Genetic associations with micronutrient levels identified in immune and gastrointestinal networks

Genes and Nutrition

Volumn 9, Issue 4, 2014, Pages

  Morine, Melissa J ^a   Monteiro, Jacqueline Pontes ^b   Wise, Carolyn ^c   Teitel, Candee ^c   Pence, Lisa ^c   Williams, Anna ^c   Ning, Baitang ^c   McCabe Sellers, Beverly ^d   Champagne, Catherine ^e   Turner, Jerome ^f   Shelby, Beatrice ^f   Bogle, Margaret ^d   Beger, Richard D ^c   Priami, Corrado ^a   Kaput, Jim ^g  

^a UNIVERSITY OF TRENTO   (Italy)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^d AGRICULTURAL RESEARCH SERVICE   (United States)

^e PENNINGTON BIOMEDICAL RESEARCH CENTER   (United States)

^f Boys Girls and Adults Community Development Center Phillips County Community Partners   (United States)

^g NESTLÉ RESEARCH CENTER   (Switzerland)

Author keywords

Community based participatory research; Genetic analysis; Network analysis; Systems nutrition

Indexed keywords

EID: 84904437208     PISSN: 15558932     EISSN: 18653499     Source Type: Journal    
DOI: 10.1007/s12263-014-0408-4     Document Type: Article

References (70)

1. Afacan NJ, Fjell CD, Hancock REW (2012) A systems biology approach to nutritional immunology - focus on innate immunity. Mol Asp Med 33:14-25. doi:10.1016/j.mam.2011.10.013
2. Auffray C, Chen Z, Hood L (2009) Systems medicine: the future of medical genomics and healthcare. Genome Med 1:2. doi:10.1186/gm2
3. Baeke F, Gysemans C, Korf H, Mathieu C (2010) Vitamin D insufficiency: implications for the immune system. Pediatr Nephrol 25:1597-1606. doi:10.1007/s00467-010-1452-y
4. Barker DJ, Gluckman PD, Godfrey KM et al (1993) Fetal nutrition and cardiovascular disease in adult life. Lancet 341:938-941. doi:10.1016/0140- 6736(93)91224-A (Pubitemid 23109122)
5. Beadle G, Tatum E (1941) Genetic control of biochemical reactions in neurospora. Proc Natl Acad Sci USA 27:499-506
6. Beall CM (2007) Two routes to functional adaptation: Tibetan and Andean high-altitude natives. Proc Natl Acad Sci USA 104(Suppl.): 8655-8660. doi:10.1073/pnas.0701985104
7. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Stat Method 57:289-300
8. Bhaskaram P (2002) Micronutrient malnutrition, infection, and immunity: an overview. Nutr Rev 60:S40-S45
9. Bindea G, Mlecnik B, Hackl H et al (2009) ClueGO: a cytoscape plug-into decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091-1093. doi:10.1093/bioinformatics/btp101
10. Brody EN, Gold L (2000) Aptamers as therapeutic and diagnostic agents. J Biotechnol 74:5-13
11. Brody E, Gold L, Mehan M et al (2012) Life's simple measures: unlocking the proteome. J Mol Biol 422:595-606. doi:10.1016/j.jmb.2012.06.021
12. Bustamante CD, Burchard EG, De la Vega FM (2011) Genomics for the world. Nature 475:163-165. doi:10.1038/475163a
13. Chen R, Mias GI, Li-Pook-Than J et al (2012) Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148:1293-1307. doi:10.1016/j.cell.2012.02.009
14. Cheng CY, Reich D, Coresh J et al (2010) Admixture mapping of obesity-related traits in African Americans: the Atherosclerosis Risk in Communities (ARIC) Study. Obes (Silver Spring) 18:563-572. doi:10.1038/oby.2009. 282
15. Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal Complex Syst 1695. http://cran.rproject.org/web/ packages/igraph/citation.html
16. Dominguez-Salas P, Moore SE, Cole D et al (2013) DNA methylation potential: dietary intake and blood concentrations of one-carbon metabolites and cofactors in rural African women. Am J Clin Nutr 97:1217-1227. doi:10.3945/ajcn.112.048462.The
17. Fenech M, El-Sohemy A, Cahill L et al (2011) Nutrigenetics and nutrigenomics: viewpoints on the current status and applications in nutrition research and practice. J Nutrigenet Nutrigenomics 4:69-89. doi:10.1159/000327772
18. Gardy JL, Lynn DJ, Brinkman FSL, Hancock REW (2009) Enabling a systems biology approach to immunology: focus on innate immunity. Trends Immunol 30:249-262. doi:10.1016/j.it.2009.03.009
19. Gluckman PD, Hanson MA, Buklijas T et al (2009) Epigenetic mechanisms that underpin metabolic and cardiovascular diseases. Nat Rev Endocrinol 5:401-408. doi:10.1038/nrendo.2009.102
20. Gold L (1995) Oligonucleotides as research diagnostic, and therapeutic agents. J Biol Chem 270:13581-13584
21. Gold L, Ayers D, Bertino J et al (2010) Aptamer-based multiplexed proteomic technology for biomarker discovery. PLoS One 5:e15004. doi:10.1371/journal.pone.0015004
22. Gold L, Walker JJ, Wilcox SK, Williams S (2011) Advances in human proteomics at high scale with the SOMAscan proteomics platform. N Biotechnol. doi:10.1016/j.nbt.2011.11.016
23. Goldstein DB (2009) Common genetic variation and human traits. N Engl J Med 360:1696-1698. doi:10.1056/NEJMp0806284
24. Hamza TH, Chen H, Hill-Burns EM et al (2011) Genome-wide gene-environment study identifies glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee. PLoS Genet 7:e1002237. doi:10.1371/journal.pgen.1002237
25. Harris SC, Fang H, Su Z et al (2009) FDA bioinformatics tool for public use - ArrayTrack™. Methods Mol Biol 563:379-398. doi:10.1007/978-1-60761- 175-2-20
26. Hemani G, Yang J, Vinkhuyzen A et al (2013) Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs. Am J Hum Genet 93:865-875. doi:10.1016/j.ajhg.2013.10.005
27. Højsgaard S, Halekoh U, Yan J (2006) The R package geepack for generalized estimating equations. J Stat Softw 15:1-11 (Pubitemid 43037444)
28. Illig T, Gieger C, Zhai G et al (2010) A genome-wide perspective of genetic variation in human metabolism. Nat Genet 42:137-141. doi:10.1038/ng.507
29. Kalupahana NS, Moustaid-moussa N (2011) Overview of symposium "systems genetics in nutrition and obesity research" 1(2):3-5. doi:10.3945/jn.110.130104.512
30. Kaput J, Rodriguez RL (2004) Nutritional genomics: the next frontier in the postgenomic era. Physiol Genomics 16:166-177 (Pubitemid 38420031)
31. Kaput J, Swartz D, Paisley E et al (1994) Diet-disease interactions at the molecular level: an experimental paradigm. J Nutr 124:1296S-1305S (Pubitemid 24283390)
32. Kaput J, Klein KG, Reyes EJ et al (2004) Identification of genes contributing to the obese yellow Avy phenotype: caloric restriction, genotype, diet x genotype interactions. Physiol Genomics 18:316-324 (Pubitemid 39319515)
33. Karlsson FH, Nookaew I, Petranovic D, Nielsen J (2011) Prospects for systems biology and modeling of the gut microbiome. Trends Biotechnol 29:251-258. doi:10.1016/j.tibtech.2011.01.009
34. Kleemann R, Bureeva S, Perlina A et al (2011) A systems biology strategy for predicting similarities and differences of drug effects: evidence for drug-specific modulation of inflammation in atherosclerosis. BMC Syst Biol 5:125. doi:10.1186/1752-0509-5-125
35. Kraemer S, Vaught JD, Bock C et al (2011) From SOMAmer-based biomarker discovery to diagnostic and clinical applications: a SOMAmer-based, streamlined multiplex proteomic assay. PLoS One 6:e26332. doi:10.1371/journal.pone.0026332
36. Kussmann M, Krause L, Siffert W (2010) Nutrigenomics: where are we with genetic and epigenetic markers for disposition and susceptibility? Nutr Rev 68(Suppl. 1):S38-S47. doi:10.1111/j.1753-4887.2010.00326.x
37. Lee Y-C, Lai C-Q, Ordovas JM, Parnell LD (2011) A database of gene-environment interactions pertaining to blood lipid traits, cardiovascular disease and type 2 diabetes. J Data Min Genomics Proteomics 2:1-8. doi:10.4172/2153-0602.1000106
38. Liu JZ, McRae AF, Nyholt DR et al (2010) A versatile gene-based test for genome-wide association studies. Am J Hum Genet 87:139-145. doi:10.1016/j.ajhg. 2010.06.009
39. Ma H, Sorokin A, Mazein A et al (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 3:135. doi:10.1038/msb4100177
40. Maggini S, Wintergerst ES, Beveridge S, Hornig DH (2007) Selected vitamins and trace elements support immune function by strengthening epithelial barriers and cellular and humoral immune responses. Br J Nutr 98(Suppl. 1):S29-S35. doi:10.1017/S0007114507832971 (Pubitemid 47558856)
41. McCabe-Sellers B, Lovera D, Nuss H et al (2008) Personalizing nutrigenomics research through community based participatory research and omics technologies. OMICS 12:263-272. doi:10.1089/omi.2008.0041 (Pubitemid 352773936)
42. Meng Q, Mäkinen V-P, Luk H, Yang X (2013) Systems biology approaches and applications in obesity, diabetes, and cardiovascular diseases. Curr Cardiovasc Risk Rep 7:73-83. doi:10.1007/s12170-012-0280-y
43. Monteiro J, Wise C, Morine M et al (2014) Methylation potential associated with diet, genotype, protein, and metabolite levels in the delta obesity vitamin study. Genes Nutr 9(3):403-418. doi:10.1007/s12263-014-0403-9
44. Morine MJ, McMonagle J, Toomey S et al (2010) Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of metabolic syndrome. BMC Bioinform 11:499. doi:10.1186/1471-2105-11-499
45. Morine MJ, Tierney AC, van Ommen B et al (2011) Transcriptomic coordination in the human metabolic network reveals links between n-3 fat intake, adipose tissue gene expression and metabolic health. PLoS Comput Biol 7:e1002223. doi:10.1371/journal.pcbi.1002223
46. Morine MJ, Toomey S, McGillicuddy FC et al (2012) Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice. J Nutr Biochem. doi:10.1016/j.jnutbio.2012.04.012
47. Nettleton JA, McKeown NM, Kanoni S et al (2010) Interactions of dietary whole-grain intake with fasting glucose - and insulin-related genetic loci in individuals of European descent. Diabetes Care 33:2684-2691. doi:10.2337/dc10-1150
48. Olson MV (2012) Human genetic individuality. Annu Rev Genomics Hum Genet 13:1-27. doi:10.1146/annurev-genom-090711-163825
49. Ooi JH, Chen J, Cantorna MT (2012) Vitamin D regulation of immune function in the gut: why do T cells have vitamin D receptors? Mol Asp Med 33:77-82. doi:10.1016/j.mam.2011.10.014
50. Ordovás JM, Robertson R, Cléirigh EN (2011) Gene-gene and gene-environment interactions defining lipid-related traits. Curr Opin Lipidol 22:129-136. doi:10.1097/MOL.0b013e32834477a9
51. Ostroff R, Foreman T, Keeney TR et al (2010) The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J Proteomics 73:649-666. doi:10.1016/j.jprot.2009.09.004
52. Patel CJ, Bhattacharya J, Butte AJ (2010) An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus. PLoS One 5:e10746. doi:10.1371/journal.pone.0010746
53. Patel CJ, Chen R, Butte AJ (2012a) Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease. Bioinformatics 28:i121-i126. doi:10.1093/bioinformatics/bts229
54. Patel CJ, Cullen MR, Ioannidis JPA, Butte AJ (2012b) Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels. Int J Epidemiol 41:828-843. doi:10.1093/ije/dys003
55. Ramos E, Rotimi C (2009) The A's, G's, C's, and T's of health disparities. BMC Med Genomics 2:29. doi:10.1186/1755-8794-2-29
56. Reichardt J, Bornholdt S (2006) Statistical mechanics of community detection. Phys Rev E Stat Nonlin Soft Matter Phys 74:016110
57. Roux AVD (2011) Complex systems thinking and current impasses in health disparities research. Am J Public Health 101:1627-1634. doi:10.2105/AJPH.2011. 300149.Complex
58. Schulz LO, Bennett PH, Ravussin E et al (2006) Effects of traditional and western environments on prevalence of type 2 diabetes in Pima Indians in Mexico and the U.S. Diabetes Care 29:1866-1871. doi:10.2337/dc06-0138 (Pubitemid 44156644)
59. Slikker W Jr, Paule MG, Wright LK et al (2007) Systems biology approaches for toxicology. J Appl Toxicol 27:201-217. doi:10.1002/jat.1207 (Pubitemid 46663415)
60. So L, Fruman DA (2012) PI3K signaling in B and T lymphocytes: new developments and therapeutic advances. Biochem J 442:465-481. doi:10.1042/BJ20112092.PI3K
61. Stahl EA, Wegmann D, Trynka G et al (2012) Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis. Nat Genet 44:483-489. doi:10.1038/ng.2232
62. Ströhle A, Wolters M, Hahn A (2011) Micronutrients at the interface between inflammation and infection-ascorbic acid and calciferol. Part 2: calciferol and the significance of nutrient supplements. Inflamm Allergy Drug Targets 10:64-74
63. Suhre K, Shin SY, Petersen AK et al (2011) Human metabolic individuality in biomedical and pharmaceutical research. Nature 477:54-60. doi:10.1038/nature10354
64. Tanaka T, Ngwa JS, van Rooij FJA et al (2013) Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake. Am J Clin Nutr 97:1395-1402. doi:10.3945/ajcn.112.052183
65. Valentini L, Schaper L, Buning C et al (2008) Malnutrition and impaired muscle strength in patients with Crohn's disease and ulcerative colitis in remission. Nutrition 24:694-702. doi:10.1016/j.nut.2008.03.018
66. Von Bertalanffy L (1950) The theory of open systems in physics and biology. Science 111(2872):23-29
67. Waterland RA, Kellermayer R, Laritsky E et al (2010) Season of conception in rural Gambia affects DNA methylation at putative human metastable epialleles. PLoS Genet 6:e1001252. doi:10.1371/journal.pgen.1001252
68. Williams RP (1956) Biochemical individuality: the basis for the genetotrophic concept. Keats, New Canaan
69. Xu J, Wise C, Varma V et al (2010) Two new ArrayTrack libraries for personalized biomedical research. BMC Bioinform 11(Suppl. 6):S6. doi:10.1186/1471-2105-11-S6-S6
70. Yu X, Wallqvist A, Reifman J (2012) Inferring high-confidence human protein-protein interactions. BMC Bioinform 13:79. doi:10.1186/1471-2105-13-79