Abstract: Most epidemiologic studies of the role of HDL in atherosclerosis have emphasized HDL levels, but there is increasing evidence that HDL functioning may be critically important as well. It is clear that HDL from different individuals can differ strikingly in both structural and functional characteristics. In particular, there is evidence that HDL can lose its well-documented atheroprotective characteristics and even become pro-inflammatory. Studies of HDL function in humans are complicated by genetic heterogeneity and environmental factors. We propose to identify novel genes and pathways contributing to HDL functions using naturally occurring variations among inbred strains of mice. Two broad classes of HDL functioning will be examined. The first has to do with lipid transport, and particularly reverse cholesterol transport, and the second with anti-inflammatory and antioxidant properties of HDL. In preliminary studies, we have discovered large variations among inbred strains in both lipid transport functions and anti-inflammatory functions. The underlying genes and pathways will be identified using novel strategies capable of high-resolution genetic mapping and a systems-based approach that integrates genetics, gene expression and clinical traits. In contrast to classical linkage mapping in mice, our novel, association- based approach allows direct identification of likely candidate genes. We also utilize mathematical analyses to model causal relationships and entire gene networks. To validate candidate genes and pathways, we will employ a variety of in vitro and in vivo approaches, including cultured hepatocytes, transgenic mice, and gene targeted mice.