采用蛋白组学技术分析质粒介导siRNA的“Off-target”效应

siRNA的"脱靶效应"(off-target effects)是RNA干扰应用研究领域的热点问题.采用蛋白组学技术对质粒介导的siRNA稳定沉默原癌基因c-myc可能存在的"off-target"效应进行初步研究,为siRNA靶向特异性的系统评价奠定理论与实验基础.构建靶向c-myc的siRNA真核表达质粒p-Mat01-1及其错配质粒p-Mis09-1,空质粒pEGFP-C1为对照,并稳定转染MCF-7人乳腺癌细胞.通过RT-PCR和Western印迹分析结果显示p-Mat01-1稳定转染克隆中c-myc/c-MYC的表达降低.采用2-DE及LC-ESI-MS/MS等方法,研究了p-Mat01-1与pEGFP-C1稳定转染克隆的蛋白组表达差异.结果显示,p-Mat01-1稳定转染克隆中有47个c-myc非调控蛋白点表达升高或降低,约占423个随机检测蛋白点的11.1%.这些蛋白涉及细胞骨架、代谢、增殖、信号传导、分子伴侣、氧化还原等多条途径.实验结果表明,质粒介导靶向c-myc的siRNA在MCF-7细胞中存在明显的"off-target"效应,提示在设计siRNA实验及应用研究时应系统考察其靶向特异性.     

siRNA脱靶效应类型与规避策略

小干扰RNAs(small interfere RNAs,siRNAs)能够特异性沉默靶基因,现已广泛应用于阐明基因功能,鉴定药物靶点,开发比目前更有效的治疗药物。然而siRNA脱靶效应(off-target effects,OTEs)导致基因沉默实验中表型效应解释复杂化,引起siRNA治疗毒副作用。与siRNA有关的脱靶效应有microRNA样脱靶效应、免疫刺激、RNAi元件饱和三种类型。综述了siRNA脱靶效应类型及减轻脱靶效应的方法,以增强该技术的实用性。     

Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast

To better understand off-target effects of widely prescribed psychoactive drugs, we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a model system. Because the known human targets of these drugs do not exist in yeast, we could employ the yeast gene deletion collections and parallel fitness profiling to explore potential off-target effects in a genome-wide manner. Among 214 tested, documented psychoactive drugs, we identified 81 compounds that inhibited wild-type yeast growth and were thus selected for genome-wide fitness profiling. Many of these drugs had a propensity to affect multiple cellular functions. The sensitivity profiles of half of the analyzed drugs were enriched for core cellular processes such as secretion, protein folding, RNA processing, and chromatin structure. Interestingly, fluoxetine (Prozac) interfered with establishment of cell polarity, cyproheptadine (Periactin) targeted essential genes with chromatin-remodeling roles, while paroxetine (Paxil) interfered with essential RNA metabolism genes, suggesting potential secondary drug targets. We also found that the more recently developed atypical antipsychotic clozapine (Clozaril) had no fewer off-target effects in yeast than the typical antipsychotics haloperidol (Haldol) and pimozide (Orap). Our results suggest that model organism pharmacogenetic studies provide a rational foundation for understanding the off-target effects of clinically important psychoactive agents and suggest a rational means both for devising compound derivatives with fewer side effects and for tailoring drug treatment to individual patient genotypes.     

Off-target effects of cytidine base editor and adenine base editor:What can we do?

<正>DNA is the blueprint of life,instructing the growth,development,and reproduction of an organism.Genome sequencing uncovers the codes of life,whereas genome editing could rewrite the codes,thus then leads to revolutionary advances in all aspects of life sciences,such as uncovering regulatory     

Carp transferrin can protect spermatozoa against toxic effects of cadmium ions

Cadmium is a widespread heavy metal that enters the aquatic environment and affects many processes involved in fish reproduction such as sperm motility. Fish seminal plasma proteins can protect spermatozoa against toxic effects of heavy metals. The objective of this study was to demonstrate the ability of a major carp seminal plasma protein-transferrin (TF) to bind cadmium ions and to neutralize the toxic effect of cadmium on carp sperm motility. To obtain a high quantity of carp seminal plasma TF necessary for the experiment, immunoaffinity chromatography as a one-step isolation procedure was established. The titration of TF with cadmium ions spectrophotometrically at 247nm revealed that TF binds cadmium ions at only one spectrophotometrically-sensitive binding site, which suggests that TF is capable of neutralizing the cadmium toxic effect. Indeed, the addition of carp TF to carp semen incubated with 50ppm cadmium for 48h led to about a four-times higher percentage of sperm motility (30.3±1.1%) in comparison to samples incubated with only 50ppm cadmium (8.2±5.2%). Similarly, higher values of other parameters of sperm movement measured by a computer-assisted sperm motility analysis system (VSL, VCL and ALH) were observed at the presence of transferrin. In conclusion, our study provides the first evidence that transferrin from carp seminal plasma can protect sperm motility from cadmium toxicity.     

IgG4 can induce an M2-like phenotype in human monocyte-derived macrophages through FcγRI

Antibodies evoke cellular responses through the binding of their Fc region to Fc receptors, most of which contain immunoreceptor tyrosine-based activation motif domains and are thus considered “activating.” However, there is a growing appreciation of these receptors for their ability to deliver an inhibitory signal as well. We previously described one such phenomenon whereby interferon (IFN)γ signaling is inhibited by immune complex signaling through FcγRI. To understand the implications of this in the context of therapeutic antibodies, we assessed individual IgG subclasses to determine their ability to deliver this anti-inflammatory signal in monocyte-derived macrophages. Like IgG1, we found that IgG4 is fully capable of inhibiting IFNγ-mediated events. In addition, F(ab’)2 fragments that interfere with FcγRI signaling reversed this effect. For mAbs developed with either an IgG1 or an IgG4 constant region for indications where inflammation is undesirable, further examination of a potential Fc-dependent contribution to their mechanism of action is warranted.     

Concentrations of copper thought to be toxic to Escherichia coli can induce the viable but nonculturable condition.

We have determined that concentrations of copper considered to be toxic can induce a fraction of a population of Escherichia coli to enter the viable but nonculturable (VBNC) condition. Copper-induced VBNC cells could be resuscitated for up to 2 weeks after entering the VBNC state.     

Senescent phenotype can be reversed by reduction of caveolin status

Hyporesponsiveness to growth factors is one of the fundamental characteristics of senescent cells. We previously reported that the up-regulation of caveolin attenuates the growth factor response and the subsequent downstream signal cascades in senescent human diploid fibroblasts. Therefore, in the present experiment, we investigated the modulation of caveolin status in senescent cells to determine the effect of caveolin on mitogenic signaling efficiency and cell cycling. We reduced the level of caveolin-1 in senescent human diploid fibroblasts using its antisense oligonucleotides and small interfering RNA, and this resulted in the restoration of normal growth factor responses such as the increased phosphorylation of Erk, the nuclear translocation of p-Erk, and the subsequent activation of p-Elk upon epidermal growth factor stimulation. Moreover, DNA synthesis and the re-entry of senescent cells into cell cycle were resumed upon epidermal growth factor stimulation concomitantly with decreases in p53 and p21. Taken together, we conclude that the loss of mitogenic signaling in senescent cells is strongly related to their elevated levels of caveolin-1 and that the functional recovery of senescent cells at least in the terms of growth factor responsiveness and cell cycle entry might be achieved simply by lowering the caveolin level.     

Site-directed RNA editing (SDRE): Off-target effects and their countermeasures

Site-directed RNA editing (SDRE) is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing. The past few years have witnessed a surge of interest in SDRE, with SDRE tools emerging at a breathtaking pace. However, off-target effects of SDRE remain a tough problem, which constitutes a major hurdle to their clinical applications. Here we discuss the diverse strategies for combating off-target editing, drawing lessons from the published studies as well as our ongoing research. Overall, SDRE is still at its infancy, with significant challenges and exciting opportunities ahead.     

Ecto- and arbuscular mycorrhizal symbiosis can induce tolerance to toxic pulses of phosphorus in jarrah (Eucalyptus marginata) seedlings

In common with many plants native to low P soils, jarrah (Eucalyptus marginata) develops toxicity symptoms upon exposure to elevated phosphorus (P). Jarrah plants can establish arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) associations, along with a non-colonizing symbiosis described recently. AM colonization is known to influence the pattern of expression of genes required for P uptake of host plants and our aim was to investigate this phenomenon in relation to P sensitivity. Therefore, we examined the effect on hosts of the presence of AM and ECM fungi in combination with toxic pulses of P and assessed possible correlations between the induced tolerance and the shoot P concentration. The P transport dynamics of AM (Rhizophagus irregularis and Scutellospora calospora), ECM (Scleroderma sp.), non-colonizing symbiosis (Austroboletus occidentalis), dual mycorrhizal (R. irregularis and Scleroderma sp.), and non-mycorrhizal (NM) seedlings were monitored following two pulses of P. The ECM and A. occidentalis associations significantly enhanced the shoot P content of jarrah plants growing under P-deficient conditions. In addition, S. calospora, A. occidentalis, and Scleroderma sp. all stimulated plant growth significantly. All inoculated plants had significantly lower phytotoxicity symptoms compared to NM controls 7 days after addition of an elevated P dose (30 mg P kg^?1 soil). Following exposure to toxicity-inducing levels of P, the shoot P concentration was significantly lower in R. irregularis-inoculated and dually inoculated plants compared to NM controls. Although all inoculated plants had reduced toxicity symptoms and there was a positive linear relationship between rank and shoot P concentration, the protective effect was not necessarily explained by the type of fungal association or the extent of mycorrhizal colonization.     

Iron overload can induce mild copper deficiency

Dietary copper in the U.S. often is lower than that proved insufficient for men and women under controlled conditions. Iron overload can have adverse effects on copper nutriture and can produce cardiac disease in people. The hypothesis that iron can interfere with copper utilization to produce adverse effects related to cardiovascular function was tested.

Rats were fed a diet high in iron and marginal, but not deficient in copper for comparison with similar diets containing iron at the recommended amount. Copper and iron were measured by atomic absorption spectroscopy; cholesterol was measured by fluorescence, ceruloplasmin was measured by oxidase activity and hematology was done by an automated cell counter. When dietary copper was 2.0 mg/kg of diet, high iron decreased (p<0.008) cardiac and hepatic copper, plasma copper and ceruloplasmin, and increased (p<0.02) cardiac weight, hepatic iron and plasma cholesterol. When dietary copper was increased to 2.5 mg/kg, copper in heart and plasma decreased (p<0.04) and hepatic iron increased (p=0.001) with high iron but other effects disappeared. No harmful changes in hematology, such as hematocrit, mean corpuscular volume, etc. were found. High iron increased the dietary copper requirement of the animals. People with iron overload may benefit from copper supplementation, particularly if they habitually consume a diet low in copper.     

CD40 ligation in vivo can induce T cell independent antitumor effects even against immunogenic tumors

Antitumor effects of CD40 ligation appear to involve distinct antitumor effector cells in different experimental models. In this study, we tested whether T cells were required for antitumor effects of agonistic anti-CD40 mAb (alphaCD40) against immunogenic versus poorly immunogenic tumors. Treatment of mice bearing poorly immunogenic B16 melanoma and its more immunogenic variant, B16-hsp72.1, with alphaCD40 resulted in a similar level of tumor growth suppression. Depletion of T cells did not reduce the antitumor effects in these 2 tumor models. To generate antitumor T cell responses, C57BL/6 mice were immunized with irradiated B16-hsp72.1. Treatment of these vaccinated mice challenged with a high dose of B16-hsp72.1 tumor cells with alphaCD40 induced tumor growth suppression, which was reduced by T-cell depletion, demonstrating that T cells were involved in the antitumor effect of alphaCD40. However, immunized mice depleted of T cells and treated with alphaCD40 were still able to suppress tumor growth as compared to tumor growth in immunized, T cell-depleted mice not treated with alphaCD40, suggesting that T cells were not required for the antitumor effect of alphaCD40. To confirm a lack of correlation between tumor immunogenicity and T-cell requirement in antitumor effects of CD40 ligation, we found that alphaCD40 induced tumor growth suppression in nude and SCID/beige mice bearing highly immunogenic tumors such as Meth A sarcoma, suggesting that macrophages may play a role. Indeed, both poorly immunogenic and highly immunogenic tumors were sensitive to in vitro growth inhibition by macrophages from alphaCD40-treated mice. Taken together, our results indicate that antitumor effects induced by alphaCD40, even against immunogenic tumors, can be observed in the absence of T cells and may involve macrophages.     

Changes in photon flux can induce stomatal patchiness

Images of chlorophyll fluorescence were used to detect the occurrence of stomatal patchiness in leaves from eight species under variable photon flux conditions. Pronounced stomatal patchiness was induced within 5–10 min after PFD was changed from intermediate (～450 μmol quanta m^?2 s^?1) to low (～150 μmol quanta m^?2 s^?1) levels. This effect was completely reversible by returning PFD to intermediate levels. The pattern of heterogeneous fluorescence for each leaf was usually similar during repeated applications of medium and low PFD. In three species, stomatal patchiness could only be induced in slightly water-stressed plants. Leaves of more severely water-stressed Xanthium strumarium plants in low air humidity exhibited oscillations in fluorescence that corresponded with oscillatory changes in leaf diffusion conductance for water vapour. Stomatal patchiness was also induced by illuminating dark-adapted leaves with low PFD (below 200–300 μmol quanta m^?2 s^?1). Infiltration of leaves with distilled water showed that heterogeneous chlorophyll fluorescence was caused by changes in stomatal apertures.     

Only noise can induce chaos in discrete populations

Motivated by the papers from Ellner and Turchin 2005 and Dennis et al. 2003 we investigate the possibility to detect chaos in noisy ecological systems. One message of our paper is that if a dynamic model is available and if this model predicts chaotic behaviour, one should consider its discrete-state, noisy version when fitting numerical predictions to observations. We emphasize that deterministic discrete-state models behave periodically, thus only the interaction of these deterministic skeletons with random noise can produce non-regular dynamics. We detect and describe a relatively sharply defined range of the noise (the grey zone) where the gradual transition from periodic to chaotic behaviour happens. This zone, the upper border of which can be predicted analytically, is identified in experimental data as well as in numerical simulations. In the grey zone the global, statistical behaviour will approach the statistics produced by the chaotic, continuous model, and in this sense we claim that noise can produce chaos.     

Gravity can induce epinastic bending of isolated leaves

Abstract Isolated leaves of Plectranthus fruticosus were grown in cubic plastic cuvettes, and were supplied via their cut petioles with nutrient solution and indole-3-acetic acid (10^?6m ). Holes bored in the cuvette walls allowed the petioles to be oriented at approximately 60°, 90° or 120° to the vertical. Growth of the leaves initially oriented at angles of 60° and 90°, which simulated the situation in the intact plant, did not result in epinastic bending of the petiole. Inversion of the leaves (adaxial surface of the petiole downwards) and orientation of the adaxial/abaxial surfaces of the horizontal petiole parallel to the gravity vector, however, yielded strong epinastic bending of the petioles. In the latter case, this bending was not in the direction of the gravity vector (evidence for point (iii), below). Furthermore, epinastic bending occurred, when the isolated leaves were rotated on a clinostat (petioles parallel to the rotation axis or inclined to the rotation axis at an angle of 30°; 3 r.p.m.). Since a possible influence of the shoot was excluded, it is concluded that (i) perception and response are restricted to the leaf, (ii) gravity alone is sufficient to induce epinasty, (iii) a gravitropic component of the response can probably be excluded. The clinostat induced epinasty may not have been caused by nullifying the effect of gravity but due to continuous gravistimulation of the leaf.     

Tensin can induce JNK and p38 activation

Cells organize diverse types of specialized adhesion sites upon attachment to extracellular matrix (ECM) components. One of the physiological roles of such cell-ECM interactions is to initiate and regulate adhesion-mediated signal transduction responses. The association of cells with fibronectin fibrils has been shown to regulate the JNK and p38 signaling pathways. We tested whether tensin, a cytoskeletal component localized to both focal contacts and fibronectin-associated fibrillar adhesions, can induce these signaling pathways. We found that tensin overexpression resulted in activation of both the c-Jun amino-terminal kinase (JNK) and p38 pathways. Tensin-mediated JNK activation was independent of the activities of the small GTP binding proteins Rac and Cdc42, but did depend on SEK, a kinase involved in the JNK pathway. We suggest that tensin may directly activate the JNK and p38 pathways, acting downstream or independent of the activities of the small GTP binding proteins Rac and Cdc42.     

Superinfections can induce evolutionarily stable coexistence of pathogens

Parasites reproduce and are subject to natural selection at several different, but intertwined, levels. In the recent paper, Gilchrist and Coombs (Theor. Popul. Biol. 69:145–153, 2006) relate the between-host transmission in the context of an SI model to the dynamics within a host. They demonstrate that within-host selection may lead to an outcome that differs from the outcome of selection at the host population level. In this paper we combine the two levels of reproduction by considering the possibility of superinfection and study the evolution of the pathogen’s within-host reproduction rate p. We introduce a superinfection function φ = φ(p,q), giving the probability with which pathogens with trait q, upon transmission to a host that is already infected by pathogens with trait p, “take over” the host. We consider three cases according to whether the function q → φ(p,q) (i) has a discontinuity, (ii) is continuous, but not differentiable, or (iii) is differentiable in q = p. We find that in case (i) the within-host selection dominates in the sense that the outcome of evolution at the host population level coincides with the outcome of evolution in a single infected host. In case (iii), it is the transmission to susceptible hosts that dominates the evolution to the extent that the singular strategies are the same as when the possibility of superinfections is ignored. In the biologically most relevant case (ii), both forms of reproduction contribute to the value of a singular trait. We show that when φ is derived from a branching process variant of the submodel for the within-host interaction of pathogens and target cells, the superinfection functions fall under case (ii). We furthermore demonstrate that the superinfection model allows for steady coexistence of pathogen traits at the host population level, both on the ecological, as well as on the evolutionary time scale.