Target mRNA Levels Research Articles

A Pilot Study of Lower Doses of Ibrutinib in Patients (pts) with Chronic Lymphocytic Leukemia (CLL)

A Pilot Study of Lower Doses of Ibrutinib in Patients (pts) with Chronic Lymphocytic Leukemia (CLL)

One Bout of Aerobic Exercise Elicits Alterations in The Expression of Mitochondrial Unfolded Protein Response (UPRmt) Markers in Skeletal Muscle

Muscle contractions during aerobic exercise stimulate molecular pathways to promote the production of new mitochondria, and improve their function. These adaptations translate into improved oxygen consumption and metabolic capacity of skeletal muscle. However, the increased drive for mitochondrial biogenesis during contractile activity causes an accumulation of misfolded proteins, disrupting mitochondrial homeostasis. The action of the UPRmt, a cytoprotective stress response pathway, is required to mitigate the associated proteotoxicity. This protein quality control mechanism favours the transcription of mitochondrial chaperones and proteases to refold and degrade the defective proteins, while inhibiting global protein translation. However, the regulation and activity of the UPRmt in helping skeletal muscle adapt to exercise stress during and after an acute bout of exercise has yet to be determined. Thus, to investigate this, mice were separated into sedentary (SED), acute exercise (AE) and acute exercise with recovery (AER) groups (n=4/group). The exercise consisted of 90-minutes of treadmill running at 15m/min. Tibialis anterior muscles were extracted from the AE groups immediately following exercise and from the AER group 3 hours post-exercise. Total RNA was isolated and mRNA levels were measured using qPCR. In line with previous data, PGC-1α mRNA increased by 50% in the AE group and increased further to 3.4-fold in the AER group. Activating transcription factor 5 (ATF5), an important regulator of UPRmt gene expression, did not change with acute exercise or recovery. ATF4, another transcription factor for stress-responsive genes, was also unchanged at the end of exercise, but was upregulated by 28% in the recovery period. mRNA levels of downstream targets of ATF5, Lon protease (LonP) and chaperones (HSP60 and GRP75) were upregulated by 18%, 24% and 77%, respectively. HSP60 mRNA returned to control levels during recovery, while GRP75 and LonP mRNAs remained elevated in the AER group. Our data indicate that acute exercise influences the expression of genes involved in both mitochondrial biogenesis and those of the UPRmt, contributing to the maintenance of organelle proteostasis in exercised muscle. Investigating the regulatory mechanisms governing this acute mitochondrial stress response is critical, as preservation of cellular function in the face of exercise-induced stress is essential for metabolic adaptations in muscle and thus, for whole-body homeostasis.

Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics.

Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.

Fetal sex modulates placental microRNA expression, potential microRNA-mRNA interactions, and levels of amino acid transporter expression and substrates: INFAT\xa0study subpopulation analysis of n-3 LCPUFA intervention during pregnancy and associations with offspring body composition

BackgroundPreviously, we revealed sexually dimorphic mRNA expression and responsiveness to maternal dietary supplementation with n-3 long-chain polyunsaturated fatty acids (LCPUFA) in placentas from a defined INFAT study subpopulation. Here, we extended these analyses and explored the respective placental microRNA expression, putative microRNA-mRNA interactions, and downstream target processes as well as their associations with INFAT offspring body composition.ResultsWe performed explorative placental microRNA profiling, predicted microRNA-mRNA interactions by bioinformatics, validated placental target microRNAs and their putative targets by RT-qPCR and western blotting, and measured amino acid levels in maternal and offspring cord blood plasma and placenta. microRNA, mRNA, protein, and amino acid levels were associated with each other and with offspring body composition from birth to 5 years of age. Forty-six differentially regulated microRNAs were found. Validations identified differential expression for microRNA-99a (miR-99a) and its predicted target genes mTOR, SLC7A5, encoding L-type amino acid transporter 1 (LAT1), and SLC6A6, encoding taurine transporter (TauT), and their prevailing significant sexually dimorphic regulation. Target mRNA levels were mostly higher in placentas from control male than from female offspring, whereas respective n-3 LCPUFA responsive target upregulation was predominantly found in female placentas, explaining the rather balanced expression levels between the sexes present only in the intervention group. LAT1 and TauT substrates tryptophan and taurine, respectively, were significantly altered in both maternal plasma at 32 weeks’ gestation and cord plasma following intervention, but not in the placenta. Several significant associations were observed for miR-99a, mTOR mRNA, SLC7A5 mRNA, and taurine and tryptophan in maternal and cord plasma with offspring body composition at birth, 1 year, 3 and 5 years of age.ConclusionsOur data suggest that the analyzed targets may be part of a sexually dimorphic molecular regulatory network in the placenta, possibly modulating gene expression per se and/or counteracting n-3 LCPUFA responsive changes, and thereby stabilizing respective placental and fetal amino acid levels. Our data propose placental miR-99, SLC7A5 mRNA, and taurine and tryptophan levels in maternal and fetal plasma as potentially predictive biomarkers for offspring body composition.

Insight into the mechanism of tetrachlorobisphenol A (TCBPA)-induced proliferation of breast cancer cells by GPER-mediated signaling pathways.

Tetrachlorobisphenol A (TCBPA), a chlorinated derivative of bisphenol A, is an endocrine disruptor based on interaction with nuclear estrogen receptor alpha (ERα). However, there is only limited data on the mechanisms through which TCBPA-associated estrogenic activity is related to the membrane G protein-coupled estrogen receptor (GPER) pathway. In this study, three human breast cancer cell lines-MCF-7, SKBR3, and MDA-MB-231cells were used to evaluate whether, as well as how, TCBPA at concentration range of 0.001-50μM affect cell proliferation. The role of GPER signaling in TCBPA-induced cell proliferation was studied by analyzing the protein expression and mRNA levels of relevant signal targets. The results showed that low concentrations of TCBPA significantly induced the proliferation of MCF-7, SKBR3, and MDA-MB-231cells, with MCF-7cells being the most sensitive to TCBPA exposure. Low-concentration TCBPA also upregulated the expression of GPER, CyclinD1, c-Myc, and c-Fos proteins, as well as increased the phosphorylation of extracellular signal-regulated-kinase 1/2 (Erk1/2) and protein kinase B (Akt). Additionally, the mRNA levels of genes associated with estrogen signaling pathways also increased upon exposure to TCBPA. However, the phosphorylation of Erk1/2 and Akt decreased when the cells were treated with GPER inhibitor G15 and phosphatidylinositide 3-kinase (PI3K) inhibitor wortmannin (WM) prior to TCBPA exposure. Besides, the increased proliferation of breast cancer cells induced by TCBPA were also inhibited. In ERα-positive MCF-7cells, TCBPA also upregulated ERα expression, and ERα was found to interact with GPER-mediated signaling. The results indicate that GPER activates the PI3K/Akt and Erk1/2 signal cascades to drive the cell proliferation observed for low concentrations of TCBPA. The presented results suggest a new mechanism by which TCBPA exerts estrogenic action in breast cancer cells, namely, GPER signaling in an ERα-independent manner, and also highlights the potential risks to human health of the usage of TCBPA.

Alcohol induces mitochondrial derangements in alveolar macrophages by upregulating NADPH oxidase 4.

Excessive alcohol users have increased risk of developing respiratory infections in part due to oxidative stress-induced alveolar macrophage (AM) phagocytic dysfunction. Chronic ethanol exposure increases cellular oxidative stress in AMs via upregulation of NADPH oxidase (Nox) 4, and treatment with the peroxisome proliferator-activated receptor gamma (PPARγ) ligand, rosiglitazone, decreases ethanol-induced Nox4. However, the mechanism by which ethanol induces Nox4 expression and the PPARγ ligand reverses this defect has not been elucidated. Since microRNA (miR)-92a has been predicted to target Nox4 for destabilization, we hypothesized that ethanol exposure decreases miR-92a expression and leads to Nox4 upregulation. Previous studies have implicated mitochondrial-derived oxidative stress in AM dysfunction. We further hypothesized that ethanol increases mitochondrial-derived AM oxidative stress and dysfunction via miR-92a, and that treatment with the PPARγ ligand, pioglitazone, could reverse these derangements. To test these hypotheses, a mouse AM cell line, MH-S cells, was exposed to ethanol invitro, and primary AMs were isolated from a mouse model of chronic ethanol consumption to measure Nox4, mitochondrial target mRNA (qRT-PCR) and protein levels (confocal microscopy), mitochondria-derived reactive oxygen species (confocal immunofluorescence), mitochondrial fission (electron microscopy), and mitochondrial bioenergetics (extracellular flux analyzer). Ethanol exposure increased Nox4, enhanced mitochondria-derived oxidative stress, augmented mitochondrial fission, and impaired mitochondrial bioenergetics. Transfection with a miR-92a mimic invitro or pioglitazone treatment invivo diminished Nox4 levels, resulting in improvements in these ethanol-mediated derangements. These findings demonstrate that pioglitazone may provide a novel therapeutic approach to mitigate ethanol-induced AM mitochondrial derangements.

Adiponectin agonist ADP355 ameliorates doxorubicin-induced cardiotoxicity by decreasing cardiomyocyte apoptosis and oxidative stress

Doxorubicin (DOX) is an anthracycline derivative and widely used as an anticancer drug. However, the severe cardiotoxicity of DOX limits its application. ADP355 is an adiponectin-based active peptide with anti-liver fibrosis and atherosclerosis properties. It remains unclear the effects and involved mechanisms of ADP355 in DOX-induced cardiotoxicity. C57BL/6J mice were intraperitoneally injected DOX once a week to induce heart failure while receiving ADP355 treatment daily for 4 weeks. At the end of experiment, blood and heart tissues were collected. We found that ADP355 markedly improved DOX-induced cardiac dysfunction and histopathological damage, and decreased serum creatine kinase, lactate dehydrogenase and hydroxybutyrate dehydrogenase levels. The anti-apoptotic activity of ADP355 was indicated by reduction in TUNEL-positive cells and cleaved caspase-3 expression, along with decreased BCL2-associated X protein/B cell lymphoma 2 (BAX/BCL2) levels in heart tissues. Additionally, ADP355 markedly increased DOX-decreased cell viability by reducing BAX/BCL2, but inhibited reactive oxygen species production in H9c2 cells. Mechanistically, ADP355 attenuated expression of DOX-reduced nuclear factor-erythroid 2-related factor 2 (Nrf2) and superoxide dismutase 2, as well as mRNA levels of Nrf2 downstream targets. Furthermore, ADP355 activated sirtuin 2 and its target genes. In conclusion, we demonstrate that ADP355 alleviates DOX-induced cardiotoxicity by inhibiting myocardial apoptosis and oxidative stress through Nrf2 and sirtuin 2 signaling pathways. These findings suggest that ADP355 can be a promising candidate for the treatment of cardiac dysfunction.

Anorexic action of fusarenon-x in the hypothalamus and intestine

There is a lack of information available on the anorexic action of fusarenon-x (FX), which is a sesquiterpenoid mycotoxin. In this study, we investigated the changes in the hypothalamus and small intestine related to appetite after oral FX exposure. The time-course change of food intake after oral FX exposure (0.5, 1.0, and 2.5 mg/kg bw) in B6C3F1 mice showed that 2.5 mg/kg bw of FX significantly suppressed food intake during 3–6 h compared to the control. Furthermore, the total food intake for 24 h was lower in the group exposed to FX than in the control. The FX exposure (2.5 mg/kg bw for 3 h) significantly increased mRNA levels of anorexic hormones (pro-opiomelanocortin (POMC) and cocaine- and amphetamine-regulated transcription (CART)) without changing the mRNA levels of orexigenic hormones. In addition, FX exposure indicated significantly higher mRNA levels of possible downstream targets of anorexic POMC neurons, such as the melanocortin 4 receptor (MC4R), brain-derived neurotrophic factor (BDNF) and tyrosine kinase receptor B (TrkB), in the hypothalamus compared to the control. FX exposure also significantly increased the mRNA level of inflammatory cytokines (tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β)) and activated nuclear factor-kappa B (NF-κB), which is a regulatory factor for POMC in the hypothalamus. In the intestine, FX exposure did not affect the mRNA level of anorexic peptide YY but significantly elevated that of anorexic cholecystokinin (CCK) and regulatory factors for CCK (calcium-sensing receptor (CaSR), the transient receptor potential ankyrin-1 channel (TRPA1), and transient receptor potential cation channel subfamily M member 5 (TRPM5)). These results suggest that FX sequentially induces inflammatory cytokine expression, NF-κB activation, and POMC expression in the hypothalamus. FX also induces CCK expression in the intestine possibly via induction of CaSR, TRPM5, and TRPA1 expression. These changes will eventually lead to the anorexic action of FX.

MicroRNA-93-5p promotes hepatocellular carcinoma progression via a microRNA-93-5p/MAP3K2/c-Jun positive feedback circuit

Cumulative evidence suggests that microRNAs (miRNAs) promote gene expression in cancers. However, the pathophysiologic relevance of miRNA-mediated RNA activation in hepatocellular carcinoma (HCC) remains to be established. Our previous miRNA expression profiling in seven-paired HCC specimens revealed miR-93-5p as an HCC-related miRNA. In this study, miR-93-5p expression was assessed in HCC tissues and cell lines by quantitative real-time PCR and fluorescence in situ hybridization. The correlation of miR-93-5p expression with survival and clinicopathological features of HCC was determined by statistical analysis. The function and potential mechanism of miR-93-5p in HCC were further investigated by a series of gain- or loss-of-function experiments in vitro and in vivo. We identified that miR-93-5p, overexpressed in HCC specimens and cell lines, leads to poor outcomes in HCC cases and promotes proliferation, migration, and invasion in HCC cell lines. Mechanistically, rather than decreasing target mRNA levels as expected, miR-93-5p binds to the 3'-untranslated region (UTR) of mitogen-activated protein kinase kinase kinase 2 (MAP3K2) to directly upregulate its expression and downstream p38 and c-Jun N-terminal kinase (JNK) pathway, thereby leading to cell cycle progression in HCC. Notably, we also demonstrated that c-Jun, a downstream effector of the JNK pathway, enhances miR-93-5p transcription by targeting its promoter region. Besides, downregulation of miR-93-5p significantly retarded tumor growth, while overexpression of miR-93-5p accelerated tumor growth in the HCC xenograft mouse model. Altogether, we revealed a miR-93-5p/MAP3K2/c-Jun positive feedback loop to promote HCC progression in vivo and in vitro, representing an RNA-activating role of miR-93-5p in HCC development.

Autophagy Upregulation by the TFEB Inducer Trehalose Protects against Oxidative Damage and Cell Death Associated with NRF2 Inhibition in Human RPE Cells.

Trehalose is a natural dietary molecule that has shown antiaging and neuroprotective effects in several animal models of neurodegenerative diseases. The role of trehalose in the management of age-related macular degeneration (AMD) is yet to be investigated and whether trehalose could be a remedy for the treatment of diseases linked to oxidative stress and NRF2 dysregulation. Here, we showed that incubation of human retinal pigment epithelial (RPE) cells with trehalose enhanced the mRNA and protein expressions of TFEB, autophagy genes ATG5 and ATG7, as well as protein expressions of macroautophagy markers, LC3B and p62/SQTM1, and the chaperone-mediated autophagy (CMA) receptor LAMP2. Cathepsin D, a hydrolytic lysosomal enzyme, was also increased by trehalose, indicating higher proteolytic activity. Moreover, trehalose upregulated autophagy flux evident by an increase in the endogenous LC3B level, and accumulation of GFP-LC3B puncta and free GFP fragments in GFP-LC3 – expressing cells in the presence of chloroquine. In addition, the mRNA levels of key molecular targets implicated in RPE damage and AMD, such as vascular endothelial growth factor- (VEGF-) A and heat shock protein 27 (HSP27), were downregulated, whereas NRF2 was upregulated by trehalose. Subsequently, we mimicked in vitro AMD conditions using hydroquinone (HQ) as the oxidative insult on RPE cells and evaluated the cytoprotective effect of trehalose compared to vehicle treatment. HQ depleted NRF2, increased oxidative stress, and reduced the viability of cells, while trehalose pretreatment protected against HQ-induced toxicity. The cytoprotection by trehalose was dependent on autophagy but not NRF2 activation, since autophagy inhibition by shRNA knockdown of ATG5 led to a loss of the protective effect. The results support the transcriptional upregulation of TFEB and autophagy by trehalose and its protection against HQ-induced oxidative damage in RPE cells. Further investigation is, therefore, warranted into the therapeutic value of trehalose in alleviating AMD and retinal diseases associated with impaired NRF2 antioxidant defense.

Intratumoral use of self-delivering RNAi to reprogram the tumor microenvironment and boost the antitumor response.

e15206 Background: Immunotherapy targeting immune checkpoints has shown significant benefit in many cancers. However, systemic delivery can result in severe auto-immune toxicities, the risk increasing with the combination of checkpoint inhibiting antibodies. Local delivery of immunotherapies allows for multiple combination therapies, while potentially preventing significant systemic toxicities. One approach is to use self-delivering RNAi technology, INTASYL™, which has been shown to be safe and effective in clinical applications following local administration. Here we show the use of the INTASYL platform as a checkpoint inhibiting immunotherapy for intratumoral applications, through a series of preclinical in vivo studies. Methods: INTASYL compounds were made against mouse PD-1, TIGIT, PD-L1 and BRD4. INTASYL comprises an asymmetric duplex, a small duplex region (≤ 15 base pairs), a single-stranded phosphorothioate tail and chemical modifications to confer stability resulting in efficient cellular uptake allowing in situ delivery. The efficacy and immunomodulation of these INTASYL compounds was evaluated in the Hepa1-6 and CT26 murine syngeneic tumor models following intratumoral administration. Tumor volumes were recorded throughout the study. Tumor-Infiltrating-Lymphocytes (TILs) were isolated twenty-four hours post the last dose and examined for gene silencing by RT-qPCR. Tumor microenvironment (TME) and T cell activation were analyzed by flow cytometry. Results: Results showed dose-dependent attenuated tumor growth compared to control groups. Relevant changes in the TME included an increase of CD8+ T cells and an increase of activation markers on TILs. Tumor growth reduction correlated with silencing of target mRNA and immune effector cell levels and activation. Conclusions: These studies demonstrate the feasibility of using INTASYL compounds intratumorally to overcome the immunosuppressive TME, resulting in changes in T cell composition and activation, and inhibition of tumor growth. Together, these novel findings support using intratumoral INTASYL as a viable approach to immunotherapy and warrants further investigation in patients.

SUN-646 A Novel Population of FOXO1-Expressing Cells in the Stomach Controls Cell Plasticity by Regulating the Cyclin CCNE1

A promising new therapy for type 1 diabetes is the reprogramming of gut enteroendocrine cells into cells that produce insulin. The mechanism by which gut epithelial cells are converted into cells that make insulin remains unknown. We have previously found that elimination of Foxo1 in neurogenin3 (Ngn3)-expressing cells of the intestine generates glucose-sensing, insulin-producing cells that are capable of reversing streptozotocin-induced diabetes. Others have reported that stomach cells have a similar property when made to express β-cell factors Ngn3, Pdx1, and MafA. Using mice bearing a Foxo1-GFP knock-in allele, we traced Foxo1-expressing cells in the gut to subpopulations of Ngn3+, as well as acid-secreting parietal stomach cells. To study these cells, we established a 2D co-culture method in which primary stomach cells are isolated from mice and cultured with embryonic fibroblasts. Deletion of Foxo1 in this system generated cells immunoreactive for insulin and C-peptide. Interestingly, Foxo1 ablation also altered the abundance of other gastric cell populations, including more parietal cells and decreased expression of stem cell marker, Lgr5. Tissue-specific elimination of Foxo1 in vivo in either Ngn3+ or parietal cells also resulted in the appearance of insulin+ cells, increased parietal cells, and reduced Lgr5 mRNA. To determine how Foxo1 regulated these changes, we used cells isolated from reporter mice that change from red to green after genetic recombination to collect Foxo1-deleted primary stomach cells using FACS. While the mRNA levels of many known Foxo1 targets did not change, cyclin E1 (CCNE1), which regulates G1 to S-phase progression of the cell cycle, was significantly decreased. Conversely, primary stomach cells overexpressing Foxo1 had increased levels of CCNE1. Finally, using ChIP-seq, we found that Foxo1 binds directly to the CCNE promoter in a nutrient-dependent manner. In summary, we show that Foxo1 is expressed in a subpopulation of stomach parietal cells and that it regulates their function through the cell cycle regulator, CCNE1.

Drug Delivery to Various Body Organs via Non-blood Circulatory Pathway

Delivery of nucleic acid therapeutics to target body organs requires injection of nanocarriers into the bloodstream. However, as such nanocarriers would also be delivered to non-target organs, low delivery efficiency to target organs and risk of unexpected effects are clear limitations of this technology. We recently applied iontophoresis (IP) for direct delivery of nucleic acid therapeutics to various organs. IP relies on a weak electric current for noninvasive transdermal drug delivery. We found that IP can deliver hydrophilic macromolecules and nanoparticles into the skin. We previously succeeded in transdermal delivery of siRNA, and subsequent knockdown (70%) of target mRNA levels in the skin via IP of siRNA (Int. J. Pharm., 383, 2010, Kigasawa et al.). Moreover, we found that cell signal activation and cleavage of intercellular junctions are induced by IP (J. Biol. Chem., 289, 2014, Hama et al.). We hypothesized that this phenomenon should be observed in not only skin but also other organs, and subsequently carried out IP of nucleic acid therapeutics to various body organs including liver, pancreas and kidney. This technique resulted in delivery of nucleic acid therapeutics into the various target body organs, and subsequent knockdown of target genes. These results suggest that direct delivery to target body organs via non-blood circulatory pathway is possible. This technology may offer a solution to the various limitations associated with current drug delivery systems (DDS).

Identification of Novel Targets of RBM5 in the Healthy and Injured Brain

The tumor suppressor RNA-binding motif 5 (RBM5) regulates the expression levels and cassette exon-definition (i.e. splicing) of a select set of mRNAs in a tissue-specific manner. Most RBM5-regulated targets were identified in oncological investigations and frequently involve genes which mediate apoptotic cell death. Little is known about the role of RBM5 in the brain. Also, it is unclear if a brain injury may be required to detect RBM5 mediated effects on pro-apoptotic genes due to their low expression levels in the healthy adult CNS at baseline. Conditional/floxed (brain-specific) gene deleter mice were generated to elucidate CNS-specific RBM5 mRNA targets. Male/female mice were subjected to a severe controlled cortical impact (CCI) traumatic brain injury (TBI) in order to increase the background expression of pro-death mRNAs and facilitate testing of the hypothesis that RBM5 inhibition decreases post-injury upregulation of caspases/FAS in the CNS. As expected, a CCI increased caspases/FAS mRNA in the injured cortex. RBM5 KO did not affect their levels or splicing. Surprisingly, KO increased the mRNA levels of novel targets including casein kinase 2 alpha prime interacting protein (Csnka2ip/CKT2) – a gene not thought to be expressed in the brain, contrary to findings here. Twenty-two unique splicing events were also detected in KOs including increased block-inclusion of cassette exons 20–22 in regulating synaptic membrane exocytosis 2 (Rims2). In conclusion, here we used genome-wide transcriptomic analysis on healthy and injured RBM5 KO mouse brain tissue to elucidate the first known gene targets of this enigmatic RBP in this CNS.

Differential inhibition of target gene expression by human microRNAs

microRNA (miRNA) target genes are commonly computationally predicted, yet how dependable predictions are remains unclear, as most predicted target genes have not been rigorously tested experimentally. In addition, the degree to which a miRNA differentially inhibits the expression of its targets is underappreciated. We selected human miR‐1, miR‐122, and miR‐124 as representatives to investigate the reliability of miRNA target predictions and to examine how miRNAs suppress their target genes. We first constructed target gene reporter libraries for the miRNAs based on three prediction programs: TargetScan, miRanda, and PicTar, and used reporter assays in cell cultures to directly evaluate whether as well as how strongly a predicted target gene is repressed by its cognate miRNA. We found that all three programs have approximately 72–85% success rates in predicting genuine miRNA targets, and that miRNAs inhibit different targets to various degrees. We then performed statistical and correlation analyses to examine how well parameters offered by the online programs and features in target mRNAs might predict the degrees of repression by miRNAs. To show that endogenous miRNAs act through the same mechanism, we correlated our reporter assay results with publically available mRNA expression data in vivo. Overexpression of miR‐1, miR‐122, or miR‐124 further led to differential reduction of target mRNA levels in cell cultures. Our studies systematically investigated hundreds of miRNA target genes, shed light onto the performance of miRNA target gene prediction programs, and suggested a new mechanism by which differential target repression by miRNAs regulates gene expression in vivo.Support or Funding InformationThis work was supported in part by the National Natural Science Foundation of China [grant number 31570843].

4EHP and GIGYF1/2 Mediate Translation-Coupled Messenger RNA Decay

Current models of mRNA turnover indicate that cytoplasmic degradation is coupled with translation. However, our understanding of the molecular events that coordinate ribosome transit with the mRNA decay machinery is still limited. Here, we show that the 4EHP–GIGYF1/2 complexes trigger co-translational mRNA decay as a result of perturbed elongation. Human cells lacking 4EHP and GIGYF1/2 proteins accumulate transcripts known to be degraded in a translation-dependent manner or with prominent ribosome pausing. These include among others, mRNAs encoding secretory and membrane-bound proteins or α- and β-tubulin subunits. In addition, 4EHP–GIGYF1/2 complexes fail to reduce target mRNA levels in the absence of ribosome stalling or upon disruption of their interaction with the mRNA cap structure, DDX6 or GYF domain-associated factors. Our studies reveal how a repressor complex linked to neurological disorders minimizes the protein output of a subset of mRNAs.

MicroRNAs Cause Accelerated Decay of Short-Tailed Target mRNAs.

MicroRNAs (miRNAs) specify the recruitment of deadenylases to mRNA targets. Despite this recruitment, we find that miRNAs have almost no effect on steady-state poly(A)-tail lengths of their targets in mouse fibroblasts, which motivates the acquisition of pre-steady-state measurements of the effects of miRNAs on tail lengths, mRNA levels, and translational efficiencies. Effects on translational efficiency are minimal compared to effects on mRNA levels, even for newly transcribed target mRNAs. Effects on target mRNA levels accumulate as the mRNA population approaches steady state, whereas effects on tail lengths peak for recently transcribed target mRNAs and then subside. Computational modeling of this phenomenon reveals that miRNAs cause not only accelerated deadenylation of their targets but also accelerated decay of short-tailed target molecules. This unanticipated effect of miRNAs largely prevents short-tailed target mRNAs from accumulating despite accelerated target deadenylation. The net result is a nearly imperceptible change to the steady-state tail-length distribution of targeted mRNAs.

Functional characterization of one sex pheromone receptor (AlucOR4) in Apolygus lucorum (Meyer-Dür)

Traps baited with female-produced sex pheromones have been very effective in the monitoring and management of mirid bugs in numerous field trials. However, none of the target odorant receptors for sex pheromone components in Apolygus lucorum have been identified. Here, we identified one candidate sex pheromone receptor, AlucOR4, from A. lucorum. Quantitative real-time PCR (qPCR) analysis revealed that AlucOR4 was antennae-enriched and male-biased in adult A. lucorum. Xenopus oocyte expression system assays demonstrated that AlucOR4/AlucOrco was sensitive to two major sex pheromone constituents and exhibited high sensitivity to (E)-2-hexenyl butyrate (E2HB) and lower sensitivity to hexyl butyrate (HB). The expression level of target mRNA was significantly reduced (>80%) in dsAlucOR4-injected bugs after five days. The electroantennogram (EAG) responses of male antennae to E2HB and HB were also reduced significantly (~40%). Our findings suggest that AlucOR4 is essential to sex pheromone perception in A. lucorum.

Design of curdlan-based pH-sensitive polymers with endosome buffering functionality for siRNA delivery

Developing nucleic acid-based tools to control disease-relevant gene expression in human disorders, such as siRNAs, opens up potential opportunities for therapeutics. Because of their high molecular weight and polyanionic nature, synthetic siRNAs fail to cross biological membranes by passive diffusion and therefore, generally require transmembrane siRNA delivery technologies to access the cytoplasm of target cells. To create a biocompatible siRNA delivery agent, we chemically modified natural polysaccharide curdlan derivative 6AC-100 in a regioselective manner to introduce different ratios of imidazole rings in the amino units (denoted as Curimi) and evaluated their siRNA binding ability, cytotoxicity, endosome buffering capacity and siRNA transfection efficiency. The novel curdlan based Curimi polymers formed nanoparticles with siRNA at pH 7.4 in range of 85–105 nm and their size distribution increased along with decreasing pH condition. The zeta potential increased by lowering pH value as well. Curimi polymers showed lower toxicity and higher buffering capacity compared to 6AC-100, and efficiently delivered siRNA against to PLK1 into cancer cells, and subsequently, significantly inhibited target mRNA level. Our result suggested that novel curdlan based Curimi polymers may be used as efficient siRNA carrier for cancer therapy.

CARF, As An Oncogene, Promotes Colorectal Cancer Stemness By Activating ERBB Signaling Pathway.

IntroductionThe role of CARF, a calcium-responsive transcription factor, in colorectal cancer initiation and development is still unknown. Here, we report that CARF promotes colorectal cancer stemness through ERBB signaling pathway.Materials and methodsBoth colorectal cancer cell lines and primary cells were used in this study. The levels of target mRNA and protein in the cells were examined by qRT-PCR and Western blot. Gene manipulation was achieved by the lentivirus delivery system. Luciferase reporter gene assay was employed to analyze the transcriptional activity of the promoter. ChIP assay was performed for the examination of the binding between CARF and the promoters of MAPK8 and JUN. Kaplan-Meier survival curve was generated by the R2 program. Correlation analysis was performed using Spearman correlation analysis.ResultsAberrant upregulation of CARF has been found in tumor tissues of colorectal cancer patients and associated with poor prognosis. Ectopic expression of CARF promoted the sphere-formation activities, as well as the expression of stem cell markers in colorectal cancer cells and knockdown of CARF, inhibited these activities. The mechanistic analysis showed that CARF directly binds to the promoter of MAPK8 and JUN, promotes the expression of MAPK8 and JUN, activates the ERBB signaling pathway, and thereby promotes the maintenance of the stemness in colorectal cancer cells.ConclusionCARF, as an oncogene, promotes colorectal cancer stemness by activating ERBB signaling pathway. The ERBB signaling pathway that serves as the main downstream effector of CARF could be an efficient drug target for colorectal cancer caused by aberrant expression of CARF.