整合分析多组学数据筛选疾病靶点的精准医学策略

随着高通量测序技术的不断发展与完善,对于不同层次和类型的生物组学数据的获取及分析方法也日趋成熟与完善。基于单组学数据的疾病研究已经发现了诸多新的疾病相关因子,而整合多组学数据研究疾病靶点的工作方兴未艾。生命体是一个复杂的调控系统,疾病的发生与发展涉及基因变异、表观遗传改变、基因表达异常以及信号通路紊乱等诸多层次的复杂调控机制,利用单一组学数据分析致病因子的局限性愈发显著。通过对多种层次和来源的高通量组学数据的整合分析,系统地研究临床发病机理、确定最佳疾病靶点已经成为精准医学研究的重要发展方向,将为疾病研究提供新的思路,并对疾病的早期诊断、个体化治疗和指导用药等提供新的理论依据。本文详细介绍了基因组、转录组和表观组等系统组学研究在疾病靶点筛选方面出现的新技术手段和研究进展,并对它们之间的整合分析新策略和优势进行了讨论。     

Making the most of 'omics' for crop breeding

Adoption of new breeding technologies is likely to underpin future gains in crop productivity. The rapid advances in 'omics' technologies provide an opportunity to generate new datasets for crop species. Integration of genome and functional omics data with genetic and phenotypic information is leading to the identification of genes and pathways responsible for important agronomic phenotypes. In addition, high-throughput genotyping technologies enable the screening of large germplasm collections to identify novel alleles from diverse sources, thus offering a major expansion in the variation available for breeding. In this review, we discuss these advances, which have opened the door to new techniques for construction and screening of breeding populations, to increase ultimately the efficiency of selection and accelerate the rates of genetic gain.     

Metabolomics and its application to studying metal toxicity

Here we explain the omics approach of metabolomics and how it can be applied to study a physiological response to toxic metal exposure. This review aims to educate the metallomics field to the tool of metabolomics. Metabolomics is becoming an increasingly used tool to compare natural and challenged states of various organisms, from disease states in humans to toxin exposure to environmental systems. This approach is key to understanding and identifying the cellular or biochemical targets of metals and the underlying physiological response. Metabolomics steps are described and overviews of its application to metal toxicity to organisms are given. As this approach is very new there are yet only a small number of total studies and therefore only a brief overview of some metal metabolomics studies is described. A frank critical evaluation of the approach is given to provide newcomers to the method a clear idea of the challenges and the rewards of applying metabolomics to their research.     

Invitrogen & HUPO enter partnership

Neuroblastoma (NB) is one of the most common solid tumors of childhood and displays a remarkable diversity in both biologic characteristics and clinical outcomes. Availability of high-throughput ‘omics technologies and their subsequent application towards oncology has provided insight into the complex pathways of tumor formation and progression. Investigation of NB ‘omics profiles may better define tumor behavior and provide targeted therapy with the goal of improving outcomes in patients with high-risk disease. Utilization of these technologies in NB has already led to advances in classification and risk stratification. The gradual emergence of NB-directed proteomics adds a layer of intricacy to the analysis of biologic organization but may ultimately provide a better comprehension of this complex disease. In this review, we cite specific examples of how NB-directed proteomics has provided information regarding novel biomarkers and possible therapeutic targets. We finish by examining the impact of high-throughput ‘omics in the field of NB and speculate on how these emerging technologies may further be incorporated into the discipline.     

Autophagy regulation by inorganic,organic, and organic/inorganic hybrid nanoparticles: Organelle damage,regulation factors,and potential pathways

The rapid development of nanotechnology requires a more thorough understanding of the potential health effects caused by nanoparticles (NPs). As a programmed cell death, autophagy is one of the biological effects induced by NPs, which maintain intracellular homeostasis by degrading damaged organelles and removing aggregates of defective proteins through lysosomes. Currently, autophagy has been shown to be associated with the development of several diseases. A significant number of research have demonstrated that most NPs can regulate autophagy, and their regulation of autophagy is divided into induction and blockade. Studying the autophagy regulation by NPs will facilitate a more comprehensive understanding of the toxicity of NPs. In this review, we will illustrate the effects of different types of NPs on autophagy, including inorganic NPs, organic NPs, and organic/inorganic hybrid NPs. The potential mechanisms by which NPs regulate autophagy are highlighted, including organelle damage, oxidative stress, inducible factors, and multiple signaling pathways. In addition, we list the factors influencing NPs-regulated autophagy. This review may provide basic information for the safety assessment of NPs.     

黑曲霉组学研究进展

黑曲霉作为重要的工业发酵菌株,被广泛用于多种有机酸和工业用酶的生产。随着组学技术的日益发展和成熟,黑曲霉的基因组、转录组、蛋白质组、代谢组等组学数据不断增长,宣告着黑曲霉生物过程研究大数据时代的到来。从单一组学的数据分析、多组学的比较到以基因组代谢网络模型为中心的多组学整合研究,人们对黑曲霉高效生产机制的理解不断深入和系统,这为通过遗传改造和过程调控对菌株的生产性能进行理性的全局优化提供了可能。本文回顾和总结了近年来黑曲霉的组学研究进展,并提出黑曲霉组学研究未来的发展方向。     

Impact of labile metal nanoparticles on cellular homeostasis. Current developments in imaging,synthesis and applications

BackgroundThe use of nanomaterials is constantly increasing in electronics, cosmetics, food additives, and is emerging in advanced biomedical applications such as theranostics, bio-imaging and therapeutics. However their safety raises concerns and requires appropriate methods to analyze their fate in vivo.Scope of reviewIn this review, we describe the current knowledge about the toxicity of labile metal (ZnO, CuO and Ag) nanoparticles (NPs) both at the organism and cellular levels, and describe the pathways that are triggered to maintain cellular homeostasis. We also describe advanced elemental imaging approaches to analyze intracellular NP fate. Finally, we open the discussion by presenting recent developments in terms of synthesis and applications of Ag and CuO NPs.Major conclusionsLabile metal nanoparticles (MeNPs) release metal ions that trigger a cellular response involving biomolecules binding to the ions followed by regulation of the redox balance. In addition, specific mechanisms are set up by the cell in response to physiological ions such as Cu(I) and Zn(II). Among all types of NPs, labile MeNPs induce the strongest inflammatory responses which are most probably due to the combined effects of the NPs and of its released ions. Interestingly, recent developments in imaging technologies enable the intracellular visualization of both the NPs and their ions and promise new insights into nanoparticle fate and toxicity.General significanceThe exponential use of nanotechnologies associated with the difficulties of assessing their impact on health and the environment has prompted scientists to develop novel methodologies to characterize these nanoobjects in a biological context.     

Leveraging algal omics to reveal potential targets for augmenting TAG accumulation

Ongoing global efforts to commercialize microalgal biofuels have expedited the use of multi-omics techniques to gain insights into lipid biosynthetic pathways. Functional genomics analyses have recently been employed to complement existing sequence-level omics studies, shedding light on the dynamics of lipid synthesis and its interplay with other cellular metabolic pathways, thus revealing possible targets for metabolic engineering. Here, we review the current status of algal omics studies to reveal potential targets to augment TAG accumulation in various microalgae. This review specifically aims to examine and catalog systems level data related to stress-induced TAG accumulation in oleaginous microalgae and inform future metabolic engineering strategies to develop strains with enhanced bioproductivity, which could pave a path for sustainable green energy.     

纳米氧化锌和接种丛枝菌根真菌对大豆生长及营养吸收的影响

纳米氧化锌是应用最广的人工纳米颗粒(nanoparticles,NPs)之一,具有一定生物毒性。丛枝菌根(arbuscular mycorrhizal,AM)真菌能与陆地上80%以上的高等植物形成丛枝菌根共生体,并能改善宿主植物矿质营养,提高其抗逆性。然而纳米ZnO与丛枝菌根的关系尚不清楚。通过温室沙培盆栽试验,研究了施加不同水平纳米ZnO(0、500、1000、2000、3000 mg/kg)和接种AM真菌Acaulospora mellea对大豆生长及营养状况的影响。结果表明,3000 mg/kg的纳米ZnO显著抑制大豆植株生长,表现出植物毒性,在其他水平时没有显著影响。纳米ZnO在施加水平500、1000 mg/kg时没有抑制AM真菌对大豆根系的侵染,但是高施加水平(2000 mg/kg)时对AM真菌产生毒害,几乎完全抑制大豆根系菌根侵染。接种AM真菌仅在500 mg/kg纳米ZnO时显著促进大豆生长,增加大豆植株对P、K、N的吸收,降低根系Zn含量。纳米ZnO可能会持续释放锌离子,并抑制大豆根系对矿质营养元素的吸收,从而产生生物毒性,而AM真菌与大豆根系的共生可起到有益作用。     

Mechanisms of Toxicity of Ag Nanoparticles in Comparison to Bulk and Ionic Ag on Mussel Hemocytes and Gill Cells

Silver nanoparticles (Ag NPs) are increasingly used in many products and are expected to end up in the aquatic environment. Mussels have been proposed as marine model species to evaluate NP toxicity in vitro. The objective of this work was to assess the mechanisms of toxicity of Ag NPs on mussel hemocytes and gill cells, in comparison to ionic and bulk Ag. Firstly, cytotoxicity of commercial and maltose stabilized Ag NPs was screened in parallel with the ionic and bulk forms at a wide range of concentrations in isolated mussel cells using cell viability assays. Toxicity of maltose alone was also tested. LC50 values were calculated and the most toxic Ag NPs tested were selected for a second step where sublethal concentrations of each Ag form were tested using a wide array of mechanistic tests in both cell types. Maltose-stabilized Ag NPs showed size-dependent cytotoxicity, smaller (20 nm) NPs being more toxic than larger (40 and 100 nm) NPs. Maltose alone provoked minor effects on cell viability. Ionic Ag was the most cytotoxic Ag form tested whereas bulk Ag showed similar cytotoxicity to the commercial Ag NPs. Main mechanisms of action of Ag NPs involved oxidative stress and genotoxicity in the two cell types, activation of lysosomal AcP activity, disruption of actin cytoskeleton and stimulation of phagocytosis in hemocytes and increase of MXR transport activity and inhibition of Na-K-ATPase in gill cells. Similar effects were observed after exposure to ionic and bulk Ag in the two cell types, although generally effects were more marked for the ionic form. In conclusion, results suggest that most observed responses were due at least in part to dissolved Ag.     

Carbon nanotubes,but not spherical nanoparticles,block autophagy by a shape-related targeting of lysosomes in murine macrophages

Nanoparticles (NPs) can be toxic, depending on their physico-chemical characteristics. Macroautophagy/autophagy could represent a potential underlying mechanism of this toxicity. We therefore set up a study aimed to characterize in depth the effects, on autophagy, of macrophage exposure to NPs, with a particular attention paid to the role of NP physico-chemical characteristics (specifically chemical composition, shape, size, length, crystal phase, and/or surface properties). We demonstrate that exposure to carbon nanotubes (CNT) but not to spherical NPs leads to the blockage of the autophagic flux. We further identified lysosomal dysfunction, in association with the downregulation of SNAPIN expression, as the underlying mechanism responsible for the CNT-induced autophagy blockade. These results identify for the first time the shape as a major determinant of the interaction of NPs with the autophagy pathway. Moreover, identifying the lysosomes and SNAPIN as primary targets of MWCNT toxicity opens new directions in the interpretation and understanding of nanomaterial toxicity.     

硫化镉纳米粒子对原核生物的毒理作用

硫化镉纳米粒子（cadmium sulfide nanoparticles,CdS NPs）是一种重要的半导体,具有突出的光电特性、可调带隙和化学稳定性,在分析化学、生物医学、荧光成像和生物传感器等方面具有潜在应用价值。生物合成CdS NPs具有可控、低成本、环境友好等优势而被广泛研究。然而CdS NPs本身兼具纳米材料毒性及重金属硫化物毒性,其对原核微生物的毒性研究受到广泛关注。本文以大肠杆菌为例,对CdS NPs在原核生物细胞内的毒性机理研究进展进行了综述,包括CdS NPs的生物合成机制、CdS NPs对大肠杆菌的毒害作用以及大肠杆菌对该毒害作用的防御机制,着重论述了细菌在合成CdS NPs过程中Cd²⁺及CdS对合成细菌本身的毒理作用及该细菌所产生的相应应激机制。本文旨在更好、更全面地评估CdS NPs的毒性,促进抗CdS NPs的原核生物在相关领域的发展和应用。     

Cytotoxicity,permeability, and inflammation of metal oxide nanoparticles in human cardiac microvascular endothelial cells

Wide applications and extreme potential of metal oxide nanoparticles (NPs) increase occupational and public exposure and may yield extraordinary hazards for human health. Exposure to NPs has a risk for dysfunction of the vascular endothelial cells. The objective of this study was to assess the cytotoxicity of six metal oxide NPs to human cardiac microvascular endothelial cells (HCMECs) in vitro. Metal oxide NPs used in this study included zinc oxide (ZnO), iron(III) oxide (Fe₂O₃), iron(II,III) oxide (Fe₃O₄), magnesium oxide (MgO), aluminum oxide (Al₂O₃), and copper(II) oxide (CuO). The cell viability, membrane leakage of lactate dehydrogenase, intracellular reactive oxygen species, permeability of plasma membrane, and expression of inflammatory markers vascular cell adhesion molecule-1, intercellular adhesion molecule-1, macrophage cationic peptide-1, and interleukin-8 in HCMECs were assessed under controlled and exposed conditions (12–24 h and 0.001–100 μg/ml of exposure). The results indicated that Fe₂O₃, Fe₃O₄, and Al₂O₃ NPs did not have significant effects on cytotoxicity, permeability, and inflammation response in HCMECs at any of the concentrations tested. ZnO, CuO, and MgO NPs produced the cytotoxicity at the concentration-dependent and time-dependent manner, and elicited the permeability and inflammation response in HCMECs. These results demonstrated that cytotoxicity, permeability, and inflammation in vascular endothelial cells following exposure to metal oxide nanoparticles depended on particle composition, concentration, and exposure time.     

Exposure to Cobalt Causes Transcriptomic and Proteomic Changes in Two Rat Liver Derived Cell Lines

Cobalt is a transition group metal present in trace amounts in the human diet, but in larger doses it can be acutely toxic or cause adverse health effects in chronic exposures. Its use in many industrial processes and alloys worldwide presents opportunities for occupational exposures, including military personnel. While the toxic effects of cobalt have been widely studied, the exact mechanisms of toxicity remain unclear. In order to further elucidate these mechanisms and identify potential biomarkers of exposure or effect, we exposed two rat liver-derived cell lines, H4-II-E-C3 and MH1C1, to two concentrations of cobalt chloride. We examined changes in gene expression using DNA microarrays in both cell lines and examined changes in cytoplasmic protein abundance in MH1C1 cells using mass spectrometry. We chose to closely examine differentially expressed genes and proteins changing in abundance in both cell lines in order to remove cell line specific effects. We identified enriched pathways, networks, and biological functions using commercial bioinformatic tools and manual annotation. Many of the genes, proteins, and pathways modulated by exposure to cobalt appear to be due to an induction of a hypoxic-like response and oxidative stress. Genes that may be differentially expressed due to a hypoxic-like response are involved in Hif-1α signaling, glycolysis, gluconeogenesis, and other energy metabolism related processes. Gene expression changes linked to oxidative stress are also known to be involved in the NRF2-mediated response, protein degradation, and glutathione production. Using microarray and mass spectrometry analysis, we were able to identify modulated genes and proteins, further elucidate the mechanisms of toxicity of cobalt, and identify biomarkers of exposure and effect in vitro, thus providing targets for focused in vivo studies.