Anti-cytokine autoantibodies: Epiphenomenon or critical modulators of cytokine action

Low amounts of high-affinity autoantibodies to various cytokines have been detected in sera from healthy donors. Their levels, although highly variable, are increased in the circulation of patients subjected to cytokine therapy or suffering from a variety of immunoinflammatory diseases. It has been suggested that these autoantibodies play a regulatory role in the intensity and duration of an immune response. The antibodies may prevent the binding of a cytokine to its specific cell surface receptor thereby neutralizing its biological activityin vivo. They may also act as carrier proteins preventing the rapid elimination of a cytokine from the circulation and thus increase its bioactivity. Additionally or alternatively, autoantibodies may modulate cytokine-induced intracellular signal transduction pathways or trigger complement-mediated cytotoxicity towards cells carrying membrane-bound cytokines. The autoantibodies may exert their regulatory role in compliance with other factors that control cytokine activity, including soluble cytokine receptors, cell surface decoy receptors, and receptor antagonists. Although not favored by many investigators, a less sophisticated role for naturally occurring anti-cytokine autoantibodies should be considered as well. Recent evidence has shown that autoantibodies are generated at a high frequency as part of a response to foreign antigens. These antibodies are produced by B cells arising from the process of somatic mutation. Thus anti-cytokine autoantibodies may be the result of a “leaky” B cell response triggered by immunoinflammatory processes. High-titered autoantibodies induced by cytokine therapy are of clinical concern since their occurrence is often associated with the loss of response to treatment. Moreover, they may also neutralize endogenously produced cytokines with possible pathological consequences. In this paper we have reviewed the available information on the biological and clinical significance of both naturally occurring and therapeutically induced anti-cytokine autoantibodies in animals and man with the emphasis on antibodies directed to interferons.     

Impact of glycosylation on the effect of cytokines. A special focus on oncology

The clinical use of cytokines is largely confined to the field of cancer treatment. Industrial procedures for the preparation of cytokines may or may not affect the glycosylation status of several cytokines. The glycosylation of cytokines may be of importance for the accomplishment of their biological functions, including their biological stability, their interaction with specific receptors and their pharmacokinetic behavior. The purpose of this review is thus to describe and discuss the role of cytokine glycosylation, based on experimental data, and with the clinical perspective on oncology. There is no general rule governing the effects induced by the presence of glycosylation on cytokine activity. Among different cytokines concerned by glycosylation status, data concerning G-CSF are sufficient to translate experimental findings into clinical evidence. For this cytokine, glycosylation confers advantages for both stability and biological activity. Although at weight equivalence, the glycosylated form confers greater biological activity than the non-glycosylated form, clinical studies have demonstrated that efficacy remains the same when glycosylated and non-glycosylated G-CSF are prescribed at bioequivalent doses.     

Current techniques in protein glycosylation analysis. A guide to their application.

The importance of glycosylation in biological events and the role it plays in glycoprotein function and structure is an area in which there is growing interest. In order to understand how glycosylation affects the shape or function of a protein it is however important to have suitable techniques available to obtain structural information on the oligosaccharides attached to the protein. For many years the complexity of the structures required sophisticated analytical techniques only available to a few specialist laboratories. In many cases these techniques were not available or required a large amount of material and therefore the number of glycoproteins which were fully characterised were relatively few. In recent years there have been substantial developments in the analysis of glycosylation which has significantly changed the capability to fully characterise molecules of biological interest. A number of different techniques are available which differ in terms of their complexity, the amount of information which is available from them, the skill needed to perform them and their cost. It is now possible for many laboratories who do not specialise in glycosylation analysis to obtain some information although this may be incomplete. These developments do, however, also make complete characterisation of a glycoprotein a much less daunting task and in many cases this can be performed more easily and with less starting material than was previously required. In this review a summary will be given of current techniques and their suitability for different types of analysis will be considered.     

Measurement of cytokines by bioassays: theory and application

A large number of cytokines have been characterized, of which several have proved successful in the clinic as biotherapeutic agents for malignant, infectious or autoimmune diseases. As biologically active proteins, they cannot be fully characterized by physicochemical methods alone. Thus, biological assays (bioassays) have become increasingly important for their biological characterization and potency determinations. Since cytokines exert various biological activities in vitro, cultured cell line-based bioassay methods have mainly been developed to quantify potency. Such bioassays, like all biological systems, are inherently variable. Thus, measurement of potency of a particular cytokine must be made relative to a common, stable, reference preparation of the same cytokine to permit valid inter-assay and inter-laboratory comparisons. The development and establishment of appropriate primary reference preparations as World Health Organization (WHO) International standards (IS) and reference reagents (RR) is essential for the standardization of bioassays. This review addresses the practical and statistical considerations for the development of valid bioassays, the preparation and use of WHO IS and RR and, in brief, the types of bioassay methods applicable to potency measurements of individual cytokines. More extensive details for the potency determinations of tumor necrosis factor-alpha (TNF-alpha), related cytokines, and biotherapeutic anti-TNF-alpha products are provided.     

The Value of Forests to World Food Security

We assembled information on the contribution and value of forests to world food security. An assessment was made of the role of forests and non-timber products in the food system of developing countries. We estimated that upwards of 300 million people annually earn part or all of their livelihood and food from forests. A total of about $90 billion in non-timber products are harvested each year. Forests also help to protect land, water, and biological resources, and they play an important role in maintaining the productivity of agricultural and environmental systems.     

Signalling by the βc family of cytokines

The GM-CSF, IL-3 and IL-5 family of cytokines, also known as the βc family due to their receptors sharing the signalling subunit βc, regulates multiple biological processes such as native and adaptive immunity, inflammation, normal and malignant hemopoieis, and autoimmunity. Australian scientists played a major role in the discovery and biological characterisation of the βc cytokines and their recent work is revealing unique features of cytokine receptor assembly and signalling. Furthermore, specific antibodies have been generated to modulate their function. Characterisation of the structural and dynamic requirements for the activation of the βc receptor family and the molecular definition of downstream signalling pathways are providing new insights into cytokine receptor signalling as well as new therapeutic opportunities.     

Cytokine receptor activation at the cell surface

Cytokines are well recognized for the pleiotropic nature of their signaling and biological activities on many cell types and their role in health and disease. Recent years have seen a steady stream of new cytokine receptor crystal structures including those that are activated by GM-CSF, type I interferon, and a variety of interleukins. Highlights include the observation of a dodecameric signaling complex for the GM-CSF receptor, electron microscopy imaging of an intact gp130/IL-6/IL-6Rα ternary receptor complex bound to its signal transducing Janus kinase and visualization of novel cytokine recognition mechanisms in the interleukin-17 and type I interferon families. This increasing knowledge in cytokine structural biology is driving new opportunities for developing novel therapies to modulate cytokine function in a diverse range of diseases including malignancies and chronic inflammation.     

Endotoxin detection and elimination in biotechnology

Endotoxins liberated by gram-negative bacteria are frequent contaminants of aqueous and physiological solutions. Because of their potent biological effects in vivo and in vitro, their detection and removal are essential for the safe parenteral administration of products produced from natural sources, as well as those produced by recombinant DNA technology. Traditional methods of endotoxin detection include the U.S. Pharmacopeia rabbit test and the Limulus amebocyte lysate test. Elimination of endotoxins, however, continues to be a problem. Standard methods of sterilization, such as autoclaving or sterile filtration, have little effect on endotoxin levels. Various techniques for the prevention of endotoxin contamination and endotoxin removal have been discussed. The overall role of endotoxin prevention, detection, and elimination in biotechnology is emphasized.     

CytReD: A database collecting human cytokinome information

The cytokines/related receptors system represents a complex regulatory network that is involved in those chronic inflammatory processes which lead to many diseases as cancers. We developed a Cytokine Receptor Database (CytReD) to collect information on cytokine receptors related to their biological activity, gene data, protein structures and diseases in which these and their ligands are implicated. This large set of information may be used by researchers as well as by physicians or clinicians to identify which cytokines, reported in the literature, are important in a given disease and, therefore, useful for purposes of diagnosis or prognostic. AVAILABILITY: The database is available for free at http://www.cro-m.eu/CytReD/     

Diversity and biogeography of marine actinobacteria

The actinomycetes, although not all the Actinobacteria, are easy to isolate from the marine environment. However, their ecological role in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate strains for search and discovery of new drugs. However, the marine environment has become a prime resource in search and discovery for novel natural products and biological diversity, and marine actinomycetes turn out to be important contributors. Similarly, striking advances have been made in marine microbial ecology using molecular techniques and metagenomics, and actinobacteria emerge as an often significant, sometimes even dominant, environmental clade. Both approaches - cultivation methods and molecular techniques - are leading to new insights into marine actinobacterial biodiversity and biogeography. Very different views of actinobacterial diversity emerge from these, however, and the true extent and biogeography of this are still not clear. These are important for developing natural product search and discovery strategies, and biogeography is a hot topic for microbial ecologists.     

Reconstruction of genetic association networks from microarray data: a partial least squares approach

MOTIVATION: Gene association/interaction networks provide vast amounts of information about essential processes inside the cell. A complete picture of gene-gene associations/interactions would open new horizons for biologists, ranging from pure appreciation to successful manipulation of biological pathways for therapeutic purposes. Therefore, identification of important biological complexes whose members (genes and their products proteins) interact with each other is of prime importance. Numerous experimental methods exist but, for the most part, they are costly and labor intensive. Computational techniques, such as the one proposed in this work, provide a quick 'budget' solution that can be used as a screening tool before more expensive techniques are attempted. Here, we introduce a novel computational method based on the partial least squares (PLS) regression technique for reconstruction of genetic networks from microarray data. RESULTS: The proposed PLS method is shown to be an effective screening procedure for the detection of gene-gene interactions from microarray data. Both simulated and real microarray experiments show that the PLS-based approach is superior to its competitors both in terms of performance and applicability. AVAILABILITY: R code is available from the supplementary web-site whose URL is given below.     

Soluble receptors for IL-1 and IL-4: biological activity and therapeutic potential.

Cytokine research has yielded a range of products which have now reached the stage of clinical trials and a plethora of novel therapeutics may be expected. Recently, cytokine receptors have also become an area of intensive research. Preliminary results indicate that recombinant soluble receptors can interfere with the biological functions of cytokines and thus may be appropriate for the treatment of certain pathological conditions where cytokine activity needs to be modulated.     

Transabiotic factors in an aqueous environment (a review)

Excretion of metabolites is a characteristic feature of any alive organism. A big group of these products--second metabolites--because of their variability, quantity and physico-biological activity have a special importance in aquatic environment. Exometabolites of some organisms become an important part of environment for the others. The authors discussed the origin and evolution of exometabolites from simple waste products to biologically active substances. Quantitative and qualitative aspects of metabolic excretion by organisms in water conditions are analysed. The data on composition, origin and biological function of some second metabolites of different groups of aquatic organisms are presented. The authors propose a classification of second metabolites according to their functional significance. The role of metabolites and decay products in the development of chemical information streams in hydrobiocoenosis is analysed. Metabolites (soluble organic substances) form a field of chemical information for biotic community. The most important functions of this field are communication and conditioning. The authors emphasize the importance of investigations of chemical bioinformation field in aquatic ecosystems.     

应用化学基因组信息预测小分子化合物的潜在生物靶标的理论方法

在后基因组时代,化学基因组技术在药物作用靶点的确认、小分子化合物对通路的作用,以及小分子先导化合物的识别等方面都有着广泛的应用,为新药研发提供了新的技术方法。本文主要介绍了当前几种基于化学基因组信息来预测小分子化合物潜在生物靶标的理论方法（包括化学相似性搜索方法、反向分子对接方法、数据挖掘方法以及生物活性谱图分析方法）,并分析了这些方法的优缺点以及应用前景。     

Electron crystallography of proteins in membranes

Electron crystallography has played a vital role in advancing our understanding of proteins in membranes since the 'fluid mosaic model' was proposed in 1972. It is now an established technique to reveal the structures of proteins in their natural bilayer environment and makes possible the study of biological mechanisms through freeze-trapping of transitional states. Thus, images and diffraction patterns of well-ordered, planar and tubular protein-lipid crystals are yielding atomic models, which tell us how the proteins in situ are designed and carry out their membrane-specific tasks. Recent methodological advances and the inclusion of tomographic and cryo-sectioning techniques are enabling detailed information to be obtained from increasingly smaller and more disordered membrane assemblies, extending the potential of this approach.     

From researcher to farmer: The use of extension programs to transfer biological control technology in developed countries

Effective use of biological control by the pest manager requires knowledge of the biologies of the pests and natural enemies, and their interactions with their environment and agronomic practices. Manufacturers provide information for products such as microbial pesticides and entomophagous arthropods used in augmentative biological control. However, information about process-oriented methods such as classical (importation) biological control and conservation of natural enemies is not often available to the farmer. Governmental extension programs are one method for providing practical biological control information, but availability in developed countries varies considerably. Examples of transfer of biological control information are provided for New Zealand, Canada, and Australia. In the United States, the Extension Service, a branch of the U.S. Department of Agriculture, provides partial funding and coordination for pest management educational programs conducted at the national, regional, state and local levels. In a twelve-state region of the North Central United States, university extension and research entomologists have developed a coordinated program to educate county extension personnel, farmers, and private consultants about the use of biological controls in pest management. The details of this model program are discussed. The paper concludes with a discussion of the educational constraints that must be overcome to successfully increase the adoption of biological control.     

Structural analysis in nonsymbiotic hemoglobins: What can we learn from inner cavities?

Plants contain three classes of hemoglobins which are not associated with nitrogen fixing bacteria, and have been accordingly termed nonsymbiotic hemoglobins. The function of nonsymbiotic hemoglobins is as yet mostly unknown. A NO dioxygenase activity has been proposed and demonstrated for some of them in vitro. In this context, a sound molecular mechanism that relates the structure with the biological activity is crucial to suggest a given physiological role. Insight into such a mechanism is now facilitated by recent progress made in both experimental and computational techniques. These studies have highlighted a number of key structural features implicated in the function of nonsymbiotic hemoglobins. The bis-histidyl hexacoordination of the heme in both its ferric and ferrous states provides a powerful and general tool to modulate reactivity, protein dynamics, and shape of the cavities. In addition, the specific arrangement of distal cavity residues provides effective protection against autoxidation. Inspection of the static crystal structures available for both liganded and unliganded states seems unsufficient to explain the function of these proteins. Function appears to be intimately linked with protein flexibility, which influences the dynamical behavior of inner cavities, capable of delivering apolar reactants to the reaction site, and removing charged reaction products. In this mini review, we demonstrate how the integration of information derived from experimental assays and computational studies is valuable and can shed light into the linkage between structural plasticity of nonsymbiotic hemoglobins and their biological role.     

Soluble cytokine receptors: their role in immunoregulation

A number of cytokine receptors exist in soluble form in the biological fluids of both animals and humans, a phenomenon that might have immunoregulatory implications in vivo. Although these soluble receptors specifically inhibit binding and activity of their respective cytokines in vitro, their actual function in vivo as cytokine inhibitors or as carrier proteins is unclear. Abnormalities in the production of these substances might contribute to the pathophysiology of immune and neoplastic diseases. Besides their role in regulating cytokine activity in vivo, soluble cytokine receptors hold significant potential for therapeutic use as very specific anticytokine agents and as indicators in diagnosis and assessment of immune parameters, prognosis, disease progression, response to treatment, etc., in a variety of autoimmune and malignant diseases.