Array technology and proteomics in autoimmune diseases.

Two new technologies (tissue microarrays (TMAs) and proteomics) have generated a great amount of data in life science. High-density TMAs allow for the simultaneous analysis of proteins and RNA by various methods (immunohistochemistry, in situ hybridization, FISH) on a large scale and under highly standardized conditions. Proteomics includes a variety of techniques that are partly high throughput. These techniques aim at the innovation of proteins, the description of the domain structure, the determination of protein sequences and epitope characterization, and ultimately the definition of protein function and protein reactivities in immunologic processes. Proteins that have been characterized accordingly require validation mostly at the morphologic level of defined tissue, linking proteomics to TMAs. In autoimmune diseases, array-based antigenic fingerprinting of autoantibodies will drive the development and the selection of antigen-specific diagnostic tools and therapies. The powerful combination of genomics and proteomics formed in tissue arrays has the potential to change the way the biology of autoimmunity is studied. Novel targets of drug discovery, based on antigen-specific therapies to induce anergy, or regulatory T-cells using the targeted autoantigens of individual patients could be developed in the coming decades.

Core classification of head and neck squamous cell carcinomas: correlations between morphology, DNA ploidy and HPV infection.

AIMS: The study intended to reveal whether HPV infection is reflected by nuclear morphology and DNA cytometry parameters in head and neck squamous cell carcinomas (HNSCC). METHODS: In total, 39 HNSCC were selected for reanalysis by histomorphology applying the core classification, DNA cytometry and HPV detection. For the core classification, HE sections were assessed by a score system to evaluate the nuclear size, the mitosis size, their variabilities and the presence of tripolar or tetrapolar mitoses. HPV was analyzed by consensus PCR followed by a hybridization method for virus typing. Static DNA cytometry was applied on single cell suspension focusing particularly on the parameters DNA modal value, DNA index peak, DNA index mean, 2c deviation index and 5c exceeding rate. Statistical analysis was done by T-test or Fisher's exact test. RESULTS: The analysis revealed that HPV positive HNSCC had significantly smaller nuclei than HPV negative cases. Increasing values of the nuclear size and mitosis size were significantly associated with higher indices of the DNA cytometry analysis. CONCLUSIONS: The study confirms that the core classification can provide information on the ploidy of HNSCC and that HPV positive tumors represent a distinct morphological and genetic carcinoma subtype.

iCon-TMA for control and quantitation of immunohistochemistry and in situ molecular pathology analysis.

Reliable assessment of in situ pathology analyses like immunohistochemistry, RNA in situ hybridization, and FISH are critically important in diagnosis and treatment decisions. We describe the development of small tissue microarrays (TMA) for the internal control and quantitation of these techniques, the iCon-TMA. In its simple variant, these iCon-TMA (abbreviated from internal control TMA) consist of 2 tissue cylinders, one being clearly positive and the other clearly negative for a specific marker. In its more elaborate format, the iCon-TMAs carry additional tissue spots providing a scale for quantitatively assessable markers, e.g. representing scores of negative, weak, moderate, or strong positivity. The specimen with the yet unknown reactivity is then applied to the iCon-TMA section, and both are simultaneously processed and analyzed, thus providing a convenient measure for in situ quality control and quantitation.