Promoter-targeted double-stranded small RNAs activate PAWR gene expression in human cancer cells

Targeted Induction of Endogenous VDUP1 by Small Activating RNA Inhibits the Growth of Lung Cancer Cells

Recent studies have reported that small double-strand RNAs (dsRNAs) can activate endogenous genes via an RNA-based promoter targeting mechanism termed RNA activation (RNAa). In the present study, we showed that dsVDUP1-834, a novel small activating RNA (saRNA) targeting promoter of vitamin D₃ up-regulated protein 1 (VDUP1) gene, up-regulated expression of VDUP1 at both mRNA and protein levels in A549 lung cancer cells. We also demonstrated that dsVDUP1-834 inhibited cell proliferation in A549 lung cancer cells. Further studies showed that dsVDUP1-834 induced cell-cycle arrest by increasing p27 and p53 and decreasing cyclin A and cyclin B1. In addition, knockdown of VDUP1 abrogated dsVDUP1-834-induced up-regulation of VDUP1 gene expression and related effects. The activation of VDUP1 by dsVDUP1-834 was accompanied by an increase in dimethylation of histone 3 at lysine 4 (H3K4me2) and acetylation of histone 3 (H3ac) and a decrease in dimethylation of histone 3 at lysine 9 (H3K9me2) at the target site of VDUP1 promoter. Moreover, the enrichment of Ago2 was detected at the dsVDUP1-834 target site, and Ago2 knockdown significantly suppressed dsVDUP1-834-mediated inhibition of cell proliferation and modulation of cell-cycle regulators. Taken together, the results presented in this report demonstrate that dsVDUP1-834 induces VDUP1 gene expression by epigenetic changes, resulting in cell growth inhibition and cell-cycle arrest. Our results suggest that targeted induction of VDUP1 by dsVDUP1-834 might be a promising therapeutic strategy for the treatment of lung cancer.

RNA Activation-A Novel Approach to Therapeutically Upregulate Gene Transcription

RNA activation (RNAa) is a mechanism whereby RNA oligos complementary to genomic sequences around the promoter region of genes increase the transcription output of their target gene. Small activating RNA (saRNA) mediate RNAa through interaction with protein co-factors to facilitate RNA polymerase II activity and nucleosome remodeling. As saRNA are small, versatile and safe, they represent a new class of therapeutics that can rescue the downregulation of critical genes in disease settings. This review highlights our current understanding of saRNA biology and describes various examples of how saRNA are successfully used to treat various oncological, neurological and monogenic diseases. MTL-CEBPA, a first-in-class compound that reverses CEBPA downregulation in oncogenic processes using CEBPA-51 saRNA has entered clinical trial for the treatment of hepatocellular carcinoma (HCC). Preclinical models demonstrate that MTL-CEBPA reverses the immunosuppressive effects of myeloid cells and allows for the synergistic enhancement of other anticancer drugs. Encouraging results led to the initiation of a clinical trial combining MTL-CEBPA with a PD-1 inhibitor for treatment of solid tumors.

Small Activating RNAs: Towards the Development of New Therapeutic Agents and Clinical Treatments

Small double-strand RNA (dsRNA) molecules can activate endogenous genes via an RNA-based promoter targeting mechanism. RNA activation (RNAa) is an evolutionarily conserved mechanism present in diverse eukaryotic organisms ranging from nematodes to humans. Small activating RNAs (saRNAs) involved in RNAa have been successfully used to activate gene expression in cultured cells, and thereby this emergent technique might allow us to develop various biotechnological applications, without the need to synthesize hazardous construct systems harboring exogenous DNA sequences. Accordingly, this thematic issue aims to provide insights into how RNAa cellular machinery can be harnessed to activate gene expression leading to a more effective clinical treatment of various diseases.

Antitumor Activity of Small Activating RNAs Induced PAWR Gene Activation in Human Bladder Cancer Cells

Small double-stranded RNAs (dsRNAs) have been proved to effectively up-regulate the expression of particular genes by targeting their promoters. These small dsRNAs were also termed small activating RNAs (saRNAs). We previously reported that several small double-stranded RNAs (dsRNAs) targeting the PRKC apoptosis WT1 regulator (PAWR) promoter can up-regulate PAWR gene expression effectively in human cancer cells. The present study was conducted to evaluate the antitumor potential of PAWR gene induction by these saRNAs in bladder cancer. Promisingly, we found that up-regulation of PAWR by saRNA inhibited the growth of bladder cancer cells by inducing cell apoptosis and cell cycle arrest which was related to inhibition of anti‑apoptotic protein Bcl-2 and inactivation of the NF-κB and Akt pathways. The activation of the caspase cascade and the regulation of cell cycle related proteins also supported the efficacy of the treatment. Moreover, our study also showed that these saRNAs cooperated with cisplatin in the inhibition of bladder cancer cells. Overall, these data suggest that activation of PAWR by saRNA may have a therapeutic benefit for bladder cancer.

Expression of PAWR predicts prognosis of ovarian cancer

Background

Ovarian cancer greatly threatens the general health of women worldwide. Implementation of predictive prognostic biomarkers aids in ovarian cancer management.

Methods

Using online databases, the general expression profile, target-disease associations, and interaction network of PAWR were explored. To identify the role of PAWR in ovarian cancer, gene correlation analysis, survival analysis, and combined analysis of drug responsiveness and PAWR expression were performed. The predictive prognostic value of PAWR was further validated in clinical samples.

Results

PAWR was widely expressed in normal and cancer tissues, with decreased expression in ovarian cancer tissues compared with normal tissues. PAWR was associated with various cancers including ovarian cancer. PAWR formed a regulatory network with a group of proteins and correlated with several genes, which were both implicated in ovarian cancer and drug responsiveness. High PAWR expression denoted better survival in ovarian cancer patients (OS: HR = 0.84, P = 0.0077; PFS, HR = 0.86, P = 0.049). Expression of PAWR could predict platinum responsiveness in ovarian cancer and there was a positive correlation between PAWR gene effect and paclitaxel sensitivity. In 12 paired clinical samples, the cancerous tissues exhibited significantly lower PAWR expression than matched normal fallopian tubes. The predictive prognostic value of PAWR was maintained in a cohort of 50 ovarian cancer patients.

Conclusions

High PAWR expression indicated better survival and higher drug responsiveness in ovarian cancer patients. PAWR could be exploited as a predictive prognostic biomarker in ovarian cancer.

Enhancer II-targeted dsRNA decreases GDNF expression via histone H3K9 trimethylation to inhibit glioblastoma progression

BACKGROUND

Glial cell line-derived neurotrophic factor (GDNF) is expressed in both astrocytes and glioblastoma (GBM) cells. GDNF expression is significantly increased in GBM, and inhibiting its expression can retard GBM progression. However, there is no known method for specific inhibition of GDNF in GBM cells.

METHODS

Promoter-targeted dsRNA-induced transcriptional gene silencing or activation was recently achieved in human cells. This approach has the potential to specifically regulate gene transcription via epigenetic modifications. In this study, we designed six candidate dsRNAs targeting the enhancer or silencer in GDNF gene promoter II to check their effects on GDNF transcription and GBM progression.

RESULTS

Among these dsRNAs, enhancer II-targeted dsRNA significantly inhibited U251 GBM progression by downregulating GDNF (P < 0.05), while silencer II-targeted dsRNA exerted an opposite effect. Moreover, enhancer II-targeted dsRNA did not significantly change GDNF expression in human astrocytes (HA) and the proliferation and migration of HA cells (P > 0.05). Bisulfate PCR and chromatin immunoprecipitation analyses revealed that both DNA methylation and trimethylation of histone 3 at lysine 9 (H3K9me3) at silencer II-targeted region significantly increased, and H3K9me3 at enhancer II-targeted region significantly decreased, in U251 cells compared with HA cells in non-intervention condition (P < 0.05). Both enhancer II- and silencer II-targeted dsRNA significantly increased H3K9me3 methylation rather than DNA at the targeted site in U251 cells (P < 0.05). The expression and activity of histone methyltransferase SETDB1 increased dramatically in U251 cells compared with HA cells, and it was recruited to enhancer II targeting region after enhancer II-targeted dsRNA treatment in U251 cells (P < 0.05).

CONCLUSIONS

Our results demonstrate that a promoter-targeted dsRNA can silence or promote gene transcription depending on its targeted site in different cis-acting elements in the gene promoter. Targeted inhibition of GDNF by enhancer II-targeted dsRNA may be explored as a novel treatment for GBM.

Identifying and Classifying Shared Selective Sweeps from Multilocus Data

Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term [Formula: see text] and [Formula: see text] to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.

RNA-based therapeutics for colorectal cancer: Updates and future directions

Colorectal cancer (CRC) is one of the most common causes of cancer death worldwide. While standard chemotherapy and new targeted therapy have been improved recently, problems such as multidrug resistance (MDR) and severe side effects remain unresolved. RNAs are essential to all biological processes including cell proliferation and differentiation, cell cycle, apoptosis, activation of tumor suppressor genes, suppression of oncogenes. Therefore, there are various potential approaches to address genetic disease like CRC at the RNA level. In contrast to conventional treatments, RNA-based therapeutics such as RNA interference, antisense oligonucleotides, RNA aptamer, ribozymes, have the advantages of high specificity, high potency and low toxicity. It has gained more and more attention due to the flexibility in modulating a wide range of targets. Here, we highlight recent advances and clinical studies involving RNA-based therapeutics and CRC. We also discuss their advantages and limitations that remain to be overcome for the treatment of human CRC.

Therapeutic Potential of Small Activating RNAs (saRNAs) in Human Cancers

Background:

RNA is increasingly recognized as a powerful molecule that can be used to control gene expression. Sophisticated, well-engineered RNA-based regulators are being developed as oligotherapeutics.

Methods:

In particular, small activating RNAs (saRNAs) are promising therapeutic options for targeting human diseases. Numerous saRNAs targeting multiple cancers have been developed in preclinical models. One saRNA targeting C/EBPα is currently undergoing clinical trials in liver cancer.

Results and

Conclusion:

In this review, we describe the current working model of the intracellular mechanism of saRNA, discuss the recent progress of saRNA therapeutics in preclinical and clinical trials, and current advances in targeted delivery using aptamers in detail.

Activating the Chromatin by Noncoding RNAs

SIGNIFICANCE

The extent and breadth of transcription have recently been uncovered and this has revealed an extensive array of noncoding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realized and to date it appears that ncRNAs may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and posttranscriptional regulation, including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding. Not only enhancer RNA (eRNA) but other types of ncRNAs, including small RNA (sRNA), long-noncoding RNA (lncRNA), microRNA (miRNA), and PIWI-associated RNA (piRNA), have also been implicated in gene activation. Interestingly, they often coincide with histone modifications that favor an open chromatin. In addition, these ncRNAs can recruit key factors important for transcription, including RNA polymerase II. They may directly bind the genomic DNA or act as scaffolds; alternatively, they may loop the chromatin to enhance transcription.

CRITICAL ISSUES

Although the role of small activating (sa)RNAs has been considerably studied, the roles of miRNAs and piRNAs in gene activation still need to be substantiated and issues of specificity require further studies.

FUTURE DIRECTIONS

The ncRNA field is coming out of its infancy and we are gaining a global picture of the importance of ncRNAs. However, detailed mechanisms of action of the different ncRNAs are still to be determined. This may reveal novel ways of transcriptional regulation, which will facilitate our ability to utilize these regulatory pathways for research and therapeutic purposes. Antioxid. Redox Signal. 29, 813-831.

RNAa and Vector-Mediated Overexpression of DIRAS1 Suppresses Tumor Growth and Migration in Renal Cell Carcinoma

The downregulation of DIRAS1 has been suggested to potentially contribute to tumor development and progression in several human cancers. However, the role of DIRAS1 in renal cell carcinoma (RCC) remains elusive. In this study, we examined the DIRAS1 expression level in RCC cell lines and tissues. Both RNA activation (RNAa) and vector transfection methods were used to upregulate the expression of DIRAS1 in RCC cells. Expression analysis revealed that DIRAS1 was significantly downregulated in RCC cell lines and tissues compared with nontumorigenic renal cells and adjacent nontumor tissues individually. Promoter methylation analysis indicated that the reduced DIRAS1 expression might be partly mediated by epigenetic modulation. The RNAa-mediated overexpression of DIRAS1 inhibited cell proliferation and tumorigenicity in vitro and in vivo. The re-activation of DIRAS1 also promoted apoptosis and suppressed migration and invasion in RCC cells. The ectopic expression of DIRAS1 via an expression vector recapitulated the RNAa results. These results reveal that DIRAS1, functioning as a putative tumor suppressor in RCC cells, could potentially be a therapeutic target and RNAa could be a therapeutic strategy for RCC.

Small RNA-induced INTS6 gene up-regulation suppresses castration-resistant prostate cancer cells by regulating β-catenin signaling

Small RNAs play an important role in gene regulatory networks. The gene suppressive effect of small RNAs was previously the dominant focus of studies, but during the recent decade, small RNA-induced gene activation has been reported and has become a notable gene manipulation technique. In this study, a putative tumor suppressor, INTS6, was activated by introducing a promoter-targeted small RNA (dsRNA-915) into castration-resistant prostate cancer (CRPC) cells. Unique dynamics associated with the gene upregulation phenomenon was observed. Following gene activation, cell proliferation and motility were suppressed in vitro. Downregulation of Wnt/β-catenin signaling was observed during the activation period, and the impairment of β-catenin degradation reversed the tumor suppressor effects of INTS6. These results suggest the potential application of small activating RNAs in targeted gene therapy for CRPC.

Nuclear functions of mammalian MicroRNAs in gene regulation, immunity and cancer

MicroRNAs (miRNAs) are endogenous non-coding RNAs that contain approximately 22 nucleotides. They serve as key regulators in various biological processes and their dysregulation is implicated in many diseases including cancer and autoimmune disorders. It has been well established that the maturation of miRNAs occurs in the cytoplasm and miRNAs exert post-transcriptional gene silencing (PTGS) via RNA-induced silencing complex (RISC) pathway in the cytoplasm. However, numerous studies reaffirm the existence of mature miRNA in the nucleus, and nucleus-cytoplasm transport mechanism has also been illustrated. Moreover, active regulatory functions of nuclear miRNAs were found including PTGS, transcriptional gene silencing (TGS), and transcriptional gene activation (TGA), in which miRNAs bind nascent RNA transcripts, gene promoter regions or enhancer regions and exert further effects via epigenetic pathways. Based on existing interaction rules, some miRNA binding sites prediction software tools are developed, which are evaluated in this article. In addition, we attempt to explore and review the nuclear functions of miRNA in immunity, tumorigenesis and invasiveness of tumor. As a non-canonical aspect of miRNA action, nuclear miRNAs supplement miRNA regulatory networks and could be applied in miRNA based therapies.

Small activating RNA induced expression of VHL gene in renal cell carcinoma

Recent studies have reported that chemically synthesized double-stranded RNAs (dsRNAs), also known as small activating RNA (saRNAs), can specifically induce gene expression by targeting promoter sequences by a mechanism termed RNA activation (RNAa). In the present study, we designed 4 candidate saRNAs targeting the Von Hippel-Lindau (VHL) gene promoter. Among these saRNAs, dsVHL-821 significantly inhibited cell growth by up-regulating VHL at both the mRNA and protein levels in renal cell carcinoma 769-P cells. Functional analysis showed that dsVHL-821 induced apoptosis by increasing p53, decreasing Bcl-xL, activating caspase 3/7 and poly-ADP-ribose polymerase in a dose-dependent manner. Chromatin immunoprecipitation analysis revealed that dsVHL-821 increased the enrichment of Ago2 and RNA polymerase II at the dsVHL-821 target site. In addition, Ago2 depletion significantly suppressed dsVHL-821-induced up-regulation of VHL gene expression and related effects. Single transfection of dsVHL-821 caused long-lasting (14 days) VHL up-regulation. Furthermore, the activation of VHL by dsVHL-821 was accompanied by an increase in dimethylation of histone 3 at lysine 4 (H3K4me2) and acetylation of histone 4 (H4ac) and a decrease in dimethylation of histone 3 at lysine 9 (H3K9me2) and lysine 27 (H3K27me2) in the dsVHL-821 target region. Taken together, these results demonstrate that dsVHL-821, a novel saRNA for VHL, induces the expression of the VHL gene by epigenetic changes, leading to inhibition of cell growth and induction of apoptosis, and suggest that targeted activation of VHL by dsVHL-821 may be explored as a novel treatment of renal cell carcinoma.

Simultaneous dual targeting of Par-4 and G6PD: a promising new approach in cancer therapy? Quintessence of a literature review on survival requirements of tumor cells

The aim of this hypothesis is to propose a new approach in targeted therapy of cancer: The simultaneous, dual targeting of two single molecules, Par-4 and G6PD, rather than inhibition of full-length signaling pathways.

RATIONALE

Targeted inhibition of especially two survival signaling pathways (PI3K/AKT/mTOR and MAPK/ERK) is frequently tried, however, a major breakthrough has not yet been reported. Inhibition of complete pathways naturally goes along with a variety of dose-limiting side effects thus contributing to poor efficacy of the administered drugs. This essay offers a synopsis of relevant studies to support the above mentioned idea-targeting of two single molecules which either are crucial for tumor growth and cancer-cell-survival: on one side, Par-4-activation selectively triggers apoptosis of tumor cells thus reversing their characteristic feature-immortality. On the other side inhibition of G6PD breaks the energy supply of tumor cells, weakens their defence against oxidative stress and thereby enhances the sensitivity of tumor cells to oxidative agents (e.g. chemotherapy). Advantage of the proposed dual Par-4/G6PD-therapy is good tolerability and-especially when administered along with conventional therapy-less frequent emergence of resistance.

Demystifying the mechanistic and functional aspects of p21 gene activation with double-stranded RNAs in human cancer cells

BACKGROUND

The recently identified phenomenon of double-stranded RNA (dsRNA)-mediated gene activation (RNAa) has been studied extensively, as it is present in humans, mice, and Caenorhabditis elegans, suggesting that dsRNA-mediated RNAa is an evolutionarily conserved mechanism. Previous studies have shown that dsP21-322 can induce tumor suppressor gene p21 expression in several human cancer cells. Nonetheless, the role of dsRNAs in the activation of gene expression, including their target molecules and associated key factors, remains poorly understood.

METHODS

Oligonucleotides were used to overexpress dsRNAs and dsControl. Real-time PCR and Western blotting were used to detect corresponding mRNA and protein expression, respectively. Fluorescence microscopy was used to examine the kinetics of dsRNA subcellular distribution. Luciferase reporter assays were performed to verify dsRNA target molecules. Chromatin immunoprecipitation (ChIP) assays were carried out to determine whether histone modification and other associated key factors are involved in saRNA-mediated p21 expression.

RESULTS

We demonstrated that dsRNA-mediated p21 induction in human cell lines is a common phenomenon. This process occurs at the transcriptional level, and the complementary p21 promoter is the intended dsRNA target. Additionally, ChIP assays indicated that p21 activation was accompanied by an increased enrichment of AGO1 and the trimethylation of histone H3K4 at dsRNA-targeted genomic sites.

CONCLUSION

These data systematically reveal the mechanistic and functional aspects of ncRNA-mediated p21 activation in human cancer cells, which may be a useful tool to analyze gene function and aid in the development of novel drug targets for cancer therapeutics.

Small activating RNA upregulates NIS expression: promising potential for hepatocellular carcinoma endoradiotherapy

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Currently, the clinical strategies available for the treatment of HCC remain insufficient for the poor prognosis. Sodium/iodide symporter (NIS)-based radioiodine therapy is proposed as a promising therapeutic strategy for the treatment of HCC. However, it is difficult for HCC cells to trap iodine for the lower expression of NIS. Small activating RNA (saRNA) is a newly identified small double-stranded RNA (dsRNA) that can induce endogenous gene expression by targeting promoter sequences. Here, we designed an saRNA (saRNA-482) that targeted the NIS promoter sequences. In the cultured HepG2 cells and Hep3B cells, the expressions of NIS were upregulated after transfection of saRNA-482. In addition, the uptake of ¹²⁵I increased in the cultured HepG2 and Hep3B cells transfected with saRNA-482. Furthermore, the cell viabilities were significantly inhibited in the saRNA-482-transfected HepG2 and Hep3B cells after ¹³¹I treatment. Meanwhile, the apoptosis of saRNA-482-transfected HepG2 and Hep3B cells significantly increased after ¹³¹I treatment. The results suggest that RNA activation-mediated upregulation of NIS may have an endoradiotherapeutic potential in the treatment of HCC.

miR-6734 Up-Regulates p21 Gene Expression and Induces Cell Cycle Arrest and Apoptosis in Colon Cancer Cells

Recently, microRNAs have been implicated in the regulation of gene expression in terms of both gene silencing and gene activation. Here, we investigated the effects of miR-6734, which has a sequence homology with a specific region of p21WAF1/CIP1 (p21) promoter, on cancer cell growth and the mechanisms involved in this effect. miR-6734 up-regulated p21 expression at both mRNA and protein levels and chromatin immunoprecipitation analysis using biotin-labeled miR-6734 confirmed the association of miR-6734 with p21 promoter. Moreover, miR-6734 inhibited cancer cell growth and induced cell cycle arrest and apoptosis in HCT-116 cells, which was abolished by knockdown of p21. The phosphorylation of Rb and the cleavage of caspase 3 and PARP were suppressed by miR-6734 transfection in HCT-116 cells and these effects were also reversed by p21 knockdown. In addition, miR-6734 transfection caused prolonged induction of p21 gene and modification of histones in p21 promoter, which are typical aspects of a phenomenon referred to as RNA activation (RNAa). Collectively, our results demonstrated that miR-6734 inhibits the growth of colon cancer cells by up-regulating p21 gene expression and subsequent induction of cell cycle arrest and apoptosis, suggesting its role as an important endogenous regulator of cancer cell proliferation and survival.

Small activating RNA binds to the genomic target site in a seed-region-dependent manner

RNA activation (RNAa) is the upregulation of gene expression by small activating RNAs (saRNAs). In order to investigate the mechanism by which saRNAs act in RNAa, we used the progesterone receptor (PR) gene as a model, established a panel of effective saRNAs and assessed the involvement of the sense and antisense strands of saRNA in RNAa. All active saRNAs had their antisense strand effectively incorporated into Ago2, whereas such consistency did not occur for the sense strand. Using a distal hotspot for saRNA targeting at 1.6-kb upstream from the PR transcription start site, we further established that gene activation mediated by saRNA depended on the complementarity of the 5' region of the antisense strand, and that such activity was largely abolished by mutations in this region of the saRNA. We found markedly reduced RNAa effects when we created mutations in the genomic target site of saRNA PR-1611, thus providing evidence that RNAa depends on the integrity of the DNA target. We further demonstrated that this saRNA bound the target site on promoter DNA. These results demonstrated that saRNAs work via an on-site mechanism by binding to target genomic DNA in a seed-region-dependent manner, reminiscent of miRNA-like target recognition.

Upregulation of PAWR by small activating RNAs induces cell apoptosis in human prostate cancer cells

RNA activation (RNAa) is a promising discovery whereby expression of a particular gene can be induced by targeting its promoter using small double-stranded RNAs (dsRNAs) also termed small activating RNAs (saRNAs). We previously reported that several small dsRNAs targeting the PRKC apoptosis WT1 regulator (PAWR) promoter can upregulate PAWR gene expression effectively in human cancer cells. The present study was conducted to evaluate the antitumor potential of PAWR gene induction by these saRNAs in prostate cancer cells. Promisingly, we found that upregulation of PAWR by saRNA inhibited the growth of prostate cancer cells by inducing cell apoptosis which was related to inactivation of the NF-κB and Akt pathways. The decreased anti‑apoptotic protein Bcl-2 and activation of the caspase cascade and poly(ADP-ribose) polymerase (PARP) also supported the efficacy of the treatment. Overall, these data suggest that activation of PAWR by saRNA may have a therapeutic benefit for prostate and other types of cancer.

Differential Regulation of Vascular Endothelial Growth Factors by Promoter-targeted shRNAs

Vascular endothelial growth factors (VEGFs) and their receptors (VEGF-R) are central regulators of vasculogenesis, angiogenesis, and lymphangiogenesis. They contribute to many vascular-related pathologies, and hence VEGF-targeted therapies have been widely sought after. In this study, the authors investigated the ability of promoter-targeted small hairpin RNAs (shRNAs) to regulate VEGF-A, VEGF-C and VEGF-R1 in different cell lines. The authors identified shRNAs that can upregulate hVEGF-C at both the mRNA and protein levels, and differentially regulate hVEGF-A depending on the cell type. Likewise, the authors identified shRNA that downregulated VEGF-R1 gene expression. Hence, promoter-targeted shRNAs can affect endogenous gene expression not only bimodally, but also differentially in a cell-type specific manner. Importantly, all three genes tested were regulated by at least one shRNA, supporting the idea that nuclear RNA interference is a widespread phenomenon. The level of regulation across the panel of shRNAs varied maximally from a 2.2-fold increase to a 4-fold decrease. This level of change should be useful in fine-tuning and modulating target gene expression, which for potent molecules, such as VEGF-A and VEGF-C, can be very beneficial. These promoter-targeted shRNAs may facilitate the design and development of targeted, context-dependent strategies for both pro- and antiangiogenic therapies for the treatment of vascular-related pathologies.

Promoter Targeting RNAs: Unexpected Contributors to the Control of HIV-1 Transcription

In spite of prolonged and intensive treatment with combined antiretroviral therapy (cART), which efficiently suppresses plasma viremia, the integrated provirus of HIV-1 persists in resting memory CD4⁺ T cells as latent infection. Treatment with cART does not substantially reduce the burden of latent infection. Once cART is ceased, HIV-1 replication recrudesces from these reservoirs in the overwhelming majority of patients. There is increasing evidence supporting a role for noncoding RNAs (ncRNA), including microRNAs (miRNAs), antisense (as)RNAs, and short interfering (si)RNA in the regulation of HIV-1 transcription. This appears to be mediated by interaction with the HIV-1 promoter region. Viral miRNAs have the potential to act as positive or negative regulators of HIV transcription. Moreover, inhibition of virally encoded long-asRNA can induce positive transcriptional regulation, while antisense strands of siRNA targeting the NF-κB region suppress viral transcription. An in-depth understanding of the interaction between ncRNAs and the HIV-1 U3 promoter region may lead to new approaches for the control of HIV reservoirs. This review focuses on promoter associated ncRNAs, with particular emphasis on their role in determining whether HIV-1 establishes active or latent infection.

RNA activation: promise as a new weapon against cancer

RNA activation (RNAa) is a novel mechanism in which short RNA duplexes, referred to as small activating RNAs (saRNAs), enable sequence-specific gene activation capable of lasting up to 2 weeks. RNAa was named in contrast to RNA interference (RNAi). Although many mysteries remain, increasing evidence demonstrates that RNAa not only provides a novel mechanism for the study of gene function and regulation, but also holds exciting potential for clinical translation to therapeutic modality against cancers. In this review, we will focus on the potential applications of RNAa in cancer studies and therapeutics.

The varied roles of nuclear argonaute-small RNA complexes and avenues for therapy

Argonautes are highly conserved proteins found in almost all eukaryotes and some bacteria and archaea. In humans, there are eight argonaute proteins evenly distributed across two clades, the Ago clade (AGO1-4) and the Piwi clade (PIWIL1-4). The function of Ago proteins is best characterized by their role in RNA interference (RNAi) and cytoplasmic post-transcriptional gene silencing (PTGS) – which involves the loading of siRNA or miRNA into argonaute to direct silencing of genes at the posttranscriptional or translational level. However, nuclear-localized, as opposed to cytoplasmic, argonaute-small RNA complexes may also orchestrate the mechanistically very different process of transcriptional gene silencing, which results in prevention of transcription from a gene locus by the formation of silent chromatin domains. More recently, the role of argonaute in other aspects of epigenetic regulation of chromatin, alternative splicing and DNA repair is emerging. This review focuses on the activity of nuclear-localized short RNA-argonaute complexes in a mammalian setting and discusses recent in vivo studies employing nuclear-directed sRNA for therapeutic interventions. These studies heed the potential development of RNA-based drugs which induce epigenetic changes in the cell.

Upregulation of RECK gene expression by small double-stranded RNA targeting the promoter region

Recent studies have demonstrated that small double-stranded RNAs (dsRNAs) complementary to the promoter region of target genes enhance the expression of those genes following transfection into cells. Here we show that expression of the matrix metalloproteinase (MMP) inhibitor RECK is activated in the cultured tumor cell lines by transfection with dsRNA complementary to the promoter of the RECK gene, leading to suppression of the expression of MMPs and it inhibited tumor cell invasion. These results support the suggestion that dsRNA complementary to the promoter region of tumor suppressor genes would have potential as a novel antitumor agent.

RNA-mediated gene activation

The regulation of gene expression by non-coding RNAs (ncRNAs) has become a new paradigm in biology. RNA-mediated gene silencing pathways have been studied extensively, revealing diverse epigenetic and posttranscriptional mechanisms. In contrast, the roles of ncRNAs in activating gene expression remains poorly understood. In this review, we summarize the current knowledge of gene activation by small RNAs, long non-coding RNAs, and enhancer-derived RNAs, with an emphasis on epigenetic mechanisms.