Overgrowth caused by misexpression of a microRNA with dispensable wild-type function

The diagnostic, prognostic role and molecular mechanism of miR-328 in human cancer

MicroRNA are non-coding small RNAs that bind to their target mRNA and cause mRNA degradation or translation inhibition. MiRNA dysregulation is linked to a variety of human cancers and has a role in the genesis and development of cancer pathology. MiR-328 has been reported to be involved in various human cancers. And miR-328 is considered a key regulator in human cancer. It participates in biological processes such as proliferation, apoptosis, invasion, migration, and EMT. The present review will combine the basic and clinical studies to find that miR-328 promotes tumorigenesis and metastasis in human cancer. And we will describe the diagnostic, prognostic, and therapeutic value of miR-328 in various human cancers.

Micromanaging pattern formation: miRNA regulation of signaling systems in vertebrate development

Early embryogenesis requires the establishment of fields of progenitor cells with distinct molecular signatures. A balance of intrinsic and extrinsic cues determines the boundaries of embryonic territories and pushes progenitor cells toward different fates. This process involves multiple layers of regulation, including signaling systems, transcriptional networks, and post-transcriptional control. In recent years, microRNAs (miRNAs) have emerged as undisputed regulators of developmental processes. Here, we discuss how miRNAs regulate pattern formation during vertebrate embryogenesis. We survey how miRNAs modulate the activity of signaling pathways to optimize transcriptional responses in embryonic cells. We also examine how localized RNA interference can generate spatial complexity during early development. Unraveling the complex crosstalk between miRNAs, signaling systems and cell fate decisions will be crucial for our understanding of developmental outcomes and disease.

A comprehensive in vivo screen for anti-apoptotic miRNAs indicates broad capacities for oncogenic synergy

microRNAs (miRNAs) are ~21-22 nucleotide (nt) RNAs that mediate broad post-transcriptional regulatory networks. However, genetic analyses have shown that the phenotypic consequences of deleting individual miRNAs are generally far less overt compared to their misexpression. This suggests that miRNA deregulation may have broader phenotypic impacts during disease situations. We explored this concept in the Drosophila eye, by screening for miRNAs whose misexpression could modify the activity of pro-apoptotic factors. Via unbiased and comprehensive in vivo phenotypic assays, we identify an unexpectedly large set of miRNA hits that can suppress the action of pro-apoptotic genes hid and grim. We utilize secondary assays to validate that a subset of these miRNAs can inhibit irradiation-induced cell death. Since cancer cells might seek to evade apoptosis pathways, we modeled this situation by asking whether activation of anti-apoptotic miRNAs could serve as "second hits". Indeed, while clones of the lethal giant larvae (lgl) tumor suppressor are normally eliminated during larval development, we find that diverse anti-apoptotic miRNAs mediate the survival of lgl mutant clones in third instar larvae. Notably, while certain anti-apoptotic miRNAs can target apoptotic factors, most of our screen hits lack obvious targets in the core apoptosis machinery. These data highlight how a genetic approach can reveal distinct and powerful activities of miRNAs in vivo, including unexpected functional synergies during disease or cancer-relevant settings.

Expression of miR-30c and BCL-9 in gastric carcinoma tissues and their function in the development of gastric cancer

microRNA-30c (miR-30c) is a member of the miR-30s family, which is known to serve important roles in the occurrence and development of numerous tumor types. Our previous microarray analysis of extracted RNA from tissue samples was conducted to examine the expression of miR-30c and predict miR-30c target genes. In the present study, it was determined that the expression of miR-30c was differentially expressed in 82 paired gastric cancer (GC) and paracancerous tissues. Cellular expression of miR-30c in two GC cell lines MKN-45, MKN-74 and one non-cancer cell line GES-1 was modified using the miR-30c-mimic and miR-30c-inhibitor reagents, in a series of transfection experiments. Following transfection of cancer and non-cancer cell lines with the miR-30c-mimic, cell proliferation and apoptosis rates were increased. Compared with the NC group, MKN-74 cell proliferation was significantly inhibited (P<0.05) following transfection with the miR-30c-mimic at 48 and 24 h, GES-1 was significantly inhibited (P<0.05) at 24 and 48 h, and apoptosis was significantly reduced in transfected MKN-74 cells (P<0.05). The clinicopathological data and the expression of BCL-9 and miR-30c in patients with GC were used to identify associations. The expression levels of miR-30c were associated with age. Western blot analysis demonstrated that the BCL-9 expression levels in MKN-74 cells were higher following transfection with the miR-30c-mimic, and were lower following transfection with the miR-30c-inhibitor, both compared with the negative control group. It was concluded that compared with the negative control group, the expression of miR-30c was low in GC tissues and may be involved in GC development via regulation of proliferation, apoptosis and the cell cycle.

MiR-422a targets MAPKK6 and regulates cell growth and apoptosis in colorectal cancer cells

The important role of miR-422a in tumor has been reported in several studies. Recent research discovered that the expression of miR-422a was significantly decreased in colorectal cancer tissues, providing miR-422a as a tumor suppressor in CRC. However, the concrete mechanism of miR-422a regulating CRC cell is still unclear. In this study, we demonstrated that miR-422a could inhibit CRC cell growth and promote cell apoptosis via in vitro analyses. Moreover, computational methods were adopted to identify the targets of miR-422a. We found MAPKK6 was the direct target of miR-422a. Consequently, we further elucidated that miR-422a inhibited CRC cell growth and induced cell apoptosis by inhibiting p38/MAPK pathway. Besides that, we established the tumor xenograft model using nude mice and the inhibitory effects on tumor volumes and weights by miR-422a mimic transfection were also detected. Taken together, these findings demonstrated miR-422a exerted anti-cancer activities on CRC, which could be potentially used for CRC prognosis prediction and treatment.

Are microRNAs true sensors of ageing and cellular senescence?

All living beings are programmed to death due to aging and age-related processes. Aging is a normal process of every living species. While all cells are inevitably progressing towards death, many disease processes accelerate the aging process, leading to senescence. Pathologies such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, cardiovascular disease, cancer, and skin diseases have been associated with deregulated aging. Healthy aging can delay onset of all age-related diseases. Genetics and epigenetics are reported to play large roles in accelerating and/or delaying the onset of age-related diseases. Cellular mechanisms of aging and age-related diseases are not completely understood. However, recent molecular biology discoveries have revealed that microRNAs (miRNAs) are potential sensors of aging and cellular senescence. Due to miRNAs capability to bind to the 3' untranslated region (UTR) of mRNA of specific genes, miRNAs can prevent the translation of specific genes. The purpose of our article is to highlight recent advancements in miRNAs and their involvement in cellular changes in aging and senescence. Our article discusses the current understanding of cellular senescence, its interplay with miRNAs regulation, and how they both contribute to disease processes.

Multiple In Vivo Biological Processes Are Mediated by Functionally Redundant Activities of Drosophila mir-279 and mir-996

While most miRNA knockouts exhibit only subtle defects, a handful of miRNAs are profoundly required for development or physiology. A particularly compelling locus is Drosophila mir-279, which was reported as essential to restrict the emergence of CO2-sensing neurons, to maintain circadian rhythm, and to regulate ovarian border cells. The mir-996 locus is located near mir-279 and bears a similar seed, but they otherwise have distinct, conserved, non-seed sequences, suggesting their evolutionary maintenance for separate functions. We generated single and double deletion mutants of the mir-279 and mir-996 hairpins, and cursory analysis suggested that miR-996 was dispensable. However, discrepancies in the strength of individual mir-279 deletion alleles led us to uncover that all extant mir-279 mutants are deficient for mature miR-996, even though they retain its genomic locus. We therefore engineered a panel of genomic rescue transgenes into the double deletion background, allowing a pure assessment of miR-279 and miR-996 requirements. Surprisingly, detailed analyses of viability, olfactory neuron specification, and circadian rhythm indicate that miR-279 is completely dispensable. Instead, an endogenous supply of either mir-279 or mir-996 suffices for normal development and behavior. Sensor tests of nine key miR-279/996 targets showed their similar regulatory capacities, although transgenic gain-of-function experiments indicate partially distinct activities of these miRNAs that may underlie that co-maintenance in genomes. Altogether, we elucidate the unexpected genetics of this critical miRNA operon, and provide a foundation for their further study. More importantly, these studies demonstrate that multiple, vital, loss-of-function phenotypes can be rescued by endogenous expression of divergent seed family members, highlighting the importance of this miRNA region for in vivo function.

Genome-wide sequencing of small RNAs reveals a tissue-specific loss of conserved microRNA families in Echinococcus granulosus

BACKGROUND

MicroRNAs (miRNAs) are important post-transcriptional regulators which control growth and development in eukaryotes. The cestode Echinococcus granulosus has a complex life-cycle involving different development stages but the mechanisms underpinning this development, including the involvement of miRNAs, remain unknown.

RESULTS

Using Illumina next generation sequencing technology, we sequenced at the genome-wide level three small RNA populations from the adult, protoscolex and cyst membrane of E. granulosus. A total of 94 pre-miRNA candidates (coding 91 mature miRNAs and 39 miRNA stars) were in silico predicted. Through comparison of expression profiles, we found 42 mature miRNAs and 23 miRNA stars expressed with different patterns in the three life stages examined. Furthermore, considering both the previously reported and newly predicted miRNAs, 25 conserved miRNAs families were identified in the E. granulosus genome. Comparing the presence or absence of these miRNA families with the free-living Schmidtea mediterranea, we found 13 conserved miRNAs are lost in E. granulosus, most of which are tissue-specific and involved in the development of ciliated cells, the gut and sensory organs. Finally, GO enrichment analysis of the differentially expressed miRNAs and their potential targets indicated that they may be involved in bi-directional development, nutrient metabolism and nervous system development in E. granulosus.

CONCLUSIONS

This study has, for the first time, provided a comprehensive description of the different expression patterns of miRNAs in three distinct life cycle stages of E. granulosus. The analysis supports earlier suggestions that the loss of miRNAs in the Platyhelminths might be related to morphological simplification. These results may help in the exploration of the mechanism of interaction between this parasitic worm and its definitive and intermediate hosts, providing information that can be used to develop new interventions and therapeutics for the control of cystic echinococcosis.

Involvement of microRNAs in infection of silkworm with bombyx mori cytoplasmic polyhedrosis virus (BmCPV)

Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) is one of the most important pathogens of silkworm. MicroRNAs (miRNAs) have been demonstrated to play key roles in regulating host-pathogen interaction. However, there are limited reports on the miRNAs expression profiles during insect pathogen challenges. In this study, four small RNA libraries from BmCPV-infected midgut of silkworm at 72 h post-inoculation and 96 h post-inoculation and their corresponding control midguts were constructed and deep sequenced. A total of 316 known miRNAs (including miRNA*) and 90 novel miRNAs were identified. Fifty-eight miRNAs displayed significant differential expression between the infected and normal midgut (P value < = 0.01 and fold change > = 2.0 or < = 0.5), among which ten differentially expressed miRNA were validated by qRT-PCR method. Further bioinformatics analysis of predicted target genes of differentially expressed miRNAs showed that the miRNA targets were involved in stimulus and immune system process in silkworm.

MicroRNA functions in insects

MicroRNAs (miRNAs) are small non-coding RNAs that are generated in all eukaryotes and viruses. Their role as master regulators of gene expression in various biological processes has only been fully appreciated over the last decade. Accumulating evidence suggests that alterations in the expression of miRNAs may lead to disorders, including developmental defects, diseases and cancer. Here, I review what is currently known about miRNA functions in insects to provide an insight into their diverse roles in insect biology.

Hsp90 globally targets paused RNA polymerase to regulate gene expression in response to environmental stimuli

The molecular chaperone Heat shock protein 90 (Hsp90) promotes the maturation of several important proteins and plays a key role in development, cancer progression, and evolutionary diversification. By mapping chromatin-binding sites of Hsp90 at high resolution across the Drosophila genome, we uncover an unexpected mechanism by which Hsp90 orchestrates cellular physiology. It localizes near promoters of many coding and noncoding genes including microRNAs. Using computational and biochemical analyses, we find that Hsp90 maintains and optimizes RNA polymerase II pausing via stabilization of the negative elongation factor complex (NELF). Inhibition of Hsp90 leads to upregulation of target genes, and Hsp90 is required for maximal activation of paused genes in Drosophila and mammalian cells in response to environmental stimuli. Our findings add a molecular dimension to the chaperone's functionality with wide ramifications into its roles in health, disease, and evolution.

Exploiting Drosophila genetics to understand microRNA function and regulation

Although a great deal is known about the identity, biogenesis, and targeting capacity of microRNAs (miRNAs) in animal cells, far less is known about their functional requirements at the organismal level. Much remains to be understood about the necessity of miRNAs for overt phenotypes, the identity of critical miRNA targets, and the control of miRNA transcription. In this review, we provide an overview of genetic strategies to study miRNAs in the Drosophila system, including loss- and gain-of-function techniques, genetic interaction strategies, and transgenic reporters of miRNA expression and activity. As we illustrate the usage of these techniques in intact Drosophila, we see certain recurrent themes for miRNA functions, including energy homeostasis, apoptosis suppression, growth control, and regulation of core cell signaling pathways. Overall, we hope that this exposition of Drosophila genetic techniques, well known to the legions of fly geneticists and used to study all genes, can inform the general miRNA community that focuses on other biochemical, molecular, computational, and structural avenues. Clearly, it is the combination of these myriad techniques that has accelerated miRNA research to its extraordinary pace.

Polycomb preferentially targets stalled promoters of coding and noncoding transcripts

The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modification of target loci. Despite our broad knowledge about composition and enzymatic activities of the protein complexes involved, our understanding still lacks important mechanistic detail and a comprehensive view on target genes. In this study we use an extensive data set of ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites (TSSs) to identify and analyze thousands of binding sites for the PcG proteins and Trithorax from a Drosophila S2 cell line. In addition of finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic PcG binding sites coinciding with nonannotated TSSs. Interestingly, this set includes previously unknown promoters for primary transcripts of microRNA genes, thereby expanding the scope of Polycomb control to noncoding RNAs essential for development, apoptosis, and growth.

MicroRNA control of signal transduction

MicroRNAs (miRNAs) are integral elements in the post-transcriptional control of gene expression. After the identification of hundreds of miRNAs, the challenge is now to understand their specific biological function. Signalling pathways are ideal candidates for miRNA-mediated regulation owing to the sharp dose-sensitive nature of their effects. Indeed, emerging evidence suggests that miRNAs affect the responsiveness of cells to signalling molecules such as transforming growth factor-beta, WNT, Notch and epidermal growth factor. As such, miRNAs serve as nodes of signalling networks that ensure homeostasis and regulate cancer, metastasis, fibrosis and stem cell biology.

Epigenetic alterations as cancer diagnostic, prognostic, and predictive biomarkers

Alterations of DNA methylation and transcription of microRNAs (miRNAs) are very stable phenomena in tissues and body fluids and suitable for sensitive detection. These advantages enable us to translate some important discoveries on epigenetic oncology into biomarkers for control of cancer. A few promising epigenetic biomarkers are emerging. Clinical trials using methylated CpG islands of p16, Septin9, and MGMT as biomarkers are carried out for predication of cancer development, diagnosis, and chemosensitivity. Circulating miRNAs are promising biomarkers, too. Breakthroughs in the past decade imply that epigenetic biomarkers may be useful in reducing the burden of cancer.

microRNA-21 negatively regulates Cdc25A and cell cycle progression in colon cancer cells

microRNAs (miRNA) are small noncoding RNAs that participate in diverse biological processes by suppressing target gene expression. Altered expression of miR-21 has been reported in cancer. To gain insights into its potential role in tumorigenesis, we generated miR-21 knockout colon cancer cells through gene targeting. Unbiased microarray analysis combined with bioinformatics identified cell cycle regulator Cdc25A as a miR-21 target. miR-21 suppressed Cdc25A expression through a defined sequence in its 3'-untranslated region. We found that miR-21 is induced by serum starvation and DNA damage, negatively regulates G(1)-S transition, and participates in DNA damage-induced G(2)-M checkpoint through down-regulation of Cdc25A. In contrast, miR-21 deficiency did not affect apoptosis induced by a variety of commonly used anticancer agents or cell proliferation under normal cell culture conditions. Furthermore, miR-21 was found to be underexpressed in a subset of Cdc25A-overexpressing colon cancers. Our data show a role of miR-21 in modulating cell cycle progression following stress, providing a novel mechanism of Cdc25A regulation and a potential explanation of miR-21 in tumorigenesis.

Multiple approach to analyzing the role of microRNAs in apoptosis

MicroRNAs (miRNAs) are noncoding RNAs whose hallmarks are the very short sequences and the ability to repress the translation and/or transcription of target genes. miRNAs can have diverse functions, including regulation of cellular differentiation, proliferation, and embryogenesis. Over the past 5 years, an increasing number of studies have linked different miRNAs with programmed cell death or apoptosis. The principal aim of this chapter is to describe a method that (1) identifies miRNAs involved in apoptosis, using a validated array profiling approach, (2) assesses the direct involvement of candidate miRNAs in apoptosis, and (3) identifies the molecular mechanisms possibly involved in apoptotic response. To disclose the possible molecular targets of miRNAs, we propose the generation of a database created using a list of presumptive miRNA targets and the changes in the transcriptome after ectopic expression of the miRNAs. Our proposed method for doing this is suitable for both discovery of apoptotic pathways that regulate miRNAs and finding new miRNAs able to induce apoptosis.

A Drosophila pasha mutant distinguishes the canonical microRNA and mirtron pathways

Canonical primary microRNA (miRNA) transcripts and mirtrons are proposed to transit distinct nuclear pathways en route to generating mature approximately 22 nucleotide regulatory RNAs. We generated a null allele of Drosophila pasha, which encodes a double-stranded RNA-binding protein partner of the RNase III enzyme Drosha. Analysis of this mutant yielded stringent evidence that Pasha is essential for the biogenesis of canonical miRNAs but is dispensable for the processing and function of mirtron-derived regulatory RNAs. The pasha mutant also provided a unique tool to study the developmental requirements for Drosophila miRNAs. While pasha adult somatic clones are similar in many respects to those of dicer-1 clones, pasha mutant larvae revealed an unexpected requirement for the miRNA pathway in imaginal disc growth. These data suggest limitations to somatic clonal analysis of miRNA pathway components.

Lessons from microRNA mutants in worms, flies and mice

It is apparent that microRNAs (miRNAs) are important components in the regulation of genetic networks in many biological contexts. Based on computational analysis, typical miRNAs are inferred to have tens to hundreds of conserved targets. Many miRNA-target interactions have been validated by various means, including heterologous tests in cultured cells and gain-of-function approaches that can yield striking phenotypes in whole animals. However, these strategies do not report on the endogenous importance of such miRNA activities. Likewise, studies of miRNA pathway mutants can suggest an endogenous role for miRNAs in a given setting, but do not identify roles for specific miRNAs. Therefore, these approaches must be complemented with the analysis of miRNA mutant alleles. In this review, we describe some of the lessons learned from studying miRNA gene deletions in worms, flies and mice, and discuss their implications for the control of endogenous regulatory networks.

microRNA control of cell-cell signaling during development and disease

MicroRNAs (miRNAs) are critical post-transcriptional regulators that may collectively control a majority of animal genes. With thousands of miRNAs identified, a pressing challenge is now to understand their specific biological activities. Many predicted miRNA:target interactions only subtly alter gene activity. It has consequently not been trivial to deduce how miRNAs are relevant to phenotype, and by extension, relevant to disease. We note that the major signal transduction cascades that control animal development are highly dose-sensitive and frequently altered in human disorders. On this basis, we hypothesize that developmental cell signaling pathways represent prime candidates for mediating some of the major phenotypic consequences of miRNA deregulation, especially under gain-of-function conditions. This perspective reviews the evidence for miRNA targeting of the major signaling pathways, and discusses its implications for how aberrant miRNA activity might underlie human disease and cancer.

A gain-of-function suppressor screen for genes involved in dorsal-ventral boundary formation in the Drosophila wing

The Drosophila wing primordium is subdivided into a dorsal (D) and a ventral (V) compartment by the activity of the LIM-homeodomain protein Apterous in D cells. Cell interactions between D and V cells induce the activation of Notch at the DV boundary. Notch is required for the maintenance of the compartment boundary and the growth of the wing primordium. Beadex, a gain-of-function allele of dLMO, results in increased levels of dLMO protein, which interferes with the activity of Apterous and results in defects in DV axis formation. We performed a gain-of-function enhancer-promoter (EP) screen to search for suppressors of Beadex when overexpressed in D cells. We identified 53 lines corresponding to 35 genes. Loci encoding for micro-RNAs and proteins involved in chromatin organization, transcriptional control, and vesicle trafficking were characterized in the context of dLMO activity and DV boundary formation. Our results indicate that a gain-of-function genetic screen in a sensitized background, as opposed to classical loss-of-function-based screenings, is a very efficient way to identify redundant genes involved in a developmental process.

RNA interference and cancer: endogenous pathways and therapeutic approaches

The endogenous RNA interference (RNAi) pathway regulates cellular differentiation and development using small noncoding hairpin RNAs, called microRNAs. This chapter will review the link between mammalian microRNAs and genes involved in cellular proliferation, differentiation, and apoptosis. Some microRNAs act as oncogenes or tumor suppressor genes, but the target gene networks they regulate are just beginning to be described. Cancer cells have altered atterns of microRNA expression, which can be used to identify the cell of origin and to subtype cancers. RNAi has also been used to identify novel genes involved in cellular transformation using forward genetic screening methods previously only possible in invertebrates. Possible strategies and obstacles to harnessing RNAi for cancer therapy will also be discussed.

An overview of the identification, detection, and functional analysis of Drosophila microRNAs

MicroRNAs (miRNAs), small noncoding RNAs that post-transcriptionally regulate gene expression, are one of the most abundant classes of gene regulators. Yet, little is known about the roles that specific miRNAs play in the development of multicellular organisms. Drosophila provides an excellent model system to explore the in vivo activities of particular miRNAs within the context of well-defined gene-expression programs that control the development of a complex organism. This chapter reviews the various approaches currently used to identify Drosophila miRNAs, detect their expression, determine their messenger RNA targets, and study their function.

Modification of miR gene expression pattern in human colon cancer cells following exposure to 5-fluorouracil in vitro

MicroRNAs (miRNAs) are small noncoding RNA molecules produced by miR genes which are able to control the expression of a large number of cellular proteins by targeting mRNAs of protein coding genes. It has been suggested that modification of miR gene expression could be an important factor in the development and maintenance of the neoplastic state. It is also reasonable to hypothesize that antineoplastic drugs could be able to alter miR gene expression pattern since most of them are able to interfere with nucleic acid metabolism and gene expression. Here we show that 5-fluorouracil (5-FU), a classical antimetabolite largely used in the clinic, is able to change significantly the expression of several miR genes. In colon cancer cells, at a clinically relevant concentration, the drug up-regulates or down-regulates in vitro the expression of 19 and 3 miR genes, respectively, by a factor of not less than two-fold. In some instances, 5-FU up-regulates miR genes that are already over-expressed in neoplastic tissues, including, for example, miR-21 that is associated with anti-apoptotic functions characterizing malignant cells. In this case, it is possible that drug-induced miR gene dysregulation could be the expression of cellular response to the toxic effects of the agent. On the contrary, in other instances the drug influences the expression of miR genes in a direction that is opposite to that induced by neoplastic transformation. A typical example is provided by miR-200b, that is up-regulated in various tumors and down-regulated by treatment with the antimetabolite. Noteworthy, it is known that miR-200b suppresses a gene that codes for a protein tyrosine phosphatase (PTPN12) that inactivates products of oncogenes, such as c-Abl, Src or Ras. In conclusion, the present results support the hypothesis that 5-FU can alter profoundly miR gene expression pattern. This effect could be responsible, at least in part, of the multi-target pleiotropic influence manifested by the drug on malignant cells.

Characterization of microRNA expression levels and their biological correlates in human cancer cell lines

MicroRNAs are small noncoding RNAs that function by regulating target gene expression posttranscriptionally. They play a critical role in developmental and physiologic processes and are implicated in the pathogenesis of several human diseases including cancer. We examined the expression profiles of 241 human microRNAs in normal tissues and the NCI-60 panel of human tumor-derived cell lines. To quantify microRNA expression, we employed a highly sensitive technique that uses stem-loop primers for reverse transcription followed by real-time PCR. Most microRNAs were expressed at lower levels in tumor-derived cell lines compared with the corresponding normal tissue. Agglomerative hierarchical clustering analysis of microRNA expression revealed four groups among the NCI-60 cell lines consisting of hematologic, colon, central nervous system, and melanoma tumor-derived cell lines clustered in a manner that reflected their tissue of origin. We identified specific subsets of microRNAs that provide candidate molecular signatures characteristic of the tumor-derived cell lines belonging to these four clusters. We also identified specific microRNA expression patterns that correlated with the proliferation indices of the NCI-60 cell lines, and we developed evidence for the identification of specific microRNAs as candidate oncogenes and tumor suppressor genes in different tumor types. Our results provide evidence that microRNA expression patterns may mark specific biological characteristics of tumors and/or mediate biological activities important for the pathobiology of malignant tumors. These findings call attention to the potential of microRNAs to provide etiologic insights as well as to serve as both diagnostic markers and therapeutic targets for many different tumor types.

MicroRNAs: recently discovered key regulators of proliferation and apoptosis in animal cells : Identification of miRNAs regulating growth and survival

The relatively recent discovery of miRNAs has added a completely new dimension to the study of the regulation of gene expression. The mechanism of action of miRNAs, the conservation between diverse species and the fact that each miRNA can regulate a number of targets and phenotypes clearly indicates the importance of these molecules. In this review the current state of knowledge relating to miRNA expression and gene regulation is presented, outlining the key morphological and biochemical features controlled by miRNAs with particular emphasis on the key phenotypes that impact on cell growth in bioreactors, namely proliferation and apoptosis.

miRNAs and apoptosis: RNAs to die for

MicroRNAs (miRNAs) are small non-coding RNAs of about 18-24 nucleotides in length that negatively regulate gene expression. Discovered only recently, it has become clear that they are involved in many biological processes such as developmental timing, differentiation and cell death. Data that connect miRNAs to various kinds of diseases, particularly cancer, are accumulating. miRNAs can influence cancer development in many ways, including the regulation of cell proliferation, cell transformation, and cell death. In this review, we focus on miRNAs that have been shown to play a role in the regulation of apoptosis. We first describe in detail how Drosophila has been utilized as a model organism to connect several miRNAs with the cell death machinery. We discuss the genetic approaches that led to the identification of those miRNAs and subsequent work that helped to establish their function. In the second part of the review article, we focus on the involvement of miRNAs in apoptosis regulation in mammals. Intriguingly, many of the miRNAs that regulate apoptosis have been shown to affect cancer development. In the end, we discuss a virally encoded miRNA that influences the cell death response in the mammalian host cell. In summary, the data gathered over the recent years clearly show the potential and important role of miRNAs to regulate apoptosis at various levels and in several organisms.

microRNAs as oncogenes and tumor suppressors

microRNAs (miRNAs) are a new class of non-protein-coding, endogenous, small RNAs. They are important regulatory molecules in animals and plants. miRNA regulates gene expression by translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-guided rapid deadenylation. Recent studies show that some miRNAs regulate cell proliferation and apoptosis processes that are important in cancer formation. By using multiple molecular techniques, which include Northern blot analysis, real-time PCR, miRNA microarray, up- or down-expression of specific miRNAs, it was found that several miRNAs were directly involved in human cancers, including lung, breast, brain, liver, colon cancer, and leukemia. In addition, some miRNAs may function as oncogenes or tumor suppressors. More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites, suggesting that miRNAs may play a more important role in the pathogenesis of a limited range of human cancers than previously thought. Overexpressed miRNAs in cancers, such as mir-17-92, may function as oncogenes and promote cancer development by negatively regulating tumor suppressor genes and/or genes that control cell differentiation or apoptosis. Underexpressed miRNAs in cancers, such as let-7, function as tumor suppressor genes and may inhibit cancers by regulating oncogenes and/or genes that control cell differentiation or apoptosis. miRNA expression profiles may become useful biomarkers for cancer diagnostics. In addition, miRNA therapy could be a powerful tool for cancer prevention and therapeutics.

Pre-B cell proliferation and lymphoblastic leukemia/high-grade lymphoma in E(mu)-miR155 transgenic mice

MicroRNAs (miRNAs) represent a newly discovered class of posttranscriptional regulatory noncoding small RNAs that bind to targeted mRNAs and either block their translation or initiate their degradation. miRNA profiling of hematopoietic lineages in humans and mice showed that some miRNAs are differentially expressed during hematopoietic development, suggesting a role in hematopoietic cell differentiation. In addition, recent studies suggest the involvement of miRNAs in the initiation and progression of cancer. miR155 and BIC, its host gene, have been reported to accumulate in human B cell lymphomas, especially in diffuse large B cell lymphomas, Hodgkin lymphomas, and certain types of Burkitt lymphomas. Here, we show that E(mu)-mmu-miR155 transgenic mice exhibit initially a preleukemic pre-B cell proliferation evident in spleen and bone marrow, followed by frank B cell malignancy. These findings indicate that the role of miR155 is to induce polyclonal expansion, favoring the capture of secondary genetic changes for full transformation.

Non-coding RNA

The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests that the majority of the genomes of mammals and other complex organisms is in fact transcribed into ncRNAs, many of which are alternatively spliced and/or processed into smaller products. These ncRNAs include microRNAs and snoRNAs (many if not most of which remain to be identified), as well as likely other classes of yet-to-be-discovered small regulatory RNAs, and tens of thousands of longer transcripts (including complex patterns of interlacing and overlapping sense and antisense transcripts), most of whose functions are unknown. These RNAs (including those derived from introns) appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover. RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species.