SELECTED EXAMPLES: MURINEMODELS OF HUMAN DISEASE Genetic and Genomic Approaches to Complex Lung Diseases Using Mouse Models Michael J. Holtzman, Edy Y. Kim, and Jeffrey D. Morton 1. INTRODUCTION Common lung diseases are likely to be multifactorial and multigenic. In addition, the lung exhibits a limited set of biological and physiological responses, so different lung diseases exhibit significant overlap in phenotype. This complexity in the development and manifestation of lung disease poses significant challenges for developing complete and accurate models of disease. Nonetheless, a layered strategy that includes in vitro and in vivo systems can offset these limitations. In vitro systems have evolved from simple organ culture to intricate procedures for cell culture that exhibit high fidelity to behavior in vivo. Similarly, in vivo systems have evolved from traditional physiology-based models in large animals and rodents to genetic modification of mice using targeted and conditional systems. Complex traits may be studied in inbred, recombinant, or congenic strains of mice, and single gene effects may be segregated naturally or experimentally. Ultimately, results from these in vitro and in vivo models identify candidate genes for further study in humans.This chapter reviews the development and application of genetic and genomic approaches to complex lung diseases, focusing on the use of mouse model systems. Although the particular strength of the murine system has been its applicability to studies conducted in vivo, suitable cell culture systems have now been established for comparative work in vitro as well.Whenever possible, the extension and correlation of findings to human studies will also be noted. The chapter is organized by disease entity, using the examples of cystic fibrosis (CF), emphysema, tuberculosis, and asthma as illustrative of well-studied targets for multidisciplinary genetic and genomic 103 From: Computational Genetics and GenomicsEdited by: G. Peltz © Humana Press Inc., Totowa, NJ approaches. In addition, the distinct characteristics of these diseases have shaped different approaches to defining underlying genetic mechanisms and so illustrate the range of available methods that can be used in mouse models of lung disease. 2. CYSTIC FIBROSIS CF is the most common autosomal-recessive disorder in Caucasian populations, with an incidence of 1 in 2500 live births (1). Thus, the identification of the CF transmembrane conductance regulator (CFTR) as the site of the underlying genetic abnormality for this disease was a seminal example of the positional cloning approach to identify and characterize a candidate gene in humans (2–4). The CFTR gene has 27 exons that span 230 kb of the long arm of human chromosome 7 (7q31.2) and encodes a transmembrane glycoprotein of 1480 amino acid residues (5). The gene product is a member of the adenosine triphosphate-binding cassette family of transporters that have conserved transmembrane and nucleotide-binding domains linked by a regulatory domain with phosphorylation sites for protein kinases Aand C (2,6). Before the identification of the CF TR gene, physiological studies showed that CF epithelia have defective cyclic adenosine monophosphate MP)-mediated chloride ion transport (7–9). Subsequent studies indicated that CFTR was the major cAMP-regulated chloride channel in the apical membrane of epithelial cells (10,11) and so had a central role in transepithelial salt transport, fluid flow, and ion concentrations in the intestine, pancreas, sweat gland, and airway epithelia (12). CF results from defective CFTR activity that disrupts transepithelial ion transport. In general, nonsense or stop mutations in CFTR result in severe disease, whereas missense mutations result in milder disease. More than 900 mutations have been identified within human CFTR. The most frequent CF mutation includes 66% of mutant CFTR alleles. This mutation deletes in-frame the phenylalanine at position 508 (F508) (13). The F508 CFTR allele produces a misfolded protein that is trapped in the endoplasmic reticulum (14–16). In contrast,another common mutation (G551D) results in a protein with normal processing but decreased chloride channel activity (17). 2.1. Murine Models of CF Anumber of mouse models of CF were developed based on targeted mutations of the Cftr gene (Table 1). Initial strategies were based on knockout technology that introduces a genomic construct into mouse embryonic stem cells. Clones that have undergone genetic recombination are implanted into pseudopregnant female mice. The resulting chimeric mice are crossed to 104 Holtzman et al. Genetic and Genomic Approaches to Complex Lung Diseases 105 produce mice that are homozygous for the targeted gene deficiency. The first mouse model disrupted the CFTR gene by introducing a stop codon in exon 10 (strain CFTRm1UNC) (12,18,19). These CFTR-deficient mice are viable but lack the lung inflammation found in human CF. Instead, these mice develop severe bowel disease that was fatal by 40 d of age. A second gene knockout model (CFTRm1HGV) used insertional mutagenesis rather than the strategy of gene replacement used for the CFTRm1UNC strain. The CFTRm1HGV mouse strain produces 10% of normal CFTR levels and has 90% long-term survival with abnormalities of the colon and vas deferens (20). The CFTRm1UNC strain has been complemented by human CFTR driven by the rat intestinal fatty acid-binding protein promoter (21). However, like the CFTRm1UNC strain