Current Pharmaceutical Design - Volume 12, Issue 29, 2006

Autoimmune diseases are multifactorial polygenic diseases involving interactions between environmental and genetic factors. Complex networks of interacting genes are affected. Sequencing of the human genome and advances in novel screening technologies of genomics and proteomics offer an opportunity of systematic research to better understand the molecular mechanisms in these diseases and to find new therapeutic targets and new diagnostic tools. Therefore the aim of this volume is to discuss this novel research strategy and experimental data derived from this technology and methodology platform of a number of autoimmune diseases by outstanding experts of different aspects of the issue. The volume starts with a contribution by Helmut Dotzlaw et al. [1] Rostock and Giessen, Germany giving an overview of the approaches used in the proteomic analyses of autoimmune diseases: during the last years investigations employing a variety of proteomic technologies have yielded a wealth of information on a number of autoimmune diseases in humans and animal models. Steffen Moeller et al. [2] Rostock, Germany and Szcezin, Poland review reports on the role of comparative genomics in research on autoimmune diseases. These novel tools have proven to be successful in inferring functional equivalence between loci of multiple genomes. Tools for projecting experimental data sets onto known functional information are a major need to support the analysis of samples produced in clinical research of autoimmune diseases. Developing quantitative and predictive models for interactions of regulatory DNA, RNAs, and proteins is the ultimate goal of system biology. Sabine Dietmann et al. [3] Neuherberg and Freising, Germany describe advances related to the problem of integrating heterogenous data sets into functional modules for animal and human cellular networks based on publicly available data resources. Protein biochips are emerging analytical tools to follow DNA microarrays as a new screening technology to identify protein-ligand interactions. The huge potential of this technology as well as future requirements such as protein microarray based diagnostics are presented by Mathias Kalbas et al. [4], Dortmund, Germany. Population studies reveal HLA class gene polymorphism associated with all the common chronic autoimmune diseases. Brigitte Müller-Hilke, and N. Avrion Mitchison [5], Rostock, Germany and London, UK summarize the knowledge of HLA promoter polymorphisms and how these translate into differential expression, T cell polarization and inflammation. The authors also discuss current strategies for pharmaceutical intervention in HLA expression. Rheumatoid Arthritis, is the most common chronic inflammatory autoimmune disorder that involves an interaction of genetic and environmental factors. Combining genetic association studies in humans and murine models with high throughput sequencing, RNA expression profiling and proteome analysis have identified some promising new targets. Saleh M. Ibrahim and Xinhua Yu [6], Rostock, Germany review the advances made dissecting the genetics of Rheumatoid Arthritis using mouse model. Multiple Sclerosis is the most prevalent chronic autoimmune disorder of the central nervous system. Goertsches et al. [7], Rostock, Germany and Szcecin, Poland discuss the state of the art in Multiple Sclerosis research at the transcriptomic level applying genomewide screening methods. Their review discribes disease pathogenicity, diagnostic markers, the identification of new therapeutic targets and a classification of patients towards the advent of tailored therapies. In the very last years, autoimmune pancreatitis has been recognized as a new distinct entity. Up to now, autoimmune pancreatitis is a rare disease, frequently associated with other autoimmune diseases. Robert Jaster and Joerg Emmrich [8], Rostock, Germany describe the characteristic features of autoimmune pancreatitis focussing on the molecular mechanisms of the disease. Jiri Trcka and Manfred Kunz [9] Rostock, Germany summarize the current knowledge about functional genome and proteome analyses addressing cutaneous autoimmune diseases like psoriasis, lupus erythematosus, systemic sclerosis, vitiligo, and alopecia areata.....

During the past five years, investigations employing a variety of proteomic technologies have yielded a wealth of information on a number of autoimmune disorders. Animal models of autoimmune disease have been examined and have provided clues that can be useful in elucidating molecular pathways and mechanisms that play a role in autoimmune disorders. Human sera and body fluids have been analyzed and have resulted in the identification of autoantibodies that can be used as diagnostic markers in specific autoimmune diseases, and proteomic fingerprints of tissues and body fluids have resulted in the identification of individual proteins or patterns of protein expression that are deregulated in autoimmune diseases. The information provided by these proteomic studies are of diagnostic and therapeutic potential. This review provides an overview of the approaches used in the proteomic analyses of autoimmune disease.

The complete DNA sequence of the human genome and of several related mammals are now available, due to the investments of enormous resources and advances in sequencing technology. Novel technologies have been developed to compare multiple genomes with each other, thus specifying regions of sequence similarity among mammals and with their pathogens. Larger blocks of sequence similarity (syntenic regions) have been determined and made publicly available. In many ways, novel insights can be gained by such data when combining external genetic or clinical information for these syntenic loci. These novel tools have proven to be successful in inferring functional equivalence between loci of multiple genomes. This review reports on the role of comparative genomics in research on autoimmune diseases, a field with strong dependencies on animal models of human diseases and the problem of an adequate information transfer between multiple organisms and research areas.

Molecular databases serve as primary information resources for the analysis of biological networks providing an essential and invaluable treasure for information exploration. Tools for projecting experimental data sets onto known functional information are a major need to support the analysis of samples produced in clinical research. A new concept is the notation of functional modules, i.e. the characterisation of sets of proteins that perform a defined biological function in cooperation. The determination and analysis of functional modules overcome the limitations of the analysis of individual genes and their properties. Although functional modules are not suitable to fully capture systems properties, they have the potential to unify the information generated by different types of experiments. We describe advances related to the problem of integrating heterogeneous data sets into functional modules for mouse and/or human cellular networks based on publicly available data resources, including advances in the design of ontologies for functional classification, problems of automatic protein functional annotation and integration of microarray data.

Protein microarrays with immobilised proteins on their surface are new analytical tools to overcome the current limits with respect to sample volume and throughput. They have a great potential as well with respect to multiplexing of complex samples, as a research tool and in diagnostics. Based on recent advances in this technology, new applications for protein microarrays in studying autoimmune diseases were described. Required tools for bioinformatical analysis of protein microarrays concerning normalisation, clustering and classification methods are discussed. The huge potential of this technology as well as future requirements such as protein microarray based diagnostics are presented.

Population studies reveal HLA class I and class II gene polymorphisms associated with all the common chronic autoimmune diseases, notably spondylarthropathies, rheumatoid arthritis, multiple sclerosis and type I diabetes. We here discuss the exceptionally high levels of nucleotide diversity in the MHC region likely to reflect not only balancing selection acting on the epitope binding sites but also natural selection operating on the promoter region. The latter possibility is supported by functional studies with promoters, higher levels of diversity in the promoters of class II than class I genes and the relatively high frequency of single nucleotide polymorphisms around transcription factor binding sites. This, we argue, reflects the need for an appropriate level of signalling at the immunological synapse. We here summarise our knowledge of HLA promoter polymorphisms and how these translate into differential expression, T cell polarisation and inflammation. We discuss current strategies for pharmaceutical intervention in HLA expression.

Rheumatoid Arthritis, RA, is a common polygenic multi-factorial chronic inflammatory disorder that involves complex interactions between genetic and environmental factors. Despite major advances, the aetiology of the disease is still not completely understood. In this post-genome era, the sequencing of the human and some murine genomes as well as advances in global screening technologies offer an opportunity to accelerate the search for new pathological pathways and to identify new therapeutic targets. Animal models of RA offer an opportunity to dissect the genetic basis of disease in a simplified genome and controlled environment with the aim of identifying new pathological pathways and thus new therapeutic targets. Linkage analysis in the mouse model has identified more than 60 Loci, controlling disease phenotypes, immune response and cytokines. This indicates that gene variations among inbred mice strains affect the disease and that those polymorphic genes could be potential therapeutic targets. However, progress in identification of susceptibility genes in mouse models is slow. The progress is hampered by the complexity of disease as well as the traditional genetic dissection strategies. In this post-genome era, the sequencing of the human and some murine genomes as well as advances in global screening technologies offer an opportunity to accelerate the progress.

Multiple sclerosis (MS) is the most prevalent chronic autoimmune, neurodegenerative disorder of the central nervous system (CNS). Despite substantial progress, treatment of MS and other autoimmune diseases is only moderately effective. It is anticipated that the treatment of autoimmune diseases with single drugs or biological approaches will in the future be complemented, or even replaced, by combination therapies, which include immunomodulation, elimination of infectious triggers and tissue repair. One proclaimed goal of biomedical research and clinical practice is the discovery of sets of genes with expression that correlates with successful outcomes of drug therapy, or with unfortunate side effects. Such information has direct consequences for selection, refinement or development of treatments and will soon be translated into clinical trials. The genome-wide RNA profile of an individual represents one complement to the comprehensive determination of disease- or drug response-related elements; comparable to a ‘sentinel’ method, it serves as a large-scale approach to MS biology. This work reviews the state of the art in MS research at the transcriptome level applying genomewide screening methods. It discusses implications in understanding disease pathogenicity, diagnostic markers, the identification of new therapeutic targets and a classification of patients towards the advent of tailored therapies.

For many years, a pathological immune response has been implicated in the development of chronic pancreatitis. However, only in the last decade autoimmune pancreatitis (AIP) has been recognized as a distinct entity with typical histopathological and immunological findings. AIP is frequently associated with other autoimmune diseases, such as Sjogren's syndrome, sclerosing extra-hepatic cholangitis and retroperitoneal fibrosis. Although AIP is rare, improved diagnostics is of significant clinical interest because of the prompt response to steroid treatment. In this review, we describe the characteristic features of AIP and focus on the molecular pathogenesis of the disease.

The use of functional genomics and proteomics technologies has dramatically increased through recent years with a special emphasis on cancer biology. However, a series of more recent reports has also addressed inflammatory diseases. These included studies on different autoimmune diseases, such as rheumatoid arthritis, lupus erythematosus, and systemic sclerosis. Gene and protein expression profiles from these studies have emphasized the role of cytokines, chemokines, and apoptosis-related molecules for the pathogenesis of autoimmune diseases. Much less is known about gene and protein patterns of these diseases in dermatology. Here we provide an overview on current knowledge about genomics and proteomics analyses of cutaneous autoimmune diseases. These diseases include psoriasis, lupus erythematosus, systemic sclerosis, vitiligo, and alopecia areata. The presented findings not only provide deeper insights into the pathogenesis of each individual disease but also show overlapping gene patterns suggestive for common pathogenic mechanisms. However, many open questions remain to be resolved since data about local gene expression pattern in affected tissues are still scarce.

The interaction of leukocytes with the vessel endothelium to facilitate the extravasation into the tissue represents a key process of the body's defense mechanisms. Excessive recruitment of leukocytes into the inflamed tissue in chronic diseases like autoimmune disorders could be prevented by interfering with the mechanisms of leukocyte extravasation. Significant progress in elucidating the molecular basis of the trafficking of leukocytes from the blood stream to the extravascular tissue has been achieved that enables new strategies for therapeutic approaches. The multistep process of leukocyte rolling, firm adhesion and transmigration through the endothelial wall is facilitated by a dynamic interplay of adhesion receptors on both leukocytes and endothelial cells as well as chemokines. In preclinical studies using various animal models, promising results have been received demonstrating that blocking of adhesion receptors of the selectin and integrin families improved the inflammation process in models of ulcerative colitis, autoimmune encephalomyelitis or contact hypersensitivity. In addition to the targeting of adhesion receptors by antibodies, small molecules that mimic epitopes of adhesion receptor ligands have been developed and successfully applied in animal models. Clinical studies revealed a limited response using antibodies to selectins or LFA-1 integrins compared with animal models. However, using humanized antibodies to the α4- integrin subunit significant efficacy has been demonstrated in autoimmune diseases like psoriasis, multiple sclerosis and inflammatory bowel disease.

Previously defined as a shotcoming to achieve uniform intramyocardial reperfusion after prolonged but reversible coronary occlusion, only recently has no-reflow phenomenon been characterized as a heterogeneous clinical condition. In fact, in about half of post-infarct patients that show no-reflow after 24 hours from coronary recanalization by either thrombolysis or PTCA, no-reflow phenomenon is spontaneously reversible. Reversible no-reflow is associated with favorable left ventricular remodeling even in the absence of significant improvement in regional contractile function. Thus, it may be a clinical marker of yet unknown mechanisms, which may favorably affect myocardial response to necrosis. Based on the pathogenesis and on the time-course of no-reflow, the phenomenon may be associated with lack of patency or with loss of anatomic integrity of microvessels, with the former being potentially reversible while the latter associated with definitive tissue damage. As a consequence, possible therapeutic strategies of no-reflow have to be designed according to not only the main target [microvessel patency or integrity], but also taking into account the timing of development of the damage. This “mini review” is focused on recent advances on the pathogenesis and clinical presentation on no-reflow. These data will give the opportunity to formulate novel interpretation and classification of the phenomenon and consequently, to propose adequate therapeutic strategies.

Electropulsation (electroporation) is a physical method for delivery of various molecules into the cells in vitro and in vivo. It is an expanding field due to its applicability in cancer therapy, where combined application of electric pulses and chemotherapeutic drugs is used for treatment of cutaneous and subcutaneous nodules of different malignancies. Another application of electropulsation in vivo is electrogene therapy, where after injection of naked plasmid DNA and delivery of electric pulses directly to the tissue the expression of gene of interest can be obtained. However, the transfection efficiency of this methodology in vivo is still lower than with viral vectors. Nevertheless, due to the lack of immunogenicity of the method, easiness of the preparation of large quantities of endotoxin free plasmid DNA, control and reproducibility of the method and the development of electropulsators approved for the clinical use, electrically-assisted nucleic- acid delivery holds a great potential for the clinical application. This aim of this minireview is to critically discuss the main limitations and obstacles associated with electrogene therapy and the failures and problems as well as the successes. Topics on electric field distribution in the tissue, electrode geometries, construction of plasmid, modulation of extracellular space, tissue damage, pro-inflammatory and immune response as well as blood flow modification associated with application of electric pulses and injection of naked DNA are presented with possible directions how to overcome these limitations. Furthermore, for successful electrogene therapy in clinical setting it is of utmost importance to elucidate the mechanisms of DNA transfer into the cells of tissues in vivo. This will enable appropriate selection of electric pulse parameters and plasmid DNA constructs for each particular intended use. In the long run, this review should encourage other scientists to consider electrically assisted gene delivery for gene therapy as it matures.