Design of proteome-based studies in combination with serology for the identification of biomarkers and novel targets

Abstract

Recently proteome analysis has rapidly developed in the post-genome era and is now widely accepted as a complementary technology to genetic profiling. The improvement in the technology of both two-dimensional electrophoresis (2-DE) analysis as well as protein identification has made proteomics a valuable and powerful tool to study human diseases. A combination of conventional proteome analysis with serology has been developed as a promising experimental approach for the discovery of serological markers in different malignancies. However, the design of proteome-based studies has to be carefully performed since there are a number of critical needs for systematic and reproducible proteome analysis. In particular, the selection of tissue and its preparation represent an important step in proteome analysis. Besides the preparation of protein samples, the 2-DE and protein identification is a further critical issue. So far proteome-based technologies have been successfully used in tumor immunnology for the identification of tumor-specific autoantigens. Similarly, this technology has been employed for the detection of virulence factors, antigens and vaccine candidates in infectious diseases, as well as for the identification of diagnostic and prognostic markers, suggesting that proteome-based analysis is a promising tool for the identification of prognostic, diagnostic markers as well as for novel therapeutic targets which could be used for treatment of diseases. The integration of proteome-based approaches with data from genomic or genetic profiling will lead to a better understanding of different diseases, which will then contribute to the direct translation of the research findings into clinical practice.

Cancer Immunomics Using Autoantibody Signatures for Biomarker Discovery

“…SERPA (also called PROTEOMEX by Seliger et al (26,27)) is based on a classical proteomics workflow associating an effective separation on 2-DE gels and an identification by MS. In SERPA, Western blotting in combination with 2-DE gels (2-D blotting) (18, 26, 28 -30) permits the transfer and immobilization of proteins from tumor tissue or tumor cell lines to a semirigid support.…”

“…During sample collection, one may keep in mind that the patient is the focus of all the efforts with a requirement to consider the social responsibility that is given when handling human samples (26). In particular, the pathological classification of the samples and the availability of patient data (age, gender, information on treatment or surgery, and grade and cytogenetic type of the tumor) are a prerequisite.…”

Decoding Serological Response to Candida Cell Wall Immunome into Novel Diagnostic, Prognostic, and Therapeutic Candidates for Systemic Candidiasis by Proteomic and Bioinformatic Analyses

“…Among the currently available techniques, the combination of proteomics with serology (immunoproteomics (30 -34)) is largely being used to screen for panels of biomarkers and therapeutic targets in patients with infectious diseases (including SC (27,31,35,36)), cancer, or autoimmune disorders (32,(37)(38)(39)(40)(41). This discipline permits characterization of the immunome of a (micro)organism, defined as the subset of the proteome of a (micro)organism that acts as a target for the immune system (42).…”

Identification of the cross-reactive and species-specific antigens between Neospora caninum and Toxoplasma gondii tachyzoites by a proteomics approach

“…Proteomics is a useful tool for obtaining a more complete understanding of the biology of parasites, and this technology will identify life cycle stage-specific proteins implicated in invasion, survival, virulence, disease pathogenesis, and transmission (Belli et al 2005). Protein expression analysis using preliminary two-dimensional gel electrophoresis (2-DE)-based protein separation technologies combined with immunoblot analysis of antigenic proteins and then coupled with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and bioinformatics analysis provides a means to identify parasite-specific proteins and antigenic proteins that represent potential vaccine candidates or targets for serodiagnosis (Klade 2002;Seliger and Kellner 2002). Moreover, the proteomics approach has greatly enhanced the possibilities for the mapping and characterization of protein populations (Cohen et al 2002).…”