Editorial [Hot Topic: Genome and Proteome Analyses of Autoimmune Diseases (Executive Editor: G. Neeck)]

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.....