ReviewChanges in miRNA expression in solid tumors: An miRNA profiling in melanomas
Introduction
Until recently, the non-coding RNAs and their functions were out of focus of investigations, primarily due to the fact that they are not converted into proteins and therefore the interpretation of their function is difficult. Now, the approach to non-protein-coding genomic sections changed fundamentally and investigations of small non-coding RNAs unfolded many, yet unpredictable, regulatory relationships.
Among non-protein-coding RNAs, the miRNA have been proven to play a key role in regulating gene expression by interacting with messenger RNA (mRNA)—either by inhibiting mRNA translation [1], [2], [3], [4] or by causing mRNA degradation [5], [6], [7]. Mature form of miRNAs are a class of conserved, approximately 21–25 nucleotides long RNAs. MiRNAs have been identified in both plants and animals, acting as key regulators of multicellular differentiation [8], [9], [10], [11]. In accordance to miRNAs control, a range of developmental events, such as timing of cell-fate decision, stem cell maintenance, apoptosis and organ morphogenesis, are suggested to play a role in the appropriate establishment of the tissue or cell type specific expression patterns along the development. Nevertheless, the majority of miRNAs expressed in many tissues, in more cases the highly tissue-specific suggested miRNAs latter proved to be expressed more broadly [12].
It is now already established that miRNAs contribute not only in developmental processes related functions, but also play an important role in the response of cells to outer signals and in adaptation to the changing environment (e.g. cellular stress [13], hypoxia [14]). Moreover, in a recent paper evidences are provided that miRNAs can be tools in the communication between different cell types. As part of the delivered “exosomal shuttled RNA”, miRNAs are present in exosomes secreted by mast cells. Through this newly discovered form of cell–cell communication, the donor cell may modulate the post-transcriptional system of target cells directly [15].
The range of different cellular pathways with miRNA-mediated regulation was estimated by Gaidatzis et al. [16]. Using bioinformatic tools a method was developed, which is able to mark significant association between a predicted miRNA target sets and their involvement in cellular pathways in human. The results confirmed the findings of other authors, that the miRNA target sites in the genes of ubiquitous, basic metabolic processes are relatively under-represented, while the genes involved in cell growth/death, development (especially in axon guidance pathway), transcriptional regulation, and intercellular communication are exposed to miRNA-driven control more frequently. Possibly, the miRNA-mediated regulation can be necessary in processes when beside the fundamental regulation, a fine balancing is also required for driving the cell to the most proper response for different signals.
Evidence is emerging that particular miRNAs may play a role in human cancer pathogenesis. The mutational and epigenetic changes in the genome leads stepwise to uncontrolled proliferation and cell death mechanisms in cancer. The dysregulation of cell proliferation with defects in differentiation of cancer cells, is a usual feature of carcinogenesis, often be accompanied the loss of tissue type-specific, unique miRNA profile. Little is known about the mechanisms underlying miRNA regulation in normal tissues and their deregulation in neoplastic processes. It remains also to be elucidated whether miRNA expression changes are the cause or the consequence of de-differentiated state. Further studies are also needed to clarify how to develop the altered miRNA fingerprint in cancer.
The estimated biological role of miRNA suggests that their expression may provide valuable diagnostic and prognostic indicators for human diseases, including solid tumors. miRNA expression changes have been described to correlate with the clinico-pathological features of the tumor in human cancers [17], [18], [19]. In classifying tumors and predicting their outcomes, the studies on miRNA-patterns are very promising. Understanding their function in gene regulation will help to develop biomarkers and new drug targets in cancer management.
Section snippets
miRNAs in the genome
The non-coding RNA represents a significant part of the genetic information in complex eukaryotes. According to the estimation, the non-protein–coding RNA can share 97–98% of the transcriptional output of a human cell. Certainly a part of these DNA segments which are transcribed but does not result protein-products belongs to intronic RNA, which constitutes 95% of the primary protein-coding transcripts (pre-mRNA) [20]. A recent paper with the purpose of finding direct experimental evidence on
miRNA processing
To understand the mechanism of miRNA-mediated silencing the basic step of their biogenesis has to be summarized. Briefly, miRNAs are a large family of endogenous, small regulatory RNAs that are generated by a two-step process from long primary miRNAs (pri-miRNAs) that are transcribed in the nucleus by the RNA polymerase II complex. At first it is processed by a complex comprised of the RNase III enzyme DROSHA and a double-stranded RNA binding domain possessing protein DGCR8 (DiGeorge syndrome
Range of methods available for measure expression of miRNAs
Different methodologies have been used to profile miRNA expression, including Northern blotting with radiolabeled probes [33], [34], oligonucleotide macroarrays [8], [35], quantitative PCR-based amplification of precursor or mature miRNAs [36], [37], [38], bead-based profiling methods [39], [40] and DNA microarrays [41], [42], [43], [44], [45], [12]. By contrast to mRNA profiling technologies, miRNA profiling must consider the short nature of microRNAs and should be able to distinguish between
Targets of miRNA
Beyond the knowledge of miRNA signature in different tumor types, it is necessary to uncover, how to act miRNAs with altered expression on their respective targets. The question is are there any pathways probably by the reason of altered miRNA expression over- or underrepresented in tumor cells, and in this way participate in manifestation of tumorous phenotype?
In accordance with the current model miRNAs affect the gene expression at the posttranscriptional level. Translational repression and
Altered expression of miRNAs in solid cancers
Although the biological functions and the target genes of miRNAs are poorly characterized, it has been confirmed that their pattern is changing during tumorigenesis. In tumor cells, both the levels of miRNA and their target gene mRNA expression are expressed differently. Conflicting reports have been published on whether the global amounts of miRNAs increase or decrease in cancers [40], [59]. Recent findings indicate the importance of the type and not the overall amount of altered miRNAs.
Unique
Lung cancer
In human lung cancers, reduced level of let-7 family was observed compared with levels in normal lung tissues. On the basis of expression of let-7 isoforms, the patients were classified into different outcome groups. In a lung cancer cell culture model was confirmed when levels of let-7a and let-7f were increased, then growth of the cancer cells was greatly reduced [71]. In Johnson's group was found that let-7 controls the activity of the critical human oncogene RAS. Accordingly, the lung tumor
Esophageal cancer
It has been shown that the miRNA processing enzyme RNASEN (an alias of Drosha, it cleaves pri-miRNA to pre-miRNA in nucleus) is overexpressed in a fraction of esophageal cancer compared to normal eosophagial epithelium. High levels of RNASEN found to associate with poor postoperative survival [78].
Hepatocellular cancer
MiR-21 is reported to be involved in the regulation of PTEN (phosphatase and tensin homolog) tumor suppressor is highly expressed in hepatocellular tumor samples and cell lines. Negative regulation of
Breast cancer
In breast cancer, the expression of various let-7 miRNAs is downregulated, which miRNA family were previously shown to control the level of RAS. Furthermore, downregulation of miR-20a, which regulates TGFBR2 was also described in breast cancer [59]. Tsuchiya and coworkers reported for the first time that miRNAs can regulate not only the essential genes for proliferation and apoptosis, but also drug metabolizing enzymes. They found an inverse correlation between miR-27b and CYP2B1. Since CYP2B1
Pituitary cancer
Bottoni and coworkers found that miR-15a and miR-16-1 are expressed at lower levels in pituitary adenomas as compared to normal pituitary tissue. Down-regulation of these miRNAs in pituitary adenomas correlates with a greater tumor diameter and a lower p43 secretion (as cofactor influence the activity of arginyl-tRNA-synthetase which is involved in inflammation and angiogenesis), suggesting that these genes may, at least in part, influence tumor growth [73].
Thyroid cancer
Kit is a tyrosine kinase receptor
Glioblastoma
Increased levels of the miR-21 have been found in glioblastomas compared with levels in normal brain tissue. Reducing the level of miR-21 in glioblastoma cells led to increased cell death in vitro. It appears that miR-21 can act as an anti-apoptoting factor by targeting the apoptosis-related genes, and in this way its overproduction could contribute to the maintenance of this tumor [87].
Oral squamous cell carcinoma
The increased expression of HMGA2 has been linked to epithelial-mesenchymal transition in oral squamous cell carcinoma. HMGA2 is a non-histone protein that bind through their AT binding motifs to the minor groove of AT-rich DNA strands. Although several proteins have been established as regulatory factors of HMGA2, Hebert and coworkers showed the upregulation of miRNA-98 under hypoxic condition and its role in the regulation of this protein which is critical in governing genotoxic response [88]
Melanoma: implication of miRNAs in diagnosis and treatment
Melanoma is one of the most aggressive cancer type in human. Melanoma transforms from melanocytes, the specialized pigment cells, which originate from neural crest. Most of melanomas arise within the epidermis where their progenitors are exposed to the UV radiation. Accordingly, the sunburn is high-ranked among the environmental risk factors. Notably, its incidence is progressively increasing in the past decades [90].
Besides the invasive growth the therapeutic resistance to available therapy
Concluding remarks, perspectives
The discovery of miRNAs and the perspectives of their regulatory potential revive a new layer in regulation of gene expression whereas many aspects of yet acquired ideas need to revaluate in cancer biology. The characteristic expression pattern observed in different tumor types and its prognostical value suggest miRNAs has a place sure enough in diagnosis and staging. The demand for reliable markers able to predict the prognosis is high, especially in cancer types such as melanoma. Otherwise,
Acknowledgement
This work was supported by grants of Hungarian Science Foundation (OTKA-67955).
References (101)
MicroRNAs: genomics, biogenesis, mechanism, and function
Cell
(2004)- et al.
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
Cell
(1993) - et al.
MicroRNAs as regulators of mammalian hematopoiesis
Semin Immunol
(2005) - et al.
Unique microRNA molecular profiles in lung cancer diagnosis and prognosis
Cancer Cell
(2006) - et al.
Prediction of plant microRNA targets
Cell
(2002) - et al.
Prediction of mammalian microRNA targets
Cell
(2003) - et al.
Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells
Cancer Cell
(2006) - et al.
Extensive modulation of a set of microRNAs in primary glioblastoma
Biochem Biophys Res Commun
(2005) - et al.
RAS is regulated by the let-7 microRNA family
Cell
(2005) - et al.
MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer
Gastroenterology
(2007)
A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors
Cell
MicroRNA expression profiles in head and neck cancer cell lines
Biochem Biophys Res Commun
Screening, early detection, and trends for melanoma: current status (2000–2006) and future directions
J Am Acad Dermatol
Gene expression profile changes between melanoma metastases and their daughter cell lines: implication for vaccination protocols
J Invest Dermatol
The functions of animal microRNAs
Nature
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans
Nature
Silencing of microRNAs in vivo with ‘antagomirs’
Nature
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
Nature
Cell-type-specific signatures of microRNAs on target mRNA expression
Proc Natl Acad Sci USA
A microRNA array reveals extensive regulation of microRNAs during brain development
RNA
Mechanisms of translational control by the 3′ UTR in development and differentiation
Semin Cell Dev Biol
The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb
Proc Natl Acad Sci USA
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
RNA
MicroRNA responses to cellular stress
Cancer Res
A microRNA signature of hypoxia
Mol Cell Biol
Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells
Nat Cell Biol
Inference of miRNA targets using evolutionary conservation and pathway analysis
BMC Bioinformat
A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia
N Engl J Med
MicroRNA gene expression deregulation in human breast cancer
Cancer Res
Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms
Bioessays
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome
Genome Res
The microRNAs of Caenorhabditis elegans
Genes Dev
Computational identification of Drosophila microRNA genes
Genome Biol
Computational prediction of miRNAs in Arabidopsis thaliana
Genome Res
MicroRNA identification based on sequence and structure alignment
Bioinformatics
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
Genome Res
miRBase: microRNA sequences, targets and gene nomenclature
Nucleic Acids Res
MicroRNA biogenesis: coordinated cropping and dicing
Nat Rev Mol Cell Biol
Identification of mammalian microRNA host genes and transcription units
Genome Res
Tissue-dependent paired expression of miRNAs
Nucleic Acids Res
Processing of primary microRNAs by the Microprocessor complex
Nature
An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells
Nature
Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation
Genome Biol
Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes
Nucleic Acids Res
Profiling microRNA expression using sensitive cDNA probes and filter arrays
Biotechniques
A high-throughput method to monitor the expression of microRNA precursors
Nucleic Acids Res
Real-time expression profiling of microRNA precursors in human cancer cell lines
Nucleic Acids Res
Real-time quantification of microRNAs by stem-loop RT-PCR
Nucleic Acids Res
MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues
Genome Res
MicroRNA expression profiles classify human cancers
Nature
Cited by (61)
MicroRNAs in Skin Fibrosis
2023, MicroRNA in Regenerative Medicine, Second EditionAssociation of DNA sequence-independent genetic regulatory mechanisms with apical periodontitis: A scoping review
2020, Archives of Oral BiologyCitation Excerpt :MiRNAs are small non-coding RNAs (∼22 nucleotides in length) that regulate gene expression at the post-transcriptional level (Fabian & Sonenberg, 2012). By base complementarity, these molecules bind to their mRNA targets’ 3′UTR regions and lead to reduced protein levels either by inducing mRNA degradation or by blocking translation (Molnár, Tamási, Bakos, Wiener, & Falus, 2008). A single miRNA might bind to hundreds of different mRNAs and, in many cases, a negative feedback loop has been shown between miRNAs and their targets, suggesting a very complex network orchestrated by these small RNA molecules (Lina et al., 2019; Yue et al., 2016).
Therapeutic Silencing of miR-214 Inhibits Tumor Progression in Multiple Mouse Models
2018, Molecular TherapyCitation Excerpt :In addition, a clinical intervention for patients with Alport syndrome, a life-threatening genetic kidney disease with no approved therapies, is currently ongoing with an anti-miR-21.20,21 Considering the relevant expression of miR-214 in malignant melanoma, breast, and pancreatic tumors,4–15 we investigated the capability of R97 or R98 anti-miR-214 or AAV8-miR-214 sponge to block the dissemination of those primary tumors in mice following systemic administrations of the compounds. Malignant melanomas and triple-negative breast cancers express high levels of miR-214, a small RNA with a proven pro-metastatic function as in Penna et al.4 Here, we used MA-2 melanoma and 4175-TGL breast cancer cells overexpressing (over) miR-214 and turbo red fluorescent protein (tRFP)4,15 to evaluate the relevance of miR-214 as therapeutic target.
miR-214 as a Key Hub that Controls Cancer Networks: Small Player, Multiple Functions
2015, Journal of Investigative DermatologyCitation Excerpt :Although normal melanocytes display low miR-214 levels, the expression of this small RNA is high in nevi, which present abnormal, although benign, melanocyte proliferation and frequently contain genetic mutations (Grichnik, 2008; Glud et al., 2009; Philippidou et al., 2010; Chen et al., 2010b; Penna et al., 2011). Importantly, miR-214 is highly expressed in primary malignant cutaneous melanomas (Molnar et al., 2008; Segura et al., 2010; Penna et al., 2011, 2013), although showing low expression levels in in situ noninvasive melanomas (Penna et al., 2011). Moreover, miR-214 correlates significantly more with acral than with non-acral melanoma subtypes (Chan et al., 2011) and is heavily expressed and associated with poor prognosis and elevated metastatic risk in ocular melanomas (Worley et al., 2008).
MicroRNAs in Skin Fibrosis
2015, MicroRNA in Regenerative Medicine