BackgroundThe differential pathophysiologic mechanisms that trigger and maintain the two forms of inflammatory bowel disease (IBD), Crohn disease (CD), and ulcerative colitis (UC) are only partially understood. cDNA microarrays can be used to decipher gene regulation events at a genome-wide level and to identify novel unknown genes that might be involved in perpetuating inflammatory disease progression.Methods and FindingsHigh-density cDNA microarrays representing 33,792 UniGene clusters were prepared. Biopsies were taken from the sigmoid colon of normal controls (n = 11), CD patients (n = 10) and UC patients (n = 10). 33P-radiolabeled cDNA from purified poly(A)+ RNA extracted from biopsies (unpooled) was hybridized to the arrays. We identified 500 and 272 transcripts differentially regulated in CD and UC, respectively. Interesting hits were independently verified by real-time PCR in a second sample of 100 individuals, and immunohistochemistry was used for exemplary localization. The main findings point to novel molecules important in abnormal immune regulation and the highly disturbed cell biology of colonic epithelial cells in IBD pathogenesis, e.g., CYLD (cylindromatosis, turban tumor syndrome) and CDH11 (cadherin 11, type 2). By the nature of the array setup, many of the genes identified were to our knowledge previously uncharacterized, and prediction of the putative function of a subsection of these genes indicate that some could be involved in early events in disease pathophysiology.ConclusionA comprehensive set of candidate genes not previously associated with IBD was revealed, which underlines the polygenic and complex nature of the disease. It points out substantial differences in pathophysiology between CD and UC. The multiple unknown genes identified may stimulate new research in the fields of barrier mechanisms and cell signalling in the context of IBD, and ultimately new therapeutic approaches.

A comparison of oligonucleotide and cDNA-based microarray systems. Physiol Genomics 16: 361-370, 2004. First published November 25, 2003 10.1152/physiolgenomics.00080.2003.-Large-scale public data mining will become more common as public release of microarray data sets becomes a corequisite for publication. Therefore, there is an urgent need to clarify whether data from different microarray platforms are comparable. To assess the compatibility of microarray data, results were compared from the two main types of high-throughput microarray expression technologies, namely, an oligonucleotide-based and a cDNA-based platform, using RNA obtained from complex tissue (human colonic mucosa) of five individuals. From 715 sequence-verified genes represented on both platforms, 64% of the genes matched in "present" or "absent" calls made by both platforms. Calls were influenced by spurious signals caused by Alu repeats in cDNA clones, clone annotation errors, or matched probes that were designed to different regions of the gene; however, these factors could not completely account for the level of call discordance observed. Expression levels in sequence-verified, platform-overlapping genes were not related, as demonstrated by weakly positive rank order correlation. This study demonstrates that there is only moderate overlap in the results from the two array systems. This fact should be carefully considered when performing large-scale analyses on data originating from different microarray platforms. noncommercial clone-based microarray system; commercial oligonucleotide-based microarray system; expression screening platform; cross-platform screening

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Both clinically and histopathologically, melanoma of childhood is a rarely encountered lesion. In addition, it has particular histopathologic diagnostic problems. Differential diagnosis of this lesion and Spitz nevus is at times very problematic, in that distant metastases and death of the patient may be the only diagnostic criteria for some cases. We present a 4-year-old girl with an atypical melanocytic neoplasm with Spitzoid features on the left subscapular region.

All of the CKs detected in amyloid deposits were basic type (type II). It seems plausible either that acidic CKs might be degraded faster than basic types in amyloidogenesis or that paraffin-embedded tissue specimens are less sensitive than frozen tissue sections. The results of our study suggest that when paraffin-embedded specimens are investigated by immunohistochemical methods, CK5 antibody is useful in the diagnosis of LA and MA.