Investigation of mRNA sequences in ulcerative colitis.

After decades of research into the epidemiology, microbiology and immunology of ulcerative colitis (UC) the aetiology has still not been elucidated. An alternative approach is to compare gene expression in mucosa affected by UC with that of normal mucosa. Differentially expressed genes may elucidate the cells and processes involved in the disease. Such genes may be reliable markers of disease which facilitate diagnosis and provide an avenue for further research. In this thesis mRNA expression in normal and UC mucosa was compared by screening a cDNA library prepared from UC mucosa with cDNA probes with the aim of identifying abnormally expressed mRNAs. cDNA probes, including subtracted probes, were prepared from normal mucosa and mucosa affected by quiescent and active colitis. Differentially hybridising clones were screened with a spleen cDNA probe which failed to eliminate immunological sequences. With the exception of one sequence that could not be identified, all differentially hybridising clones were either immunoglobulin or mitochondrial genes. K and light-chain and IgG heavy-chain were all overexpressed in active disease. Using in situ hybridisation, the signal was localised in the lamina propria. IgA heavy-chain could be either overexpressed or underexpressed in UC, possibly reflecting the degree of ulceration of the epithelium, beneath which the IgA plasma cells were localised. Mitochondrial sequences were overexpressed in quiescent colitis but underexpressed in active disease. Using in situ hybridisation, signals were localised in the crypt bases probably representing proliferating cells. However, RNA dot blot hybridisation was unable to confirm that mitochondrial sequences and the unidentified sequence were consistently abnormally expressed in other cases of UC. Finally, enriched cDNA was generated by repeated subtraction with appendix mRNA/cDNA and amplified by the polymerase chain reaction. Analysis of the enriched cDNA demonstrated substantial loss of immunoglobulin sequences. In conclusion, the only informative sequences were immunoglobulin sequences which confirmed previous findings. Screening of immunoglobulin-subtracted cDNA may overcome this problem.