Expression and cellular localization of microRNA-29b and RAX, an activator of the RNA-dependent protein kinase (PKR), in the retina of streptozotocin-induced diabetic rats.

PURPOSE: The apoptosis of retinal neurons plays a critical role in the pathogenesis of diabetic retinopathy (DR), but the molecular mechanisms underlying this phenomenon remain unclear. The purpose of this study was to investigate the cellular localization and the expression of microRNA-29b (miR-29b) and its potential target PKR associated protein X (RAX), an activator of the pro-apoptotic RNA-dependent protein kinase (PKR) signaling pathway, in the retina of normal and diabetic rats. METHODS: Retinas were obtained from normal and diabetic rats within 35 days after streptozotocin (STZ) injection. In silico analysis indicated that RAX is a potential target of miR-29b. The cellular localization of miR-29b and RAX was assessed by in situ hybridization and immunofluorescence, respectively. The expression levels of miR-29b and RAX mRNA were evaluated by quantitative reverse transcription PCR (qRT-PCR), and the expression of RAX protein was evaluated by western blot. A luciferase reporter assay and inhibition of endogenous RAX were performed to confirm whether RAX is a direct target of miR-29b as predicted by the in silico analysis. RESULTS: We found that miR-29b and RAX are localized in the retinal ganglion cells (RGCs) and the cells of the inner nuclear layer (INL) of the retinas from normal and diabetic rats. Thus, the expression of miR-29b and RAX, as assessed in the retina by quantitative RT-PCR, reflects their expression in the RGCs and the cells of the INL. We also revealed that RAX protein is upregulated (more than twofold) at 3, 6, 16, and 22 days and downregulated (70%) at 35 days, whereas miR-29b is upregulated (more than threefold) at 28 and 35 days after STZ injection. We did not confirm the computational prediction that RAX is a direct target of miR-29b. CONCLUSIONS: Our results suggest that RAX expression may be indirectly regulated by miR-29b, and the upregulation of this miRNA at the early stage of STZ-induced diabetes may have a protective effect against the apoptosis of RGCs and cells of the INL by the pro-apoptotic RNA-dependent protein kinase (PKR) signaling pathway.

Differential expression of microRNAs in mouse pain models.

BACKGROUND: MicroRNAs (miRNAs) are short non-coding RNAs that inhibit translation of target genes by binding to their mRNAs. The expression of numerous brain-specific miRNAs with a high degree of temporal and spatial specificity suggests that miRNAs play an important role in gene regulation in health and disease. Here we investigate the time course gene expression profile of miR-1, -16, and -206 in mouse dorsal root ganglion (DRG), and spinal cord dorsal horn under inflammatory and neuropathic pain conditions as well as following acute noxious stimulation. RESULTS: Quantitative real-time polymerase chain reaction analyses showed that the mature form of miR-1, -16 and -206, is expressed in DRG and the dorsal horn of the spinal cord. Moreover, CFA-induced inflammation significantly reduced miRs-1 and -16 expression in DRG whereas miR-206 was downregulated in a time dependent manner. Conversely, in the spinal dorsal horn all three miRNAs monitored were upregulated. After sciatic nerve partial ligation, miR-1 and -206 were downregulated in DRG with no change in the spinal dorsal horn. On the other hand, axotomy increases the relative expression of miR-1, -16, and 206 in a time-dependent fashion while in the dorsal horn there was a significant downregulation of miR-1. Acute noxious stimulation with capsaicin also increased the expression of miR-1 and -16 in DRG cells but, on the other hand, in the spinal dorsal horn only a high dose of capsaicin was able to downregulate miR-206 expression. CONCLUSIONS: Our results indicate that miRNAs may participate in the regulatory mechanisms of genes associated with the pathophysiology of chronic pain as well as the nociceptive processing following acute noxious stimulation. We found substantial evidence that miRNAs are differentially regulated in DRG and the dorsal horn of the spinal cord under different pain states. Therefore, miRNA expression in the nociceptive system shows not only temporal and spatial specificity but is also stimulus-dependent.

Non-coding transcript in T cells (NTT): antisense transcript activates PKR and NF-kappaB in human lymphocytes.

T cell activation is a complex process involving many steps and the role played by the non-protein-coding RNAs (ncRNAs) in this phenomenon is still unclear. The non-coding T cells transcript (NTT) is differentially expressed during human T cells activation, but its function is unknown. Here, we detected a 426 nt NTT transcript by RT-PCR using RNA of human lymphocytes activated with a synthetic peptide of HIV-1. After cloning, the sense and antisense 426 nt NTT transcripts were obtained by in vitro transcription and were sequenced. We found that both transcripts are highly structured and are able to activate PKR. A striking observation was that the antisense 426 nt NTT transcript is significantly more effective in activating PKR than the corresponding sense transcript. The transcription factor NF-kappaB is activated by PKR through phosphorylation and subsequent degradation of its inhibitor I-kappaBbeta. We also found that the antisense 426 nt NTT transcript induces more efficiently the degradation of I-kappaBbeta than the sense transcript. Thus, this study suggests that the role played by NTT in the activation of lymphocytes can be mediated by PKR through NF-kappaB activation. However, the physiological significance of the activity of the antisense 426 nt NTT transcript remains unknown.

Knockdown of PKR expression by RNAi reduces pulmonary metastatic potential of B16-F10 melanoma cells in mice: possible role of NF-kappaB.

It was suggested that PKR may act as a tumor suppressor. However, the results are still controversial. Here, we investigate the effect of PKR-specific short hairpin RNA (shRNA) expressing plasmids on pulmonary metastatic potential of B16-F10 melanoma cells in mice. Levels of both PKR mRNA and PKR protein were only significantly reduced in tumor cells transfected with plasmid-based PKR-specific shRNA. Injection of tumor cells transfected with PKR-specific shRNA expressing plasmid resulted in inhibition (85%) of metastatic nodules compared with control. Our results suggest that this effect is mediated by the transcription factor NF-kappaB. This study does not support the concept of PKR as a tumor suppressor.

PKR activation by a non-coding RNA expressed in lymphocytes of mice bearing B16 melanoma.

In recent years, non-coding RNAs (ncRNAs) have become an exciting area of research. It has been demonstrated that ncRNAs play an important role in the regulation of gene expression in eukaryotic cells. However, little is known about ncRNAs in lymphocytes. In this study, we investigated the presence of ncRNAs in lymphocytes of C57BL/6 mice bearing B16 melanoma by using the differential display reverse transcription-PCR (DD-RT-PCR). PKR is a serine/threonine kinase containing two RNA-binding domains within the N-terminal region. We took advantage of the ability of RNAs to bind PKR in order to identify ncRNAs of lymphocytes activated during tumor development. Thus, RNAs that co-immunoprecipitated with PKR were reversed transcribed, re-amplified, cloned, sequenced and the secondary structure was determined. The ability of transcripts obtained by in vitro transcription to activate PKR was also examined. We detected a highly structured transcript of 220 nt with no open reading frame (ORF) which is able to activate PKR, and it is only expressed in lymphocytes of C57BL/6 mice bearing B16 melanoma. Therefore, the 220 nt transcript may be included in the class of ncRNAs that act by modifying protein activity and our data suggest that regulation of gene expression in activated lymphocytes by this ncRNA could be mediated by PKR through the activation of the transcription factor NF-kappaB.

Activation of the RNA-dependent protein kinase (PKR) of lymphocytes by regulatory RNAs: implications for immunomodulation in HIV infection.

It has been known for decades that exogenous RNAs are able to induce cytotoxic T lymphocytes (CTLs) and immunological reactivity to a wide variety of antigens. The molecular events responsible for these effects remain unclear for more than two decades. It has been decided to revisit this phenomenon in the light of new concepts that are just emerging in Molecular Biology, such as the regulation of gene expression by noncoding RNAs, named regulatory RNAs. The immunological effects observed in lymphocytes treated with RNAs obtained from lymph nodes of immunized animals with different types of antigens including synthetic peptides of the human immunodeficiency virus type 1 (HIV-1) have been investigated. Our recent results showed that regulatory RNAs are involved in this phenomenon, which is due to the activation of the RNA-dependent protein kinase (PKR) by regulatory RNAs with subsequent activation of the transcription factor NF-kappaB. The RNA-dependent protein kinase (PKR) is a serine/threonine kinase and contains two RNA-binding domains (RBD-I and RBD-II) within the N-terminal region. PKR is activated by viral double-stranded RNA (dsRNA) and highly structured single-stranded RNAs. This review will focus on the structure and functions of PKR including its role in HIV-1 infection. Special emphasis will be placed on a regulatory RNA, named p9-RNA, isolated from lymphocytes of animals immunized with the synthetic peptide p9 (pol: 476-484) of HIV-1. It was found that the regulatory p9-RNA induces CTLs and production of IFN-gamma. These findings showed for the first time that transcriptional control of gene expression by a regulatory RNA can be mediated by PKR through the activation of the transcription factor NF-kappaB. A model for the mechanism of action of the regulatory p9-RNA responsible for the production of IFN-gamma is proposed. Elucidating the molecular mechanism of p9-RNA may contribute to determining the rationale for the use of this regulatory RNA as an immunomodulator in HIV-infected patients.

A point mutation in the RNA-binding domain I results in decrease of PKR activation in acute lymphoblastic leukemia.

RNA-dependent protein kinase (PKR) mediates the antiviral activity of interferon and also has implications in cell growth, differentiation, and apoptosis. On the other hand, the tumor suppressor function of PKR is still controversial. PKR is a serine/threonine kinase that contains two RNA-binding domains (RBD-I and RBD-II) and RBD-I is critical for its activation. Site-directed mutagenesis studies indicated that a single amino acid substitution in RBD-I is sufficient to abolish the interaction of human PKR with RNA. Also, PKR mutants that are unable to bind RNA are inactive in vitro and have no antiproliferative activity in vivo. There have been no reports of mutations in the RNA-binding domains of PKR of tumor cells taken directly from patients. We investigated the presence of mutations in the RBD-I and RBD-II of PKR gene in children with acute lymphoblastic leukemia (ALL). The RNA extracted from bone marrow samples of 15 patients with ALL (5 patients T-lineage; 10 patients B-lineage) was used for to synthesize cDNA and amplify the sequences corresponding to RBD-I and RBD-II. The PCR products were subsequently cloned and sequenced. A point mutation was detected in the RBD-I of PKR from a patient with ALL of T-cell lineage that is located at cDNA nt 50 A --> G (17 Tyr-->Cys). We also found that activation of a PKR mutant by the polyinosinic acid:polycytidylic acid (poly I:C) is impaired when compared with the wild-type PKR. Additional work is required to elucidate whether this point mutation plays a role in the formation and/or maintenance of leukemic cells. To our knowledge, this study is the first example of detection of a mutation in the RBD-I of PKR gene from tumor cells taken directly from patients.

Regulatory RNA induces the production of IFN-gamma, but not IL-4 in human lymphocytes: role of RNA-dependent protein kinase (PKR) and NF-kappaB.

Previous results with p9-RNA, obtained from lymph nodes of animals immunized with the peptide p9 of HIV-1, suggested that its effects on lymphocytes could be mediated by RNA-dependent protein kinase (PKR). Here we report that p9-RNA activates PKR leading to the degradation of the inhibitor I-kappaB alpha and the concomitant nuclear factor kappa B (NF-kappaB) activation. The fractionation of p9-RNA by affinity chromatography indicates that the poly A(+) p9-RNA is the fraction responsible for PKR activation. We also found that p9-RNA induces the production of interferon-gamma (IFN-gamma), but not interleukin (IL-4) since only IFN-gamma gene promoter contains NF-kappaB binding site. This study provides the first evidence that transcriptional control of gene expression by regulatory RNAs can be mediated by PKR through NF-kappaB activation. A model for the mechanism of action of poly A(+) p9-RNA is proposed.

Evidence for the involvement of the RNA-dependent protein kinase (PKR) in the induction of human cytotoxic T lymphocytes against a synthetic peptide of HIV-1 by regulatory RNA.

Exogenous RNA molecules can be incorporated into eukaryotic cells and can exert a variety of biological effects. We have previously showed that exogenous RNAs obtained from lymphoid organs of animals immunized with synthetic peptides of HIV-1 are able to induce cell-mediated immune responses. In this study, animals were immunized with a synthetic peptide (pol: 476-484) of HIV-1, referred to as p9, which is a cytotoxic T lymphocyte (CTL) epitope. The RNA extracted from the lymphoid organs of animals immunized with p9 was termed p9-RNA. We have demonstrated that p9-RNA is active in inducing human CTL. The p9-RNA was also able to activate the RNA-dependent protein kinase (PKR) of human lymphocytes. The polyA(+) p9-RNA was the fraction responsible for the activation of this protein kinase. We also found that p9-RNA activates the transcription factor nuclear kappa B (NF-kappaB) by inducing the degradation of its inhibitor I-kappaB. Thus, these findings suggest that p9-RNA may act as a regulatory RNA and that the induction of CTL activity by p9-RNA could be mediated by PKR through NF-kappaB activation. It is known that CTL activity plays an important role in host defense against HIV-1 infection. Elucidating the molecular mechanism of p9-RNA could contribute to determining the basis for the use of p9-RNA as an immunomodulator in HIV-infected patients.

Activation of RNA-dependent protein kinase and nuclear factor-kB by regulatory RNA from lipopolysaccharide-stimulated macrophages: implications for cytokine production.

Our previous results showed that L-RNA, extracted from lipopolysaccharide-stimulated macrophages, induces interleukin-1, interleukin-8 and tumor necrosis factor-alpha (TNF-alpha) in resident macrophages. It was demonstrated the promoter of these cytokine genes contain nuclear factor-kB (NF-kappa B) binding sites. We hypothesized that this effect of L-RNA is mediated by RNA-dependent protein kinase (PKR) through NF-kappa B activation. We found that L-RNA activates PKR and induces NF-kappa B activation through degradation of its inhibitor I-kappa B alpha. These data support the idea that L-RNA acts as a regulatory RNA. A model for the mechanism of action of L-RNA is proposed.