). www.aacrjournals.org 315 Downloaded from mcr.aacrjournals.org on September 26, 2021. © 2013 American Association for Cancer Research. Published OnlineFirst January 29, 2013; DOI: 10.1158/1541-7786.MCR-12-0649 Samantarrai et al. Over the last few years, studies on involvement of miRNA in 30 over hangs at the cleavage site (4). DGCR8/Pasha protein breast cancer have accelerated and its role as critical bio- of the microprocessor complex contains 2 dsRNA-binding markers for classification, diagnosis, prognosis, and treat- domains and is essential for miRNA processing in all ment are being established (17). Many studies have shown organisms (22). It stably interacts with pri-miRNA and acts that miRNAs, in addition to regulating the cellular levels of as a molecular ruler to determine the specific cleavage site various oncogenes or tumor suppressor genes (TSG; (23). The pre-miRNA formed is then transported from the ref. 11, 14), also act as oncogenes, termed as oncomiRs nucleus to the cytoplasm via a nuclear export factor Expor- (18) and tumor suppressors, termed as oncosuppressor tin-5 in complex with RanGTP (24). A defined length of miRNAs (19). In this review, we aim to provide a compre- the double-stranded stem and the 30 overhangs of the pre- hensive story on the miRNA signatures of cancers, especially miRNA are important for successful binding to Exportin-5, in breast cancer, their role as oncomiRs or oncosuppressors, which ensures the export of only correctly processed pre- how they regulate the genes and how they are being regulated miRNAs (25). (genomic and epigenomic alterations) to understand the Once the pre-miRNA gets transported into the cytoplasm, interplay between miRNAs and mRNAs leading to breast its further processing and RISC (RNA-inducing silencing cancer. complex) assembly is carried out by RLC (RISC loading complex). RLC is a multiprotein complex composed of the Biogenetic Pathways of miRNAs RNase III enzyme Dicer, dsRNA-binding domain proteins The mature miRNAs are generated from miRNA genes TRBP (Tar RNA-binding protein), PACT (protein activator through a multistep event (Fig. 1). The genes are transcribed of PKR), and the core component Argonaute-2 (Ago2; into a fragment of 1 to 3 kb long primary transcripts (pri- ref. 26). The pre-miRNA is cleaved by Dicer and generates miRNA), usually by RNA polymerase II (20), similar to approximately 19 to 24 nts long miRNA duplex molecule protein coding genes in the genome or by RNA polymerase (27). TRBP mediates cleavage by Dicer and also stablizes it. III (21). One pri-miRNA can contain one or several miR- Among the 2 strands of pre-miRNA, one is called the NAs. This pri-miRNA present in the nucleus is then functional guide strand and the other is called the passenger recognized and processed by a microprocessor complex strand. The guide strand gets incorporated into the RISC formed by the RNaseIII enzyme Drosha and DGCR8 and guides the RISC to its target, whereas the passenger (DiGeorge critical region 8) protein, also known as Pasha strand gets degraded. Ago2 protein facilitates the unwinding (Partner of Drosha; ref. 4). The processing results in the of pre-miRNA duplexes and RISC activation by cleaving the formation of a hairpin intermediate of about 60 to 100 nts passenger strand. The biogenesis process completes with the with a stem loop structure called pre-miRNA. Drosha is a assembly of the functional guide strand with the RISC dsRNA-specific endonuclease present in the nucleus. It is a complex. The miRNA along with RISC effector Ago2 multidomain protein and mainly contains 2 RNaseIII mediates mRNA degradation, destabilization, or translation- domains, a dsRNA-binding domain, an amino terminal al inhibition (reviewed in ref. 28). Apart from this, it has also segment of unknown function, and generates 2 nts long been shown that some miRNAs can actually increase the RNA POL miRNA Gene I/II ′ 5 EXPORTIN 5 pri-miRNA 3′ DICER DROSA DGCR8 TRBP pre-miRNA Nucleus miRNA Duplex Mature miRNA RISC Formation AGO2 Cytoplasm miRNA-RISC miRNA-RISC ORF AAAA ORF AAAA deA Target mRNA Target miRNA Ribosome Ribosome Translation repression miRNA-RISC mRNA deadenylation Target miRNA mRNA degradation Figure 1. Biogenesis pathway of miRNA in animals and their function. 316 Mol Cancer Res; 11(4) April 2013 Molecular Cancer Research Downloaded from mcr.aacrjournals.org on September 26, 2021. © 2013 American Association for Cancer Research. Published OnlineFirst
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