Using Blood Informative Transcripts in Geographical Genomics: Impact of Lifestyle on Gene Expression in Fijians

Abstract

In previous geographical genomics studies of the impact of lifestyle on gene expression inferred from microarray analysis of peripheral blood samples, we described the complex influences of culture, ethnicity, and gender in Morocco, and of pregnancy in Brisbane. Here we describe the use of nanofluidic Fluidigm quantitative RT-PCR arrays targeted at a set of 96 transcripts that are broadly informative of the major axes of immune gene expression, to explore the population structure of transcription in Fiji. As in Morocco, major differences are seen between the peripheral blood transcriptomes of rural villagers and residents of the capital city, Suva. The effect is much greater in Indian villages than in Melanesian highlanders and appears to be similar with respect to the nature of at least two axes of variation. Gender differences are much smaller than ethnicity or lifestyle effects. Body mass index is shown to associate with one of the axes as it does in Atlanta and Brisbane, establishing a link between the epidemiological transition of human metabolic disease, and gene expression profiles.

The transition from a rural to an urban environment alters expression of the human Ebola virus receptor Neiman-Pick C1: implications for the current epidemic in West Africa

“…In this study, more than one third of the transcriptome was differently expressed in the three different regions, suggesting an effect of environmental geography on gene expression. Similar findings were reported from Fiji, where there were also major differences between the peripheral blood transcriptomes of rural villagers and residents of the capital city, Suva (Nath et al 2012). In both studies, differences in genome-wide expression signature were attributed to a combination of lifestyle, geography, and biotic factors.…”

Geographical, Environmental and Pathophysiological Influences on the Human Blood Transcriptome

“…They discuss how this situation could nevertheless lead to G×E interactions at the phenotype level. Subsequently, Nath et al [43] made similar observations in Fiji, where migrant Indians and native Melanesian Fijians living in rural and urban settings were found to diverge in peripheral blood gene expression, with the most significant differences observed between rural Indians and the other three groups of residents, to some extent involving similar genes as observed in Morocco.…”

Bone Marrow–Derived Mesenchymal Stromal Cells from Patients with Sickle Cell Disease Display Intact Functionality

“…Statistical analysis of Fluidigm data was performed using SAS JMP Genomics (Cary, NC) as previously described. 17 …”