Clustered miRNAs and their role in biological functions and diseases

MicroRNAs (miRNAs) are endogenous, small non‐coding RNAs known to regulate expression of protein‐coding genes. A large proportion of miRNAs are highly conserved, localized as clusters in the genome, transcribed together from physically adjacent miRNAs and show similar expression profiles. Since a single miRNA can target multiple genes and miRNA clusters contain multiple miRNAs, it is important to understand their regulation, effects and various biological functions. Like protein‐coding genes, miRNA clusters are also regulated by genetic and epigenetic events. These clusters can potentially regulate every aspect of cellular function including growth, proliferation, differentiation, development, metabolism, infection, immunity, cell death, organellar biogenesis, messenger signalling, DNA repair and self‐renewal, among others. Dysregulation of miRNA clusters leading to altered biological functions is key to the pathogenesis of many diseases including carcinogenesis. Here, we review recent advances in miRNA cluster research and discuss their regulation and biological functions in pathological conditions.     

Micro‐RNAs meet epigenetics to make for better brains

Recent studies have highlighted the importance of regulatory non‐coding RNAs and epigenetics in controlling the differentiation of somatic stem cells. Two major pathways characterize these fields: micro‐RNAs (miRNAs) and DNA methylation. In this issue of EMBO Reports, Lv et al show that during mammalian corticogenesis, miR‐15b inhibits cytosine demethylation by targeting Tet3, a key methylcytosine dioxygenase. This leads to the epigenetic downregulation of cyclin D1. As a result, cell cycle and differentiation of neural progenitors are altered, promoting their switch to neurogenesis. Hence, Lv et al elegantly bring together miRNAs and DNA methylation in the cell cycle control of neural progenitors and neurogenesis.     

Modulators of cancer cell invasiveness

Cell invasiveness is essential for cancer metastasis. Many proteins, and more recently also non‐coding RNAs, particularly microRNAs (miRNAs), have been reported to affect the cell invasiveness of various cancers. There is an apparent gap between the high number of these macromolecules and the low number of signaling pathways experimentally verified to control cancer invasiveness. We have brought together these various proteins and RNAs because we could not find any publication that filled this important gap. We have noted 589 proteins, 28 miRNAs, and 1 long non‐coding RNA that are reported to modulate invasiveness in cells of various cancers. Interestingly, 44 proteins enhance invasiveness in cells of some cancers, but suppress it in cells of others. Almost all of the proteins that show experimentally verified activation/inhibition effects on, or binding interactions with, each other are linked together in a single network, in a “hub‐and‐spoke” architecture. The accumulated data show trends that point to anticipated future results and highlight gaps in what is known about invasiveness signaling. Identification of cancer invasiveness signaling networks is important for combination and personalized targeted therapies of cancers. J. Cell. Biochem. 111: 791–796, 2010. © 2010 Wiley‐Liss, Inc.     

Exosome biogenesis,secretion and function of exosomal miRNAs in skeletal muscle myogenesis

Exosomes are membrane‐bound extracellular vesicles that are produced in the endosomal compartment of most mammalian cell types and then released. Exosomes are effective carriers for the intercellular material transfer of material that can influence a series of physiological and pathological processes in recipient cells. Among loaded cargoes, non‐coding RNAs (ncRNAs) vary for the exosome‐producing cell and its homeostatic state, and characterization of the biogenesis and secretion of exosomal ncRNAs and the functions of these ncRNAs in skeletal muscle myogenesis remain preliminary. In this review, we will describe what is currently known of exosome biogenesis, release and uptake of exosomal ncRNAs, as well as the varied functions of exosomal miRNAs in skeletal muscle myogenesis.     

The insights of Let‐7 miRNAs in oncogenesis and stem cell potency

The ability of the classic tumour‐suppressive let‐7 family to inhibit carcinogenesis, tumour progression, recurrence and pluripotency of cancer stem cells has generated significant interest in the field of cancer research. Through suppressing and degrading downstream‐targeted mRNAs, let‐7 affected most aspects of cell biology. It is perplexing how let‐7 affects oncogenesis, as the large influx of new miRNAs and other kinds of non‐coding RNAs are continuously defined. In this review, we delineate the complex functions of let‐7 and discuss the future direction of let‐7 research.     

Induced miR‐99a expression represses Mtor cooperatively with miR‐150 to promote regulatory T‐cell differentiation

Peripheral induction of regulatory T (Treg) cells provides essential protection from inappropriate immune responses. CD4⁺ T cells that lack endogenous miRNAs are impaired to differentiate into Treg cells, but the relevant miRNAs are unknown. We performed an overexpression screen with T‐cell‐expressed miRNAs in naive mouse CD4⁺ T cells undergoing Treg differentiation. Among 130 candidates, the screen identified 29 miRNAs with a negative and 10 miRNAs with a positive effect. Testing reciprocal Th17 differentiation revealed specific functions for miR‐100, miR‐99a and miR‐10b, since all of these promoted the Treg and inhibited the Th17 program without impacting on viability, proliferation and activation. miR‐99a cooperated with miR‐150 to repress the expression of the Th17‐promoting factor mTOR. The comparably low expression of miR‐99a was strongly increased by the Treg cell inducer “retinoic acid”, and the abundantly expressed miR‐150 could only repress Mtor in the presence of miR‐99a. Our data suggest that induction of Treg cell differentiation is regulated by a miRNA network, which involves cooperation of constitutively expressed as well as inducible miRNAs.     

miR‐134 inhibits non‐small cell lung cancer growth by targeting the epidermal growth factor receptor

The epidermal growth factor receptor (EGFR) is frequently activated in a wide range of solid tumours and represents an important therapeutic target. MicroRNAs (miRNAs) have recently been recognized as a rational and potential modality for anti‐EGFR therapies. However, more EGFR‐targeting miRNAs need to be explored. In this study, we identified a novel EGFR‐targeting miRNA, miRNA‐134 (miR‐134), in non‐small‐cell lung cancer (NSCLC) cell lines. Luciferase assays confirmed that EGFR is a direct target of miR‐134. In addition, the overexpression of miR‐134 inhibited EGFR‐related signaling and suppressed NSCLC cells proliferation by inducing cell cycle arrest and/or apoptosis, suggesting that miR‐134 functions as a tumour suppressor in NSCLC. Further mechanistic investigation including RNAi and rescue experiments suggested that the down‐regulation of EGFR by miR‐134 partially contributes to the antiproliferative role of miR‐134. Last, in vivo experiments demonstrated that miR‐134 suppressed tumour growth of A549 xenograft in nude mice. Taken together, our findings suggest that miR‐134 inhibits non‐small cell lung cancer growth by targeting the EGFR.     

Small non‐coding RNA and colorectal cancer

Colorectal cancer (CRC) is the third most common malignance. Although great efforts have been made to understand the pathogenesis of CRC, the underlying mechanisms are still unclear. It is now clear that more than 90% of the total genome is actively transcribed, but lack of protein‐coding potential. The massive amount of RNA can be classified as housekeeping RNAs (such as ribosomal RNAs, transfer RNAs) and regulatory RNAs (such as microRNAs [miRNAs], PIWI‐interacting RNA [piRNAs], tRNA‐derived stress‐induced RNA, tRNA‐derived small RNA [tRFs] and long non‐coding RNAs [lncRNAs]). Small non‐coding RNAs are a group of ncRNAs with the length no more than 200 nt and they have been found to exert important regulatory functions under many pathological conditions. In this review, we summarize the biogenesis and functions of regulatory sncRNAs, such as miRNAs, piRNA and tRFs, and highlight their involvements in cancers, particularly in CRC.     

Epigenetic regulation of miR‐129‐2 and its effects on the proliferation and invasion in lung cancer cells

MicroRNAs (miRNAs) play a pivotal role in carcinogenesis. Dysregulation of miRNAs, both oncogenic miRNAs and tumour‐suppressive miRNAs, is closely associated with cancer development and progression. The levels of miRNAs could be changed epigenetically by DNA methylation in the 5′ untranslated region (UTR) of pre‐mature miRNAs. To investigate whether DNA methylation alters the expression of miR‐129 in lung cancer, we did DNA methylation assays and found that 5′ UTR region of miR‐129‐2 gene was absolutely methylated in both A549 and SPCA‐1 lung cancer cells, but totally un‐methylated in 95‐D cells. The expression of miR‐129 was restored by 5‐Aza‐2'‐deoxycytidine (DAC), a de‐methylation agent, in both A549 and SPCA‐1 cells, resulting in attenuated cell migration and invasion ability, and decreased protein level of NF‐κB, which indicates the involvement of NF‐κB pathway. To further illustrate the roles of miR‐129 in lung tumourigenesis, we overexpressed miR‐129 in lung cancer cells by transfection of miR‐129 mimics, and found arrested cell proliferation at G2/M phase of cell cycle and inhibited cell invasion. These findings strongly suggest that miR‐129 is a tumour suppressive miRNA, playing important roles in the development and progression of human lung cancer.     

The functional role of microRNAs in alcoholic liver injury

The function of microRNAs (miRNAs) during alcoholic liver disease (ALD) has recently become of great interest in biological research. Studies have shown that ALD associated miRNAs play a crucial role in the regulation of liver‐inflammatory agents such as tumour necrosis factor‐alpha (TNF‐α), one of the key inflammatory agents responsible for liver fibrosis (liver scarring) and the critical contributor of alcoholic liver disease. Lipopolysaccharide (LPS), a component of the cell wall of gram‐negative bacteria, is responsible for TNF‐α release by Kupffer cells. miRNAs are the critical mediators of LPS signalling in Kupffer cells, hepatocytes and hepatic stellate cells. Certain miRNAs, in particular miR‐155 and miR‐21, show a positive correlation in up‐regulation of LPS signalling when they are exposed to ethanol. ALD is related to enhanced gut permeability that allows the levels of LPS to increase, leads to increased secretion of TNF‐α by the Kupffer cells and subsequently promotes alcoholic liver injury through specific miRNAs. Meanwhile, two of the most frequently dysregulated miRNAs in steatohepatitis, miR‐122 and miR‐34a are the critical mediators in ethanol/LPS activated survival signalling during ALD. In this review, we summarize recent findings regarding the experimental and clinical aspects of functions of specific microRNAs, focusing mainly on inflammation and cell survival after ethanol/LPS treatment, and advances on the role of circulating miRNAs in human alcoholic disorders.     

Global microRNA level regulation of EGFR‐driven cell‐cycle protein network in breast cancer

The EGFR‐driven cell‐cycle pathway has been extensively studied due to its pivotal role in breast cancer proliferation and pathogenesis. Although several studies reported regulation of individual pathway components by microRNAs (miRNAs), little is known about how miRNAs coordinate the EGFR protein network on a global miRNA (miRNome) level. Here, we combined a large‐scale miRNA screening approach with a high‐throughput proteomic readout and network‐based data analysis to identify which miRNAs are involved, and to uncover potential regulatory patterns. Our results indicated that the regulation of proteins by miRNAs is dominated by the nucleotide matching mechanism between seed sequences of the miRNAs and 3′‐UTR of target genes. Furthermore, the novel network‐analysis methodology we developed implied the existence of consistent intrinsic regulatory patterns where miRNAs simultaneously co‐regulate several proteins acting in the same functional module. Finally, our approach led us to identify and validate three miRNAs (miR‐124, miR‐147 and miR‐193a‐3p) as novel tumor suppressors that co‐target EGFR‐driven cell‐cycle network proteins and inhibit cell‐cycle progression and proliferation in breast cancer.