Using blood informative transcripts in geographical genomics: Impact of lifestyle on gene expression in Fijians

Frontiers in Genetics

Volumn 3, Issue NOV, 2012, Pages

  Nath, Artika Praveeta ^a,b   Arafat, Dalia ^a   Gibson, Greg ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b FIJI NATIONAL UNIVERSITY   (Fiji)

Author keywords

Axes of variation; Body mass index,TLR signaling; Epidemiological transition; Gene expression profiling

Indexed keywords

EID: 84876007294     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00243     Document Type: Article

References (45)

1. Berry, M. P., Graham, C. M., McNab, F. W., Xu, Z., Bloch, S. A., Oni, T., et al. (2010). An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466, 973-977.
2. Brian, G., Ramke, J., Maher, L., Page, A., and Szetu, J. (2010). The prevalence of diabetes among adults aged 40 years and over in Fiji. N. Z. Med. J. 17, 68-75.
3. Chaussabel, D., Quinn, C, Shen, J., Patel, P., Glaser, C, Baldwin, N., et al. (2008). A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29, 150-164.
4. Cheung, V. G., Spielman, R. S., Ewens, K. G., Weber, T. M., Morley, M. (2005). Mapping determinants of human gene expression by regional and genome-wide association. Nature 437, 1365-1369.
5. Dakeshita, S., Kawai, T., Uemura, H., Hiyoshi, M., Oguma, E., Horiguchi, H., et al. (2009). Gene expression signatures in peripheral blood cells from Japanese women exposed to environmental cadmium. Toxicology 257, 25-32.
6. Eady, J. J., Wortley, G. M., Wormstone, Y. M., Hughes, J. C, Astley, S. B., Foxall, R. J., et al. (2005). Variation in gene expression profiles of peripheral blood mononuclear cells from healthy volunteers. Physiol. Genomics 11, 402-411.
7. Emilsson, V., Thorleifsson, G., Zhang, B., Leonardson, A. S., Zink, F., Zhu, J., et al. (2008). Genetics of gene expression and its effect on disease. Nature 452,423-428.
8. Feezor, R. J., Baker, H. V., Mindrinos, M., Hayden, D., Tannahill, C. L., Brownstein, B. H., et al. (2004). Whole blood and leukocyte RNA isolation for gene expression analyses. Physiol. Genomics 19,247-254.
9. Fehrmann, R. S. N., Jansen, R. C, Veldink, J. H., Westra, H.-J., Arends, D., Bonder, M. J., et al. (2011). Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet. 7, el002197. doi:10.1371/journal.pgen.l002197
10. Fink, J., Gu, F, Ling, L., Tolfvenstam, T., Olfat, F, Chin, K. C, et al. (2007). Host gene expression profiling of dengue virus infection in cell lines and patients. PLoS Negl. Trap. Dis. 1, e86. doi:10.1371/journal.pntd. 0000086
11. Freedman, J. E., Larson, M. G., Tanriverdi, K., O'Donnell, C. J., Morin, K., Hakanson, A. S., et al. (2010). Relation of platelet and leukocyte inflammatory transcripts to body mass index in the Framing-ham heart study. Circulation 13, 119-129.
12. Fry, R. C, Navasumrit, P., Valiathan, C, Svensson, J. P., Hogan, B. J., Luo, M., et al. (2007). Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers. PLoS Genet. 3, e207. doi:10.1371/joumal.pgen.0030207
13. Gibson, G. (2008). The environmental contribution to gene expression profiles. Nat. Rev. Genet. 9, 575-581.
14. Gilad, Y., Pritchard, J. K., and Thornton, K. (2009). Characterizing natural variation using next-generation sequencing technologies. Trends Genet. 25,463-471.
15. Hodge, A. M., Dowse, G. K., and Zimmet, P. Z. (1992). Obesity in Pacific populations. Pac. Health Dialog. 3, 77-86.
16. Hughes, R. G., and Marks, G. C. (2009). Against the tide of change: diet and health in the Pacific islands. J. Am. Diet. Assoc. 109, 1700-1703.
17. Idaghdour, Y, Czika, W., Shianna, K. V., Lee, S. H., Visscher, P. M., Martin, H. C, et al. (2010). Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat. Genet. 42, 62-67.
18. Idaghdour, Y, Storey, J. D., Jadallah, S. J., and Gibson, G. (2008). A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs. PLoS Genet. 4, el000052. doi:10.1371/joumal.pgen.l00005
19. Inouye, M., Silander, K., Hamalainen, E., Salomaa, V., Harald, K., Jousilahti, P., et al. (2010). An immune response network associated with blood lipid levels. PLoS Genet. 6, el001113. doi:10.1371/joumal. pgen.1001113
20. Jamison, D. T., and Mosley, W. H. (1991). Disease control priorities in developing countries: health policy responses to epidemiological change. Am. J. Public Health 81, 15-22.
21. Karlovich, C, Duchateau-Nguyen, G., Johnson, A., McLoughlin, P., Navarro, M., Fleurbaey, C, et al. (2009). A longitudinal study of gene expression in healthy individuals. BMC Med. Genomics 2, 33. doi:10.1186/1755-8794-2-33
22. Kawai, T., Morita, K., Masuda, K., Nishida, K., Shikishima, M., Ohta, M., et al. (2007). Gene expression signature in peripheral blood cells from medical students exposed to chronic psychological stress. Biol. Psychol. 76,147-155.
23. Kent, J. W Jr., Goring, H. H., Charlesworth, J. C, Drigalenko, E., Diego, V. P., Curran, J. E., et al. (2012). Genotype x age interaction in human transcriptional ageing. Mech. Ageing Dev. 133, 581-590.
24. Kim, J., and Gibson, G. (2010). Insights from GWAS into the quantitative genetics of transcription in humans. Genet. Res. 92, 361-369.
25. Lako, V. (2001). Dietary trend and diabetes: its association among indigenous Fijians 1952 to 1994. Asia. Pac. I Clin. Nutr. 10, 183-187.
26. Lai, B. V. (1986). Murmurs of dissent: Non-resistance on Fiji plantations. Hawaiian J. Hist. 20, 188-214.
27. Mason, E., Tronc, G., Nones, K., Matigian, N., Kim, J., Aranow, B. J., et al. (2010). Transmission of leukocyte gene expression profiles in population samples from Brisbane, Australia. PLoS ONE 5, e 14479. doi:10.1371/journal.pone.0014479
28. Mavoa, H. M., and McCabe, M. (2008). Sociocultural factors relating to Ton-gan's and Indigenous Fijians' pattern of eating, physical activity and body size. Asia Pac. J. Clin. Nutr. 17, 375-384.
29. Monks, S. A., Leonardson, A., Zhu, H., Cundiff, P., Pietrusiak, P., Edwards, S., et al. (2004). Genetic inheritance of gene expression in human cell lines. Am. J. Hum. Genet. 75, 1094-1105.
30. Murray, C. J., and Lopez, A. D. (1997). Mortality by cause for eight regions of the world: global burden of disease study. Lancet 349, 1269-1276.
31. Myers, A. J., Gibbs, J. R., Webster, J. A., Rohrer, K., Zhao, A., Marlowe, L. (2007). A survey of genetic human cortical gene expression. Nat. Genet. 39, 1494-1499.
32. Nakaya, H. I., Wrammert, J., Lee, E. K., Racioppi, L., Marie-Kunze, S., Haining, W N., et al. (2011). Systems biology of vaccination for seasonal influenza in humans. Nat. Immunol. 12, 786-795.
33. Peretz, A., Peck, E. C, Bammler, T. K., Beyer, R. P., Sullivan, J. H., Trenga, C. A., et al. (2007). Diesel exhaust inhalation and assessment of peripheral blood mononuclear cell gene transcription effects: an exploratory study of healthy human volunteers. Inhal. Toxicol. 19, 1107-1119.
34. Pollock, N. J. (1995). Cultural elaborations of obesity - fattening practices in Pacific societies. Asia Pac. J. Clin. Nutr. 4, 357-360.
35. Powell, J. E., Henders, A. K., McRae, A. F, Wright, M. J., Martin, N. G., Dermitzakis, E. T., et al. (2012). Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res.22,456-466.
36. Qin, S. P., Kim, J., Arafat, D., and Gibson, G. (2012). Effect of normalization on statistical and biological interpretation of gene expression profiles. Front. Genet. 3, doi:10.3389/fgene.2012.00160
37. Saito, S. (1995). 1993 National Nutrition Survey. Suva: National Food and Nutrition Centre.
38. Schadt, E. E., Molony, C, Chudin, E., Hao, K., Yang, X., Lum, P. Y, et al. (2008). Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 6, elO7. doi:10.1371/joumal. pbio.0060107
39. Schultz, J. T., Vatucawaqa, P., and Tuivaga, J. (2007). 2004 Fiji National Nutrition Survey. Suva: National Food and Nutrition Centre.
40. Siefkenm, K., Macniven, R., Schofield, G., Bauman, A., and Waqanivalu, T. (2012). Stocktake of physical activity programs in the Pacific Islands. Health Promot. Int. 27, 197-207.
41. Skelly, D. A., Ronald, J., and Akey, J. M. (2009). Inherited variation in gene expression. Annu. Rev. Genomics Hum. Genet. 10, 313-332.
42. Spurgeon, S. L., Jones, R. C, and Ramakrishnan, R. (2008). High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS ONE 3, el662. doi:10.1371/journal. pone.0001662
43. Thaman, R. R. (1988). Consumerism, the media and malnutrition in the Pacific Islands. J. Pacific Stud. 14, 68-90.
44. Ulijaszek, S. (2009). Modernization, migration and nutritional health of Pacific Island populations. Environ. Sci. 12,167-176.
45. Xu,Q.,Ni,S.,Wu,E,Liu,E,Ye,X.,Mougin, B., et al. (2011). Investigation of variation in gene expression profiling of human blood by extended principle component analysis. PLoS ONE 6, e26905.doi:10.1371/joumal. pone.0026905