PHAT Abstract, 2003

Pharmacogenomics of Asthma Therapy

Goals

There are three classes of drugs used to treat asthma: Leukotriene antagonists, beta agonists, and inhaled steroids. Our general approach, to asthma pharmacogenetics is to use pathway candidate genes to finding the important sequence variants in those genes that influence asthma treatment response. Once these genes are identified by genetic association studies and verified in at least two clinical trials populations our goal is to characterize the molecular mechanisms that are involved in their effect. We are also interested in gene-gene and gene drug interactions and we have developed a set of novel tools for managing SNP data and performing single SNP and haplotypic analyses as part of our project.

• Our first goal is to identify polymorphisms in genes in the three pathways relating to drug for the treatment of asthma. To date, we have made significant progress on variation discovery in all three pathways and relevant genes for asthma treatment in two of the three pathways. A total of 31 candidate genes have been submitted for sequencing and sequencing was performed on 32 Coriell cell lines from four ethnic groups and 16 asthmatic cell lines have been identified in the 31 sequenced genes. All of these genes have been submitted to the PharmGKB web site. In addition to identifying the sequence variants, we have substantial information on allele frequencies, haplotypes, and haplotype tagging SNPs for these 71 genes. We have also developed a set of novel tools for evaluating linkage disequilibrium patterns in these genes, for determining hardy Weinberg equilibrium and haplotype tagging SNP. These tool are available for use on our PharmgAT website (http://www.pharmgat.org).
• Our second goal is to genotype SNPs that tag all common haplotypes with a greater than 5% haplotype frequency in a variety of pharmacogenetic populations to determine the relationship of specific pathway genes to asthma treatment response. We have evaluated a total of 16 steroid pathway candidate genes and five Beta-Agonist pathway genes in at least two separate clinical trial populations. To do these analyses we needed to develop or adapt tools for haplotype imputation, haplotype tagging and data analysis. We have published on modifications of Haplo. Scor (Lake, Hum. Hered. 2003). We have several validated positive associations and have presented these data to our network colleagues and at the Pharmacogenetic network public meeting and have several manuscripts in preparation. Assessment of steroid pathway genes for bronchodilator phenotypes has revealed cross talk between these two pathways. Work on gene - gene interactions is ongoing.
• Our third and final goal is that for those genes where positive associations have been demonstrated, we investigate the molecular biology of these sequence variants and determine the functional effect of the genetic variation. We have tested one of our candidate genes by looking at a knock out of the gene in a mouse model of asthma and determined that our gene, CRH, is proinflammatory and we have submitted this work for publication. (Silveman, J. Clin. Invest, submitted)

Our molecular biology work has enabled us to characterize the effects of beta-agonist in smooth muscle cell lines isolated from b2-AR knockout mice and transgenic mice with a 10-fold over expression of b2-AR airway smooth muscle. These studies have been reported (MacGraw, J. Clin. Invest. 2003) and provide important information about the relationship of regular beta-agonist use to airways responsiveness.