Objectives
- Partner Berlin has developed and tested a highly multiplexed microarray manufacturing system capable of producing high-density cDNA arrays. Based on this EST-chip containing 38,000 non-redundant sequences, a database of normal gene expression in the GI tract has been established. The database and bioinformatics infrastructure for analysis and data curation are in place. The database of normal gene expression in the GI tract is currently being published.
- In this work package, a global assessment of differential gene regulation in inflamed GI tissue will be used to identify novel inflammation genes, that are generic or specific for certain conditions.
Description of the work
The methodology for expression screening from GI tissues using biopsy material is established. An average of two biopsies is needed for a duplicate experiment. The mRNA is reversely transcribed and labelled radioactively. The available expression database allows a description of normal variability of gene expression within the GI tract..
In addition, the presently used UniGene cluster will be replaced/enriched by an inflammation specific set of clones, which are sequence and gel verified.
Status and progress
Resources from work-package 5 were re-directed for the development of a chromosome 6-specific microarray, enriched with additional probes for inflammation related genes from other chromosomes. Resources from work-package 6 were re-directed into the development of a novel and improved nano-dispensing technology platform for microarray production and nano-well applications. Furthermore, resources from work-package 8 were used to establish protein microarrays for serum screening.
As mentioned earlier the decision was made to re-direct resources from this work-package for the development of a chromosome 6-specific microarray, enriched with additional probes for inflammation related genes from other chromosomes. This decision was made because expression levels of genes located in the linkage regions of IBD on chromosome 6 have not yet been systematically analysed. Therefore partner 1 and partner 4 agreed to develop a chromosome 6 specific cDNA microarray. This new type of microarray includes predicted genes, splices variants and predicted splice variants. One pathway (TNF) with about 100 associated genes has been designed across all chromosomes. The microarray contains approximately 3000 features including internal and external controls and enables us to investigate the interplay of genes located on chromosome 6p, including differential splicing, and their implication in several functional clusters (see below in more details). For providing high quality microarrays we earlier optimised the process of spotting high-density microarrays (>25,000 spots per array) and additional technical advances have been made in order to provide excellent spotted microarrays.
Additionally, partner Berlin has established a protein microarray platform for serum screening experiments. In the third period the generation and application of IBD protein chips in screening IBD patient serum was proposed. Initially it was planned to express about 100 IBD related proteins and to spot on glass slides, which then could be applied for screening with IBD patient serum. The technology platform and application of protein chips for serum screening has been established in this workpackage for quantitative screening and analysis with control and patient serum. Major delays occurred in the throughput of the generation of the proteins for spotting.
The extended chromosome 6 microarray
The rational for developing a chromosome 6-specific microarray was that former epidemiological, clinical and molecular studies provided strong evidence that inherited predisposition is important in the pathogenesis of chronic inflammatory diseases. Multiple linkage scans have demonstrated that a region on chromosome 6p contributes to susceptibility for Crohn's Disease and Ulcerative colitis. Moreover chromosome 6p also contributes to other chronic inflammatory diseases like Psoriasis, Sarcoidosis, Atopic dermatitis, Asthma etc.
To identify disease specific genes and to investigate their functional interplay a microarray representing known genes and ESTs, which -map to chromosome 6p has been developed and produced at the Max Planck Institute for Molecular Genetics in Berlin (partner 4) in co-operation with the Mucosal Immunology Group Kiel (partner 1).
Deliverables:
- DL6: Glass microarray with a dense inflammation gene content (initially restricted, then publicly available), DL7: List of consistently differentially regulated novel transcripts.
- Reference to Milestones and Expected Results:
Discovery of susceptibility genes in IBD - a list of genes that are differentially expressed has been generated and was verified on a population level.