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Across disease indications, there is immediate need for new drug targets. Target scarcity is reflected in a growing number of same-target drugs of marginal clinical value. Advances in RNA mechanisms of disease are revealing a windfall of targets for nucleic acids therapeutics. However, nucleic acids remain limited as pharmaceutical agents. Because enzymes are predominant drug targets, ribonucleases represent an established target class to capitalize on RNA mechanisms of disease. Analysis of the human proteome identified 122 ribonucleases. This small ribonucleome mediates the biosynthetic and catabolic processing of a large transcriptome. Thus, ribonucleases represent critical signaling targets. Similar to kinases, proteases, and epigenetic enzymes, ribonucleases are rational targets for development of therapies with novel mechanisms, expanding treatment options for improved patient outcomes.

Despite immense promise, development of microRNA (miRNA) therapeutics remains limited by pharmacodynamic challenges that have hindered progress of related oligonucleotide-based technologies. Recent discovery of enzymes that mediate miRNA metabolism represent potential pharmacological targets for directing miRNA function, circumventing barriers associated with oligonucleotides. We previously identified the Translin/Trax (TN/TX) ribonuclease complex as a pre-miRNA degrading enzyme that competes with pre-miRNA processing by Dicer. Here, we establish a high-throughput TN/TX assay and screened 2320 drug and natural product compounds for inhibitors of TN/TX. Secondary analyses demonstrate small molecule mediated inhibition of pre-miRNA degradation by TN/TX and enhanced miRNA processing by Dicer. This application of traditional enzyme-inhibitor pharmacology to the miRNA pathway establishes a druggable target for rescuing global miRNA defects, providing an important complement to current approaches towards miRNA therapeutics. More broadly, demonstrating feasibility of pharmacological targeting of the ‘ribonucleome’ is particularly important given emerging classes of regulatory RNA and growing understanding of their importance in health and disease.

Genetic defects in the microRNA (miRNA) generating enzyme, dicer, are increasingly linked to disease. Loss of miRNA in dicer deficiency is thought to be due to loss of miRNA-generating activity. Here, we demonstrate a previously unknown catabolic mechanism driving miRNA depletion in dicer deficiency. We developed a Dicer-antagonist assay revealing a pre-miRNA degrading enzyme that competes with pre-miRNA processing. We purified this pre-miRNA degrading activity using an unbiased chromatographic procedure and identified the ribonuclease complex Translin/Trax (TN/TX). In wild type dicer backgrounds, pre-miRNA processing was dominant. However, in dicer deficient contexts, TN/TX broadly suppressed miRNA. These findings indicate that miRNA depletion in dicer deficiency is due to the combined loss of miRNA-generating activity and catabolic function of TN/TX. Importantly, inhibition of TN/TX mitigated loss of both miRNA and tumor suppression with dicer haploinsufficiency. These studies reveal a potentially druggable target for restoring miRNA function in cancers and emerging dicer deficiencies.

SummaryMicroRNAs (miRNAs) control gene expression by promoting degradation or repressing translation of target mRNAs. The components of the miRNA pathway are subject to diverse modifications that can modulate the abundance and function of miRNAs. Iron is essential for fundamental metabolic processes, and its homeostasis is tightly regulated. Here we identified iron chelators as a class of activator of the miRNA pathway that could promote the processing of miRNA precursors. We show that cytosolic iron could regulate the activity of the miRNA pathway through poly(C)-binding protein 2 (PCBP2). PCBP2 is associated with Dicer and promotes the processing of miRNA precursors. Cytosolic iron could modulate the association between PCBP2 and Dicer, as well as the multimerization of PCBP2 and its ability to bind to miRNA precursors, which can alter the processing of miRNA precursors. Our findings reveal a role of iron homeostasis in the regulation of miRNA biogenesis.

In less than 10 years since its inception, RNA interference (RNAi) has had extraordinary impact on biomedical science. RNAi has been demonstrated to influence numerous biological and disease pathways. Development and adoption of RNAi technologies have been prolific ranging from basic loss-of-function tools, genome-wide screening libraries to pharmaceutical target validation and therapeutic development. However, understanding of the molecular mechanisms of RNAi is far from complete. The purpose of this brief review is to highlight key achievements in elucidating the biochemical mechanisms of the RNA-induced silencing complex and to outline major challenges for the field.

Bioluminescence imaging (BLI) is a highly sensitive tool for visualizing tumors, neoplastic development, metastatic spread, and response to therapy. Although BLI has engendered much excitement due to its apparent simplicity and ease of implementation, few rigorous studies have been presented to validate the measurements. Here, we characterize the nature of bioluminescence output from mice bearing subcutaneous luciferase-expressing tumors over a 4-week period. Following intraperitoneal or direct intratumoral administration of luciferin substrate, there was a highly dynamic kinetic profile of light emission. Although bioluminescence was subject to variability, strong correlations (r > .8, p < .001) between caliper measured tumor volumes and peak light signal, area under light signal curve and light emission at specific time points were determined. Moreover, the profile of tumor growth, as monitored with bioluminescence, closely resembled that for caliper measurements. The study shows that despite the dynamic and variable nature of bioluminescence, where appropriate experimental precautions are taken, single time point BLI may be useful for noninvasive, high-throughput, quantitative assessment of tumor burden. Mol Imaging (2004) 3, 117–124.

Short interfering RNAs (siRNAs) are valuable tools for analyzing protein function in mammalian cell culture. This success has led to high expectations for in vivo and therapeutic applications. However, the pharmacokinetic properties of siRNA are not known. Here we report the biodistribution of a phosphodiester (PO) siRNA duplex and examine the effect of phosphorothioate (PS) linkages. Our findings indicate that biodistribution of siRNA is similar to that for single-stranded antisense oligonucleotides and offer insights for use of siRNA in vivo.

The development of methods for non-invasive, real-time imaging of gene expression would provide powerful tools for biomedical research and medical diagnostics. A broadly applicable strategy for achieving this goal is the use of complementary oligonucleotide probes for recognition of mRNA. The major challenge for molecular imaging is the development of specific and efficient transducers for signaling probe-target interaction. This review summarizes the strengths and limitations of reported molecular approaches for imaging of mRNA expression and discusses the challenges to development of in vivo methods.

Assembly of the RNA-induced silencing complex (RISC) consists of loading duplex (guide-passenger) siRNA onto Argonaute (Ago2) and removing the passenger strand. Ago2 contributes critically to RISC activation by nicking the passenger strand. Here we reconstituted duplex siRNA-initiated RISC activity using recombinant human Ago2 (hAgo2) and C3PO, indicating that C3PO has a critical role in hAgo2-RISC activation. Consistently, genetic depletion of C3PO compromised RNA silencing in mammalian cells. We determined the crystal structure of hC3PO, which reveals an asymmetric octamer barrel consisting of six translin and two TRAX subunits. This asymmetric assembly is critical for the function of C3PO as an endonuclease that cleaves RNA at the interior surface. The current work supports a Dicer-independent mechanism for human RISC activation, in which Ago2 directly binds duplex siRNA and nicks the passenger strand, and then C3PO activates RISC by degrading the Ago2-nicked passenger strand.

The assembly of RNA-induced silencing complex (RISC) is a key process in small RNA-mediated gene silencing. In humans, small interfering RNAs (siRNAs) and microRNAs (miRNAs) are incorporated into RISCs containing the Argonaute (AGO) subfamily proteins Ago1-4. Previous studies have proposed that, unlike Drosophila melanogaster RISC assembly pathways, human RISC assembly is coupled with dicing and is independent of ATP. Here we show by careful reexamination that, in humans, RISC assembly and dicing are uncoupled, and ATP greatly facilitates RISC loading of small-RNA duplexes. Moreover, all four human AGO proteins show remarkably similar structural preferences for small-RNA duplexes: central mismatches promote RISC loading, and seed or 3'-mid (guide position 12-15) mismatches facilitate unwinding. All these features of human AGO proteins are highly reminiscent of fly Ago1 but not fly Ago2.

SummaryMicroRNAs (miRNAs) govern an expanding number of biological and disease processes. Understanding the mechanisms by which the miRNA pathway is regulated, therefore, represents an important area of investigation. We determined that the human miRNA-generating complex is comprised of Dicer and phospho-TRBP isoforms. Phosphorylation of TRBP is mediated by the mitogen-activated protein kinase (MAPK) Erk. Expression of phospho-mimic TRBP and TRBP phosphorylation enhanced miRNA production by increasing stability of the miRNA-generating complex. Mitogenic signaling in response to serum and the tumor promoter PMA was dependent on TRBP phosphorylation. These effects were accompanied by a coordinated increase in levels of growth-promoting miRNA and reduced expression of let-7 tumor suppressor miRNA. Conversely, pharmacological inhibition of MAPK/Erk resulted in an anti-growth miRNA profile. Taken together, these studies indicate that the MAPK/Erk pathway regulates the miRNA machinery and suggest a general principle, wherein signaling systems target the miRNA pathway to achieve biological responses.

In Drosophila melanogaster, the multidomain RNase III Dicer-1 (Dcr-1) functions in tandem with the double-stranded (ds)RNA-binding protein Loquacious (Loqs) to catalyze the maturation of microRNAs (miRNAs) from precursor (pre)-miRNAs. Here we dissect the molecular mechanism of pre-miRNA processing by the Dcr-1-Loqs complex. The tandem RNase III (RIII) domains of Dcr-1 form an intramolecular dimer such that one RIII domain cleaves the 3′ strand, whereas the other cuts the 5′ strand of pre-miRNA. We show that the functional core of Dcr-1 consists of a DUF283 domain, a PAZ domain, and two RIII domains. Dcr-1 preferentially associates with the Loqs-PB splice isoform. Loqs-PB uses the second dsRNA-binding domain to bind pre-miRNA and the third dsRNA-binding domain to interact with Dcr-1. Both domains of Loqs-PB are required for efficient miRNA production by enhancing the affinity of Dcr-1 for pre-miRNA. Thus, our results provide further insights into the functional anatomy of the Drosophila miRNA-generating enzyme.

Synthetic small interfering RNA (siRNA) has become a valuable tool for investigating gene function in cell culture. This success has led to high expectations for siRNA as a tool for in vivo investigation and as a platform for therapeutic development. siRNA in cell culture owes much of its success to years of development of traditional antisense oligonucleotides, and in vivo applications will also benefit from previous experience in this regard. However, the duplex nature of siRNA presents significant obstacles that will need to be overcome. Here, we discuss the current status of in vivo siRNA technology and describe some of the barriers to widespread application of RNAi-mediated gene silencing in mammals.

Experiments involving chemical induction of the heat shock response in simple biological systems have generated the hypothesis that protein denaturation and consequential binding of heat shock transcription factor 1 (HSF1) to proximal heat shock elements (HSEs) on heat shock protein ( hsp) genes are the result of oxidation and/or depletion of intracellular thiols. The purpose of the present investigation was to determine the role of redox signaling of HSF1 in the intact animal in response to physiological and pharmacological perturbations. Heat shock and exercise induced HSF1-HSE DNA binding in the rat myocardium ( P < 0.001) in the absence of changes in reduced glutathione (GSH), the major nonprotein thiol in the cell. Ischemia-reperfusion, which decreased GSH content ( P < 0.05), resulted in nonsignificant HSF1-HSE formation. This dissociation between physiological induction of HSF1 and changes in GSH was not gender dependent. Pharmacological ablation of GSH withl-buthionine-[ S, R]-sulfoximine (BSO) treatment increased myocardial HSF1-HSE DNA binding in estrogen-naive animals ( P = 0.007). Thus, although physiological induction of HSF1-HSE DNA binding is likely regulated by mediators of protein denaturation other than cellular redox status, the proposed signaling pathway may predominate with pharmacological oxidation and may represent a plausible and accessible strategy in the development of HSP-based therapies.

Exercise is a physiological inducer of the cardioprotective heat shock protein, Hsp70. The putative biological events involved in signaling this response exhibit sexual dimorphism. Thus, it was hypothesized that exercise-mediated induction of Hsp70 would demonstrate sex specificity. After treadmill running, male rats exhibited 2-fold greater levels of cardiac Hsp70 relative to the levels in gonadally intact female rats ( P P P P

Exercise has been demonstrated as a physiological inducer of heat shock protein (HSP)70. Many of the proposed signals of this response exhibit sexual dimorphism. Thus the present objectives were to determine whether HSP70 induction after exercise exhibits gender specificity and to elucidate the mechanisms underlying such a phenomenon. Postexercise HSP70 induction in skeletal muscle was greater in male than female rats at the level of protein and mRNA ( P = 0.005). Moreover, placebo-treated ovariectomized animals demonstrated a greater HSP70 response to exercise than those treated with estrogen ( P = 0.015 and 0.019 for protein and mRNA, respectively). These findings indicate that the gender-specific HSP70 response to exercise is mediated by the female-specific hormone estrogen. Compounds structurally related to 17β-estradiol, the major endogenous estrogen, but which do not activate the estrogen receptor, also attenuated HSP70 induction with exercise ( P < 0.01), indicating a nongenomic hormonal mechanism. These findings highlight a specific example of the biological differences between males and females and reiterate the physiological effects of sex hormones extending beyond their roles in reproductive function.

Apoptosis is an essential developmental process in which a highly concerted series of biochemical events directs cell disassembly and death. Degradation of chromosomal DNA is a defining characteristic of apoptosis, involving distinct deoxyribonucleases that initiate DNA fragmentation (initiator DNases) and metabolize residual DNA (progressive DNases). On page 327 of this issue, Nakagawa et al. ( 1 ) report an unexpected role in apoptotic DNA degradation for an enzyme that was previously known for its role in RNA interference (RNAi).

Estrogen has been shown to reduce post-exercise skeletal muscle damage. Exercise-induced muscle damage may be a factor in the elevated post-exercise expression of heat-shock proteins (HSPs). Thus, the present investigation was conducted in order to examine the influence of estrogen on post-exercise levels of HSP 72 and heat-shock cognate, HSC 73, in male and female rodents. Prior to an acute bout of treadmill running, male and female Sprague-Dawley rats received daily injections of either 40 microg x kg(-1) of beta-estradiol 3-benzoate or olive oil vehicle for 2 weeks. A two- to fourfold reduction in post-exercise HSP 72 content was observed in the heart, liver, lung and red and white vastus muscles of estradiol-treated males compared with their vehicle-injected counterparts (P0.05). Compared to the males, the females had significantly lower post-exercise HSP 72 levels which were not affected by estradiol supplementation. Moreover, estradiol administration in male rodents resulted in a HSP response similar to that of females following exercise. Thus, the results of the present investigation suggest that estrogen is the factor responsible for the observed differences in post-exercise HSP 72 levels between males and females.

A report of the Keystone Symposium on Molecular and Cellular Biology, 'MicroRNA and Cancer', Keystone, Colorado, USA, 10-15 June 2009.