Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity

• Published in: PloS one 2008-11, Vol.3 (11), p.e3802-e3802
• Main Authors: Managbanag, J R, Witten, Tarynn M, Bonchev, Danail, Fox, Lindsay A, Tsuchiya, Mitsuhiro, Kennedy, Brian K, Kaeberlein, Matt
• Format: Article
• Language: English
• Subjects: Aging; Algorithms; Biochemistry; Caenorhabditis elegans; Cancer; Cell Physiological Phenomena - genetics; Computational Biology/Systems Biology; Coronary artery disease; Data processing; Diabetes mellitus; Diet; Dietary restrictions; Gene deletion; Gene Regulatory Networks; Genes; Genes, Fungal; Genetic aspects; Genetic disorders; Genetic research; Genetics and Genomics; Genetics and Genomics/Functional Genomics; Genomes; Genomics; Health aspects; Heart diseases; Kinases; Life span; Longevity; Molecular modelling; Mutation; Nervous system diseases; Network analysis; Neurodegenerative diseases; Protein-protein interactions; Proteins; Public concern; Saccharomyces cerevisiae; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - genetics; Shortest-path problems; Yeast
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0003802

Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of network analysis of aging to be extensively validated in a biological system. The novel longevity genes identified in this study are likely to yield further insight into the molecular mechanisms of aging and age-associated disease.