Functional validation of microRNA-target RNA interactions

miRNA Expression Is Increased in Serum from Patients with Semantic Variant Primary Progressive Aphasia

Primary progressive aphasia (PPA) damages the parts of the brain that control speech and language. There are three clinical PPA variants: nonfluent/agrammatic (nfvPPA), logopenic (lvPPA) and semantic (svPPA). The pathophysiology underlying PPA variants is not fully understood, including the role of micro (mi)RNAs which were previously shown to play a role in several neurodegenerative diseases. Using a two-step analysis (array and validation through real-time PCR), we investigated the miRNA expression pattern in serum from 54 PPA patients and 18 controls. In the svPPA cohort, we observed a generalized upregulation of miRNAs with miR-106b-5p and miR-133a-3p reaching statistical significance (miR-106b-5p: 2.69 ± 0.89 mean ± SD vs. 1.18 ± 0.28, p < 0.0001; miR-133a-3p: 2.09 ± 0.10 vs. 0.74 ± 0.11 mean ± SD, p = 0.0002). Conversely, in lvPPA, the majority of miRNAs were downregulated. GO enrichment and KEGG pathway analyses revealed that target genes of both miRNAs are involved in pathways potentially relevant for the pathogenesis of neurodegenerative diseases. This is the first study that investigates the expression profile of circulating miRNAs in PPA variant patients. We identified a specific miRNA expression profile in svPPA that could differentiate this pathological condition from other PPA variants. Nevertheless, these preliminary results need to be confirmed in a larger independent cohort.

miR775 integrates light, sucrose and auxin associated pathways to regulate root growth in Arabidopsis thaliana

MicroRNAs (miRNAs), a class of single-stranded non-coding RNA of 20-24 nucleotides, regulate gene expression by target gene transcript cleavage or translation inhibition. The phytohormone auxin is a crucial regulator of almost every process involved in plant growth and development. Several studies have demonstrated the involvement of miRNA(s) in the regulation of the auxin signaling pathway and plant development. However, very few studies have identified the auxin-mediated regulation of miRNA(s). In this study, we reveal the detailed mechanism of auxin-mediated regulation of the cell wall-related miR775- Galactosyl transferase (GalT) module, which plays an important role in root growth in Arabidopsis thaliana. We also showed two interdependent mechanisms by which miR775 regulates root growth: miR775-GalT and light-mediated sucrose-dependent pathways. Treatment of GUS reporter lines with Indole Acetic Acid (IAA), sucrose, and light apparently enhanced the abundance of miR775 in root tissue. miR775 overexpressing (miR775OX) lines showed changes in root architecture, including increased primary root growth and root hair, by targeting GalT. miR775OX lines also showed tolerance toward low Pi. These results provide new insights into the auxin regulation of cell wall-related miR775 and suggest its significant role in plant root growth and development by modifying the cell wall.

MicroRNAs Regulating Autophagy in Neurodegeneration

Social and economic impacts of neurodegenerative diseases (NDs) become more prominent in our constantly aging population. Currently, due to the lack of knowledge about the aetiology of most NDs, only symptomatic treatment is available for patients. Hence, researchers and clinicians are in need of solid studies on pathological mechanisms of NDs. Autophagy promotes degradation of pathogenic proteins in NDs, while microRNAs post-transcriptionally regulate multiple signalling networks including autophagy. This chapter will critically discuss current research advancements in the area of microRNAs regulating autophagy in NDs. Moreover, we will introduce basic strategies and techniques used in microRNA research. Delineation of the mechanisms contributing to NDs will result in development of better approaches for their early diagnosis and effective treatment.

Primary transcript of miR858 encodes regulatory peptide and controls flavonoid biosynthesis and development in Arabidopsis

MicroRNAs (miRNAs) are processed products of primary miRNAs (pri-miRNAs) and regulate the target gene expression. Though the regulatory roles of the several mature plant miRNAs have been studied in detail, the functions of other regions of the pri-miRNAs are still unrecognized. Recent studies suggest that a few pri-miRNAs may encode small peptides, miRNA-encoded peptides (miPEPs); however, the functions of these peptides have not been studied in detail. We report that the pri-miR858a of Arabidopsis thaliana encodes a small peptide, miPEP858a, which regulates the expression of pri-miR858a and associated target genes. miPEP858a-edited and miPEP858a-overexpressing lines showed altered plant development and accumulated modulated levels of flavonoids due to changes in the expression of genes associated with the phenylpropanoid pathway and auxin signalling. The exogenous treatment of the miPEP858a-edited plants with synthetic miPEP858a complemented the phenotypes and the gene function. This study suggests the importance of miPEP858a in exerting control over plant development and the phenylpropanoid pathway.

Analysis of MicroRNA-Mediated Translation Activation of In Vitro Transcribed Reporters in Quiescent Cells

Quiescence (G0) is defined as an assortment of cell cycle arrested states that exhibit distinct properties. Leukemias harbor a subpopulation of G0 cells that can be enriched by growth factor deprivation or serum starvation. Target site reporters with shortened poly(A) tails show translation activation by microRNAs, via a noncanonical mechanism, when introduced into the nucleus of G0 cells. This is because recruitment by the activation causing FXR1a-microRNA-protein complex (FXR1a-microRNP) is nuclear and requires shortened poly(A) tails to avoid repressive factors and canonical translation. When introduced into the cytoplasm, target mRNAs and microRNAs are directed toward repression rather than translation activation. Leukemic cell lines are difficult to transfect but can be routinely nucleofected-where in vitro transcribed mRNA reporters and microRNAs are introduced into the nucleus of G0 leukemic cells. Nucleofection of a microRNA target reporter and either cognate, targeting microRNA, or control microRNA, into the nucleus of G0 cells, enables analysis of translation activation by microRNAs in G0. We discuss a modified protocol that we developed for transfection of mRNAs along with microRNAs to test translation regulation by microRNAs in G0 leukemic cells.

An Assessment of Database-Validated microRNA Target Genes in Normal Colonic Mucosa: Implications for Pathway Analysis

BACKGROUND

Determination of functional pathways regulated by microRNAs (miRNAs), while an essential step in developing therapeutics, is challenging. Some miRNAs have been studied extensively; others have limited information. In this study, we focus on 254 miRNAs previously identified as being associated with colorectal cancer and their database-identified validated target genes.

METHODS

We use RNA-Seq data to evaluate messenger RNA (mRNA) expression for 157 subjects who also had miRNA expression data. In the replication phase of the study, we replicated associations between 254 miRNAs associated with colorectal cancer and mRNA expression of database-identified target genes in normal colonic mucosa. In the discovery phase of the study, we evaluated expression of 18 miR-NAs (those with 20 or fewer database-identified target genes along with miR-21-5p, miR-215-5p, and miR-124-3p which have more than 500 database-identified target genes) with expression of 17 434 mRNAs to identify new targets in colon tissue. Seed region matches between miRNA and newly identified targeted mRNA were used to help determine direct miRNA-mRNA associations.

RESULTS

From the replication of the 121 miRNAs that had at least 1 database-identified target gene using mRNA expression methods, 97.9% were expressed in normal colonic mucosa. Of the 8622 target miRNA-mRNA associations identified in the database, 2658 (30.2%) were associated with gene expression in normal colonic mucosa after adjusting for multiple comparisons. Of the 133 miRNAs with database-identified target genes by non-mRNA expression methods, 97.2% were expressed in normal colonic mucosa. After adjustment for multiple comparisons, 2416 miRNA-mRNA associations remained significant (19.8%). Results from the discovery phase based on detailed examination of 18 miRNAs identified more than 80 000 miRNA-mRNA associations that had not previously linked to the miRNA. Of these miRNA-mRNA associations, 15.6% and 14.8% had seed matches for CRCh38 and CRCh37, respectively.

CONCLUSIONS

Our data suggest that miRNA target gene databases are incomplete; pathways derived from these databases have similar deficiencies. Although we know a lot about several miRNAs, little is known about other miRNAs in terms of their targeted genes. We encourage others to use their data to continue to further identify and validate miRNA-targeted genes.

Dissecting miRNA gene repression on single cell level with an advanced fluorescent reporter system

Despite major advances on miRNA profiling and target predictions, functional readouts for endogenous miRNAs are limited and frequently lead to contradicting conclusions. Numerous approaches including functional high-throughput and miRISC complex evaluations suggest that the functional miRNAome differs from the predictions based on quantitative sRNA profiling. To resolve the apparent contradiction of expression versus function, we generated and applied a fluorescence reporter gene assay enabling single cell analysis. This approach integrates and adapts a mathematical model for miRNA-driven gene repression. This model predicts three distinct miRNA-groups with unique repression activities (low, mid and high) governed not just by expression levels but also by miRNA/target-binding capability. Here, we demonstrate the feasibility of the system by applying controlled concentrations of synthetic siRNAs and in parallel, altering target-binding capability on corresponding reporter-constructs. Furthermore, we compared miRNA-profiles with the modeled predictions of 29 individual candidates. We demonstrate that expression levels only partially reflect the miRNA function, fitting to the model-projected groups of different activities. Furthermore, we demonstrate that subcellular localization of miRNAs impacts functionality. Our results imply that miRNA profiling alone cannot define their repression activity. The gene regulatory function is a dynamic and complex process beyond a minimalistic conception of "highly expressed equals high repression".

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA-target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high-throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA-target binding events in vivo drove the emergence of a slew of high-throughput multiplex strategies, which now provide a viable prospect for elucidating genome-wide miRNA-target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post-transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high-precision interference with their direct, endogenous targets. For further resources related to this article, please visit the WIREs website.

Epigenetic and miRNAs Dysregulation in Prostate Cancer: The role of Nutraceuticals

The control of cancer onset and progression is recognized to benefit from specific molecular targeting. MiRNAs are increasingly being implicated in prostate cancer, and the evidence suggests they are possible targets for molecular therapy and diagnosis. In cancer cells, growing attention has been dedicated to novel molecular mechanisms linking the epigenetic scenario to miRNA dysregulation. Currently, the rising evidence shows that nutritional and natural agents, the so-called nutraceuticals, could modulate miRNAs expression, and, as a consequence, might influence cellular responses in health or diseases conditions, including cancer. Among dietary components, plant-derived polyphenols are receiving wide interest, either for their anti-aging and anti-oxidant properties, or for their more general "cell-protective" effects. Above all, their role in preventing the occurrence/recurrence of cancer and, in particular, their potentiality in nutritional intervention for modulating the functions of miRNAs and the epigenetic mechanisms, is still under active debate. This review is focused on the more recent highlights of the impact of miRNAs dysregulation on the onset and progression of prostate cancer, their interplay with epigenetic control and their modulation by natural agents.

Current understanding of the role of microRNAs in spinocerebellar ataxias

The number of studies highlighting the role of microRNAs (miRNAs) in human physiology and diseases is growing, but many miRNA-driven regulatory mechanisms remain elusive. A proper understanding of the exact functions of individual miRNAs and their interaction with specific targets is vitally important because such knowledge might help cure diseases for which no effective treatment currently exists. Herein, we present current views on the role of the miRNA-mediated regulation of gene expression in the case of select spinocerebellar ataxias (SCAs) and their potential involvement in the pathogenesis of these diseases. Specifically, we summarize published data showing the known links between miRNAs and CAG repeat-dependent SCAs. Moreover, using the example of SCA type 3 (SCA3), we refer to the issue of prediction and validation of miRNA targets, and we demonstrate that miR-181a-1 may regulate the 3'-UTR of the ATXN3 gene.

The panorama of miRNA-mediated mechanisms in mammalian cells

MicroRNAs comprise a large family of short, non-coding RNAs that are present in most eukaryotic organisms and are typically involved in downregulating the expression of protein-coding genes. The detailed mechanisms of miRNA functioning in animals and plants have been under investigation for more than decade. In mammalian cells, miRNA guides the effector complex miRISC to bind with partially complementary sequences, usually within the 3′UTR of mRNAs, and inhibit protein synthesis with or without transcript degradation. In addition to these main mechanisms, several other modes of miRNA-mediated gene expression regulation have been described, but their scale and importance remain a matter of debate. In this review, we briefly summarize the pathway of miRNA precursor processing during miRNA biogenesis and continue with the description of the miRISC assembly process. Then, we present the miRNA-mediated mechanisms of gene expression regulation in detail, and we gather information concerning the proteins involved in these processes. In addition, we briefly refer to the current applications of miRNA mechanisms in therapeutic strategies. Finally, we highlight some of the remaining controversies surrounding the regulation of mammalian gene expression by miRNAs.

Molecular targets of HPV oncoproteins: potential biomarkers for cervical carcinogenesis

Cervical cancer is the second most common cancer among women worldwide and is responsible for 275,000 deaths each year. Persistent infection with high-risk human papillomavirus (HR-HPV) is an essential factor for the development of cervical cancer. Although the process is not fully understood, molecular mechanisms caused by HPV infection are necessary for its development and reveal a large number of potential biomarkers for diagnosis and prognosis. These molecules are host genes and/or proteins, and cellular microRNAs involved in cell cycle regulation that result from disturbed expression of HR-HPV E5, E6 and E7 oncoproteins. One of the current challenges in medicine is to discover potent biomarkers that can correctly diagnose cervical premalignant lesions and standardize clinical management. Currently, studies are showing that some of these molecules are potential biomarkers of cervical carcinogenesis, and it is possible to carry out a more accurate diagnosis and provide more appropriate follow-up treatment for women with cervical dysplasia. In this paper, we review recent research studies on cell cycle molecules deregulated by HPV infections, as well as their potential use for cervical cancer screening.

AP-1/c-Jun transcription factors: regulation and function in malignant melanoma

Malignant melanoma is an aggressive form of skin cancer with an increasing incidence worldwide. One way to address the pathology of the disease is through molecular research. In addition to the analysis of melanoma-relevant signaling pathways, the investigation of important transcription factors is a fundamental objective. The AP-1 transcription factor family is known to play an important role in melanoma progression and development. The AP-1 family member c-Jun is highly expressed and active in melanoma cells, and the mechanisms and signaling pathways regulating c-Jun protein are diverse. In addition to the common regulation and activation of c-Jun by mitogen-activated protein kinases (MAPKs), there are several other signaling pathways and interactions leading to c-Jun protein expression and thus AP-1 activation. In malignant melanoma, and many other cancer types, c-Jun has mainly oncogenic functions; however, other AP-1 proteins also have anti-oncogenic roles. Interestingly, several studies have revealed that a strong AP-1 activity in melanoma mainly depends on c-Jun. Recently, it has also been shown that the c-Jun protein is regulated and activated by several other mechanisms, including miRNAs and the cytoskeleton. In summary, there are a variety of mechanisms underlying the induction of c-Jun protein expression and activity leading to tumor progression and development, and this diverse regulatory machinery is due to the heterogeneity of different tumor types, particularly in malignant melanoma.

Integrative Analysis of miRNA and inflammatory gene expression after acute particulate matter exposure

MicroRNAs (miRNAs) are environmentally sensitive inhibitors of gene expression that may mediate the effects of metal-rich particulate matter (PM) and toxic metals on human individuals. Previous environmental miRNA studies have investigated a limited number of candidate miRNAs and have not yet evaluated the functional effects on gene expression. In this study, we wanted to identify PM-sensitive miRNAs using microarray profiling on matched baseline and postexposure RNA from foundry workers with well-characterized exposure to metal-rich PM and to characterize miRNA relations with expression of candidate inflammatory genes. We applied microarray analysis of 847 human miRNAs and real-time PCR analysis of 18 candidate inflammatory genes on matched blood samples collected from foundry workers at baseline and after 3 days of work (postexposure). We identified differentially expressed miRNAs (fold change [FC] > 2 and p < 0.05) and correlated their expression with the inflammatory associated genes. We performed in silico network analysis in MetaCore v6.9 to characterize the biological pathways connecting miRNA-mRNA pairs. Microarray analysis identified four miRNAs that were differentially expressed in postexposure compared with baseline samples, including miR-421 (FC = 2.81, p < 0.001), miR-146a (FC = 2.62, p = 0.007), miR-29a (FC = 2.91, p < 0.001), and let-7g (FC = 2.73, p = 0.019). Using false discovery date adjustment for multiple comparisons, we found 11 miRNA-mRNA correlated pairs involving the 4 differentially expressed miRNAs and candidate inflammatory genes. In silico network analysis with MetaCore database identified biological interactions for all the 11 miRNA-mRNA pairs, which ranged from direct mRNA targeting to complex interactions with multiple intermediates. Acute PM exposure may affect gene regulation through PM-responsive miRNAs that directly or indirectly control inflammatory gene expression.