This application describes a composition and method for treating inflammatory bowel disease or other autoimmune diseases. The composition utilizes a vector which contains a first promoter which controls the expression of a regulatory transcription factor and a second inducible promoter which controls the expression of the gene of interest. The preferred gene of interest encodes an isoform of TGF-beta such as TGF-beta1 or TGF-beta3. The isoform of TGF-beta does not have to be hTGF-beta and can be a latent or active isoform of TGF-beta. The preferred inducible promoter is TRE-CMV which can be induced using doxycycline. The usefulness of the composition for treating autoimmune diseases is demonstrated in the application in a murine model of inflammatory bowel disease in which intestinal inflammation was abrogated by the administration of a plasmid vector encoding active TGF-beta. The composition may be administered by a variety of delivery systems and intranasal delivery is exemplified.