microRNAs and genetic diseases

HOCTAR database: a unique resource for microRNA target prediction

microRNAs (miRNAs) are the most abundant class of small RNAs in mammals. They play an important role in regulation of gene expression by inducing mRNA cleavage or translational inhibition. Each miRNA targets an average of 100–200 genes by binding, preferentially, to their 3′ UTRs by means of partial sequence complementarity. Most miRNAs are localized within transcriptional units, termed host genes, and show similar expression behavior with respect to their corresponding host genes. Considering the impact of miRNA in the regulation of gene expression and their involvement in a growing number of human disorders, it is vital to develop sensitive computational approaches able to identify miRNA target genes. The HOCTAR database (db) is a publicly available resource collecting ranked list of predicted target genes for 290 intragenic miRNAs annotated in human. HOCTARdb is a unique resource that integrates miRNA target prediction genes and transcriptomic data to score putative miRNA targets looking at the expression behavior of their host genes. We demonstrated, by testing 135 known validated target genes (either at the translational or transcriptional level) for different miRNAs, that the miRNA target prediction lists present in HOCTARdb are highly reliable. Moreover, HOCTARdb associates biological roles to each miRNA-controlled transcriptional network by means of Gene Ontology analysis. This information is easily accessible through a user-friendly query page. The HOCTARdb is available at http://hoctar.tigem.it/. We believe that a detailed relationship between miRNAs and their target genes and a constant update of the information contained in HOCTARdb will provide an extremely valuable resource to assist the researcher in the discovery of miRNA target genes.

Pharmacogenomics of the RNA world: structural RNA polymorphisms in drug therapy

The use of pharmacogenomic biomarkers can enhance treatment outcomes. Regulatory polymorphisms are promising biomarkers that have proven difficult to uncover. They come in two flavors: those that affect transcription (regulatory single-nucleotide polymorphisms (rSNPs)) and those that affect RNA functions such as splicing, turnover, and translation (termed structural RNA SNPs (srSNPs)). This review focuses on the role of srSNPs in drug metabolism, transport, and response. An understanding of the nature and diversity of srSNPs and rSNPs enables clinical scientists to evaluate genetic biomarkers.

Epigenetic regulation of miR-196b expression in gastric cancer

MicroRNAs (miRNAs) are short noncoding RNAs that play important roles in cellular processes and disease pathogenesis via the control of specific targeted gene expression. The miR-196s miRNA is encoded at three paralogous loci in three HOX clusters and acts as an oncogenic miRNA in cancer progression. Recent studies have demonstrated that the expression of miR-196b increases cell proliferation and survival in leukemic cells. Here, we used a sequential methylation analysis to reveal that the methylation status correlated well with miR-196b expression in different cell lines. Treatment with the demethylating drug 5-Aza-dC reactivated miR-196b transcription in methylation-silenced cells. Using in vitro methylation approach, we further provide evidences that promoter hypermethylation represses miR-196b transcriptional activation tightly in human cancer cell lines. We also demonstrate that the expression of miR-196b is significantly elevated in gastric cancer and that hypomethylation status of miR-196b CpG islands frequently is observed in primary gastric tumors. Our results provide important information on miR-196s regulation and demonstrate that abnormal DNA hypomethylation induces overexpression of miR-196b in gastric cancer.

miRNeye: a microRNA expression atlas of the mouse eye

BACKGROUND

MicroRNAs (miRNAs) are key regulators of biological processes. To define miRNA function in the eye, it is essential to determine a high-resolution profile of their spatial and temporal distribution.

RESULTS

In this report, we present the first comprehensive survey of miRNA expression in ocular tissues, using both microarray and RNA in situ hybridization (ISH) procedures. We initially determined the expression profiles of miRNAs in the retina, lens, cornea and retinal pigment epithelium of the adult mouse eye by microarray. Each tissue exhibited notably distinct miRNA enrichment patterns and cluster analysis identified groups of miRNAs that showed predominant expression in specific ocular tissues or combinations of them. Next, we performed RNA ISH for over 220 miRNAs, including those showing the highest expression levels by microarray, and generated a high-resolution expression atlas of miRNAs in the developing and adult wild-type mouse eye, which is accessible in the form of a publicly available web database. We found that 122 miRNAs displayed restricted expression domains in the eye at different developmental stages, with the majority of them expressed in one or more cell layers of the neural retina.

CONCLUSIONS

This analysis revealed miRNAs with differential expression in ocular tissues and provided a detailed atlas of their tissue-specific distribution during development of the murine eye. The combination of the two approaches offers a valuable resource to decipher the contributions of specific miRNAs and miRNA clusters to the development of distinct ocular structures.

Sizing up the future of microRNA analysis

In less than 20 years, our appreciation for micro-RNA molecules (miRNAs) has grown from an original, curious observation in worms to their current status as incredibly important global regulators of gene expression that play key roles in many transformative biological processes. As our understanding of these small, non-coding transcripts continues to evolve, new approaches for their analysis are emerging. In this critical review we describe recent improvements to classical methods of detection as well as innovative new technologies that are poised to help shape the future landscape of miRNA analysis.

ARX spectrum disorders: making inroads into the molecular pathology

The Aristaless-related homeobox gene (ARX) is one of the most frequently mutated genes in a spectrum of X-chromosome phenotypes with intellectual disability (ID) as their cardinal feature. To date, close to 100 families and isolated cases have been reported to carry 44 different mutations, the majority of these (59%) being a result of polyalanine tract expansions. At least 10 well-defined clinical entities, including Ohtahara, Partington, and Proud syndromes, X-linked infantile spasms, X-linked lissencephaly with ambiguous genitalia, X-linked myoclonic epilepsy and nonsyndromic intellectual disability have been ascertained from among the patients with ARX mutations. The striking intra- and interfamilial pleiotropy together with genetic heterogeneity (same clinical entities associated with different ARX mutations) are becoming a hallmark of ARX mutations. Although males are predominantly affected, some mutations associated with malformation phenotypes in males also show a phenotype in carrier females. Recent progress in the study of the effect of ARX mutations through sophisticated animal (mice) and cellular models begins to provide crucial insights into the molecular function of ARX and associated molecular pathology, thus guiding future inquiries into therapeutic interventions.

Dicer regulates the development of nephrogenic and ureteric compartments in the mammalian kidney

MicroRNAs (miRNAs) are a large and growing class of small, non-coding, regulatory RNAs that control gene expression predominantly at the post-transcriptional level. The production of most functional miRNAs depends on the enzymatic activity of Dicer, an RNase III class enzyme. To address the potential action of Dicer-dependent miRNAs in mammalian kidney development, we conditionally ablated Dicer function within cells of nephron lineage and the ureteric bud-derived collecting duct system. Six2Cre-mediated removal of Dicer activity from the progenitors of the nephron epithelium led to elevated apoptosis and premature termination of nephrogenesis. Thus, Dicer action is important for maintaining the viability of this critical self-renewing progenitor pool and, consequently, development of a normal nephron complement. HoxB7Cre-mediated removal of Dicer function from the ureteric bud epithelium led to the development of renal cysts. This was preceded by excessive cell proliferation and apoptosis, and accompanied by disrupted ciliogenesis within the ureteric bud epithelium. Dicer removal also disrupted branching morphogenesis with the phenotype correlating with downregulation of Wnt11 and c-Ret expression at ureteric tips. Thus Dicer, and by inference Dicer-dependent miRNA activity, have distinct regulatory roles within different components of the developing mouse kidney. Furthermore, an understanding of miRNA action may provide new insights into the etiology and pathogenesis of renal cyst-based kidney disease.

miR-204 is required for lens and retinal development via Meis2 targeting

MicroRNAs (miRNAs) are small noncoding RNAs that have important roles in the regulation of gene expression. The roles of individual miRNAs in controlling vertebrate eye development remain, however, largely unexplored. Here, we show that a single miRNA, miR-204, regulates multiple aspects of eye development in the medaka fish (Oryzias latipes). Morpholino-mediated ablation of miR-204 expression resulted in an eye phenotype characterized by microphthalmia, abnormal lens formation, and altered dorsoventral (D-V) patterning of the retina, which is associated with optic fissure coloboma. Using a variety of in vivo and in vitro approaches, we identified the transcription factor Meis2 as one of the main targets of miR-204 function. We show that, together with altered regulation of the Pax6 pathway, the abnormally elevated levels of Meis2 resulting from miR-204 inactivation are largely responsible for the observed phenotype. These data provide an example of how a specific miRNA can regulate multiple events in eye formation; at the same time, they uncover an as yet unreported function of Meis2 in the specification of D-V patterning of the retina.

Human SP-A1 (SFTPA1) variant-specific 3' UTRs and poly(A) tail differentially affect the in vitro translation of a reporter gene

Human surfactant protein A (SP-A) is encoded by two functional genes (SFTPA1, SFTPA2) with a high degree of sequence identity. Sequence differences among these genes and their genetic variants have been observed at the 5' and 3' untranslated regions (UTRs). In this work, we studied the impact on translation of the SFTPA1 (hSP-A1) and SFTPA2 (hSP-A2) gene 5' UTR splice variants and 3' UTR sequence variants, in the presence or absence of poly(A) tail. We generated constructs containing the luciferase reporter gene flanked upstream by one of the hSP-A 5' UTR splice variants and/or downstream by one hSP-A 3' UTR sequence variant. mRNA transcripts were prepared by in vitro transcription and used for either in vitro translation with a rabbit reticulocyte lysate or transient transfection of the lung adenocarcinoma cell line NCI-H441. The luciferase activity results indicate that hSP-A 5' UTR and 3' UTR together have an additive effect on translation. In this context, the hSP-A1 6A(3) and 6A(4) 3' UTR variants exhibited higher translation efficiency than the 6A(2) variant (P <0.05), whereas no significant difference was observed between the two hSP-A2 3' UTRs studied (1A(0), 1A(3)). Further sequence analysis revealed that a deletion of an 11-nucleotide (nt) element in both the 6A(3) and 6A(4) 3' UTR variants changes the predicted secondary structure stability and the number of putative miRNA binding sites. Removal of this 11-nt element in the 6A(2) 3' UTR resulted in increased translation, and the opposite effect was observed when the 11-nt element was cloned in a guest 3' UTR (6A(3), 6A(4)). These results indicate that sequence differences among hSP-A gene variants may account for differential regulation at the translational level.

Improved microRNA quantification in total RNA from clinical samples

microRNAs are small regulatory RNAs that are currently emerging as new biomarkers for cancer and other diseases. In order for biomarkers to be useful in clinical settings, they should be accurately and reliably detected in clinical samples such as formalin fixed paraffin embedded (FFPE) sections and blood serum or plasma. These types of samples represent a challenge in terms of microRNA quantification. A newly developed method for microRNA qPCR using Locked Nucleic Acid (LNA)-enhanced primers enables accurate and reproducible quantification of microRNAs in scarce clinical samples. Here we show that LNA-based microRNA qPCR enables biomarker screening using very low amounts of total RNA from FFPE samples and the results are compared to microarray analysis data. We also present evidence that the addition of a small carrier RNA prior to total RNA extraction, improves microRNA quantification in blood plasma and laser capture microdissected (LCM) sections of FFPE samples.