title: Systems biology of human benzene exposure.
abstract: Toxicogenomic studies, including genome-wide analyses of susceptibility genes (genomics), gene expression (transcriptomics), protein expression (proteomics), and epigenetic modifications (epigenomics), of human populations exposed to benzene are crucial to understanding gene-environment interactions, providing the ability to develop biomarkers of exposure, early effect and susceptibility. Comprehensive analysis of these toxicogenomic and epigenomic profiles by bioinformatics in the context of phenotypic endpoints, comprises systems biology, which has the potential to comprehensively define the mechanisms by which benzene causes leukemia. We have applied this approach to a molecular epidemiology study of workers exposed to benzene. Hematotoxicity, a significant decrease in almost all blood cell counts, was identified as a phenotypic effect of benzene that occurred even below 1 ppm benzene exposure. We found a significant decrease in the formation of progenitor colonies arising from bone marrow stem cells with increasing benzene exposure, showing that progenitor cells are more sensitive to the effects of benzene than mature blood cells, likely leading to the observed hematotoxicity. Analysis of transcriptomics by microarray in the peripheral blood mononuclear cells of exposed workers, identified genes and pathways (apoptosis, immune response, and inflammatory response) altered at high (>10 ppm) and low (<1 ppm) benzene levels. Serum proteomics by SELDI-TOF-MS revealed proteins consistently down-regulated in exposed workers. Preliminary epigenomics data showed effects of benzene on the DNA methylation of specific genes. Genomic screens for candidate genes involved in susceptibility to benzene toxicity are being undertaken in yeast, with subsequent confirmation by RNAi in human cells, to expand upon the findings from candidate gene analyses. Data on these and future biomarkers will be used to populate a large toxicogenomics database, to which we will apply bioinformatic approaches to understand the interactions among benzene toxicity, susceptibility genes, mRNA, and DNA methylation through a systems biology approach.
authors.affiliation: Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720-7356, USA. luoping@berkeley.edu
authors.forename: Luoping
authors.initials: L
authors.lastname: Zhang
authors.forename: Cliona M
authors.initials: CM
authors.lastname: McHale
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Rothman
authors.forename: Guilan
authors.initials: G
authors.lastname: Li
authors.forename: Zhiying
authors.initials: Z
authors.lastname: Ji
authors.forename: Roel
authors.initials: R
authors.lastname: Vermeulen
authors.forename: Alan E
authors.initials: AE
authors.lastname: Hubbard
authors.forename: Xuefeng
authors.initials: X
authors.lastname: Ren
authors.forename: Min
authors.initials: M
authors.lastname: Shen
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Rappaport
authors.forename: Matthew
authors.initials: M
authors.lastname: North
authors.forename: Christine F
authors.initials: CF
authors.lastname: Skibola
authors.forename: Songnian
authors.initials: S
authors.lastname: Yin
authors.forename: Christopher
authors.initials: C
authors.lastname: Vulpe
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Chanock
authors.forename: Martyn T
authors.initials: MT
authors.lastname: Smith
authors.forename: Qing
authors.initials: Q
authors.lastname: Lan
mesh_terms: D001554:Benzene / Q000009:adverse effects*; D019295:Computational Biology; D044127:Epigenesis, Genetic; D006413:Hematopoietic System / Q000187:drug effects / Q000473:pathology*; D006801:Humans; D049490:Systems Biology / Q000379:methods / Q000639:trends; D043922:Toxicogenetics
chemical_list: D001554:Benzene