In utero transfer of genes to epithelial stem cells in the developing mouse and rat lungs is highly efficient. A method (transient in utero knockout [TIUKO]) for the transfer and transient expression of antisense genes in an adenovirus vector was produced to characterize developmentally important genes in the lungs and intestines. This method was applied to the Sprague-Dawley rat to evaluate developmental aspects of the CF phenotype. Treatment of rat fetuses at 15, 16, or 17 days gestation with an adenovirus-antisense CFTR yielded different phenotypes. Animals treated at 15 days gestation died shortly after birth and showed significant pathology in their intestines. Treatment later in gestation did not result in a lethal intestinal phenotype, although some changes in histology were noted immediately after birth. The lungs from rats treated at 16-17 days gestation exhibited many of the characteristics seen in CF. Airway fibrosis and parenchymal thickening with monocytic infiltrates were present as early as 90 days of age. An increase in airway reactivity to methylcholine was also documented. CF antigen (MRP8/14) expression was induced in utero. Because the TIUKO CF rats mimic human lung disease, it was used to evaluate genes that could modulate the CF phenotype. Rats deficient in CF antigen expression were treated at 16 days gestation with the adenovirus-antisense CFTR recombinant. Evaluation of airway reactivity and cell type populations in the lung demonstrated that CF antigen is involved developmentally in the lung. Its absence results in a lung phenotype different from that observed in CF antigen expressing animal. Upon treatment with antisense a unique phenotype was observed. Thus, CF antigen is involved in normal lung development and its absence affects the CF disease phenotype.