Nutrigenetics, nutrigenomics and inflammatory bowel diseases

References

• Ferguson LR. Nutrigenomics and inflammatory bowel diseases. Expert Rev. Clin. Immunol. 6(4), 573–583 (2010).
   PubMed Web of Science ®Google Scholar
• Ferguson LR. Potential value of nutrigenomics in Crohn’s disease. Nat. Rev. Gastroenterol. Hepatol. 9(5), 260–270 (2012).
   PubMed Web of Science ®Google Scholar
• Jenke AC, Zilbauer M. Epigenetics in inflammatory bowel disease. Curr. Opin. Gastroenterol. 28(6), 577–584 (2012).
   PubMed Web of Science ®Google Scholar
• Wu HJ, Wu E. The role of gut microbiota in immune homeostasis and autoimmunity. Gut. Microbes. 3(1), 4–14 (2012).
   PubMed Web of Science ®Google Scholar
• Gentschew L, Ferguson LR. Role of nutrition and microbiota in susceptibility to inflammatory bowel diseases. Mol. Nutr. Food Res. 56(4), 524–535 (2012).
   PubMed Web of Science ®Google Scholar
• Baker PI, Love DR, Ferguson LR. Role of gut microbiota in Crohn’s disease. Expert Rev. Gastroenterol. Hepatol. 3(5), 535–546 (2009).
   PubMedGoogle Scholar
• Richardson K, Lai CQ, Parnell LD, Lee YC, Ordovas JM. A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS. BMC Genomics 12, 504 (2011).
   PubMed Web of Science ®Google Scholar
• Kerkhof M, Postma DS, Brunekreef B et al. Toll-like receptor 2 and 4 genes influence susceptibility to adverse effects of traffic-related air pollution on childhood asthma. Thorax 65(8), 690–697 (2010).
   PubMed Web of Science ®Google Scholar
• Nakashima K, Hirota T, Suzuki Y et al. Association of the RIP2 gene with childhood atopic asthma. Allergol. Int. 55(1), 77–83 (2006).
   Google Scholar
• Siu H, Zhu Y, Jin L, Xiong M. Implication of next-generation sequencing on association studies. BMC Genomics 12, 322 (2011).
   Google Scholar
• Yaspan BL, Bush WS, Torstenson ES et al. Genetic analysis of biological pathway data through genomic randomization. Hum. Genet. 129(5), 563–571 (2011).
   Google Scholar
• Lees CW, Barrett JC, Parkes M, Satsangi J. New IBD genetics: common pathways with other diseases. Gut 60(12), 1739–1753 (2011).
   PubMed Web of Science ®Google Scholar
• Jostins L, Ripke S, Weersma RK et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491(7422), 119–124 (2012).
   PubMed Web of Science ®Google Scholar
• Fei M, Bhatia S, Oriss TB et al. TNF-alpha from inflammatory dendritic cells (DCs) regulates lung IL-17 A/IL-5 levels and neutrophilia versus eosinophilia during persistent fungal infection. Proc. Natl Acad. Sci USA 108(13), 5360–5365 (2011).
   PubMedGoogle Scholar
• Ng MT, Van’t Hof R, Crockett JC et al. Increase in NF-kappaB binding affinity of the variant C allele of the toll-like receptor 9-1237T/C polymorphism is associated with Helicobacter pylori-induced gastric disease. Infect. Immun. 78(3), 1345–1352 (2010).
   PubMedGoogle Scholar
• Ivanov II, McKenzie BS, Zhou L et al. The orphan nuclear receptor RORgammat directs the differentiation program of proinflammatory IL-17+ T helper cells. Cell 126(6), 1121–1133 (2006).
   PubMed Web of Science ®Google Scholar
• Di Sabatino A, Jackson CL, Pickard KM et al. Transforming growth factor beta signalling and matrix metalloproteinases in the mucosa overlying Crohn’s disease strictures. Gut 58(6), 777–789 (2009).
   PubMed Web of Science ®Google Scholar
• Cooke J, Zhang H, Greger L et al. Mucosal genome-wide methylation changes in inflammatory bowel disease. Inflamm. Bowel Dis. 18(11), 2128–2137 (2012).
   PubMed Web of Science ®Google Scholar
• Lin Z, Hegarty JP, Yu W et al. Identification of disease-associated DNA methylation in B cells from Crohn’s disease and ulcerative colitis patients. Dig. Dis. Sci. 57(12), 3145–3153 (2012).
   PubMed Web of Science ®Google Scholar
• Ferguson LR, Han DY, Fraser AG, Huebner C, Lam WJ, Morgan AR. IL23R and IL12B SNPs and haplotypes strongly sssociate with Crohn’s disease risk in a New Zealand population. Gastroenterol. Res. Pract. 2010, 539461 (2010).
   PubMed Web of Science ®Google Scholar
• Nimmo ER, Prendergast JG, Aldhous MC et al. Genome-wide methylation profiling in Crohn’s disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway. Inflamm. Bowel Dis. 18(5), 889–899 (2012).
   PubMed Web of Science ®Google Scholar
• Scarpa M, Stylianou E. Epigenetics: concepts and relevance to IBD pathogenesis. Inflamm. Bowel Dis. 18(10), 1982–1996 (2012).
   Google Scholar
• Paraskevi A, Theodoropoulos G, Papaconstantinou I, Mantzaris G, Nikiteas N, Gazouli M. Circulating MicroRNA in inflammatory bowel disease. J. Crohns Colitis 6(9), 900–904 (2012).
   PubMed Web of Science ®Google Scholar
• Clark PM, Dawany N, Dampier W, Byers SW, Pestell RG, Tozeren A. Bioinformatics analysis reveals transcriptome and microRNA signatures and drug repositioning targets for IBD and other autoimmune diseases. Inflamm. Bowel Dis. 18(12), 2315–2333 (2012).
   PubMed Web of Science ®Google Scholar
• Noble CL, Abbas AR, Lees CW et al. Characterization of intestinal gene expression profiles in Crohn’s disease by genome-wide microarray analysis. Inflamm. Bowel Dis. 16(10), 1717–1728 (2010).
   PubMed Web of Science ®Google Scholar
• Liang J, Jiang D, Jung Y et al. Role of hyaluronan and hyaluronan-binding proteins in human asthma. J. Allergy Clin Immunol. 128(2), 403–411 (2011).
   PubMed Web of Science ®Google Scholar
• Granlund A, Flatberg A, Ostvik AE et al. Whole genome gene expression meta-analysis of inflammatory bowel disease colon mucosa demonstrates lack of major differences between Crohn’s disease and ulcerative colitis. PLoS ONE 8(2), e56818 (2013).
   PubMed Web of Science ®Google Scholar
• Frank DN, Robertson CE, Hamm CM et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm. Bowel Dis. 17(1), 179–184 (2011).
   PubMed Web of Science ®Google Scholar
• Hansen JJ, Huang Y, Peterson DA et al. The colitis-associated transcriptional profile of commensal Bacteroides thetaiotaomicron enhances adaptive immune responses to a bacterial antigen. PLoS ONE 7(8), e42645 (2012).
   PubMedGoogle Scholar
• Li E, Hamm CM, Gulati AS et al. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS ONE 7(6), e26284 (2012).
   PubMed Web of Science ®Google Scholar
• Morgan XC, Tickle TL, Sokol H et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13(9), R79 (2012).
   PubMed Web of Science ®Google Scholar
• Hotte NS, Salim SY, Tso RH et al. Patients with inflammatory bowel disease exhibit dysregulated responses to microbial DNA. PLoS ONE 7(5), e37932 (2012).
   Google Scholar
• Grafors JM, Casswall TH. Exclusive enteral nutrition in the treatment of children with Crohn’s disease in Sweden: a questionnaire survey. Acta Paediatr. 100(7), 1018–1022 (2011).
   Google Scholar
• Akobeng AK, Thomas AG. Refeeding syndrome following exclusive enteral nutritional treatment in Crohn disease. J. Pediatr. Gastroenterol. Nutr. 51(3), 364–366 (2010).
   Google Scholar
• Brown AC, Rampertab SD, Mullin GE. Existing dietary guidelines for Crohn’s disease and ulcerative colitis. Expert Rev. Gastroenterol. Hepatol. 5(3), 411–425 (2011).
   PubMed Web of Science ®Google Scholar
• Khoshoo V, Sun SS, Storm H. Tolerance of an enteral formula with insoluble and prebiotic fiber in children with compromised gastrointestinal function. J. Am. Diet. Assoc. 110(11), 1728–1733 (2010).
   PubMedGoogle Scholar
• Tighe MP, Cummings JR, Afzal NA. Nutrition and inflammatory bowel disease: primary or adjuvant therapy. Curr. Opin. Clin. Nutr. Metab. Care 14(5), 491–496 (2011).
   Google Scholar
• Nolan-Clark D, Tapsell LC, Hu R, Han DY, Ferguson LR. Effects of dairy products on crohn’s disease symptoms are influenced by fat content and disease location but not lactose content or disease activity status in a New Zealand population. J. Am. Diet. Assoc. 111(8), 1165–1172 (2011).
   PubMedGoogle Scholar
• Gentschew L, Bishop KS, Han DY et al. Selenium, selenoprotein genes and Crohn’s disease in a case–control population from Auckland, New Zealand. Nutrients 4(9), 1247–1259 (2012).
   PubMed Web of Science ®Google Scholar
• Rayman MP. Selenium and human health. Lancet 379(9822), 1256–1268 (2012).
   PubMed Web of Science ®Google Scholar
• Ringstad J, Kildebo S, Thomassen Y. Serum selenium, copper, and zinc concentrations in Crohn’s disease and ulcerative colitis. Scand. J. Gastroenterol. 28(7), 605–608 (1993).
   PubMed Web of Science ®Google Scholar
• Griffin IJ, Kim SC, Hicks PD, Liang LK, Abrams SA. Zinc metabolism in adolescents with Crohn’s disease. Pediatr. Res. 56(2), 235–239 (2004).
   PubMed Web of Science ®Google Scholar
• Haritunians T, Jones MR, McGovern DP et al. Variants in ZNF365 isoform D are associated with Crohn’s disease. Gut 60(8), 1060–1067 (2011).
   PubMed Web of Science ®Google Scholar
• Wu S, Liao AP, Xia Y et al. Vitamin D receptor negatively regulates bacterial-stimulated NF-kappaB activity in intestine. Am. J. Pathol. 177(2), 686–697 (2010).
   PubMed Web of Science ®Google Scholar
• Wang TT, Dabbas B, Laperriere D et al. Direct and indirect induction by 1,25-dihydroxyvitamin D3 of the NOD2/CARD15-defensin beta2 innate immune pathway defective in Crohn disease. J. Biol. Chem. 285(4), 2227–2231 (2010).
   PubMed Web of Science ®Google Scholar
• Calder PC. Omega-3 polyunsaturated fatty acids and inflammatory processes: nutrition or pharmacology? Br. J. Clin. Pharmacol. 75(3), 645–662 (2013).
   PubMed Web of Science ®Google Scholar
• Ferguson LR, Smith BG, James BJ. Combining nutrition, food science and engineering in developing solutions to Inflammatory bowel diseases – omega-3 polyunsaturated fatty acids as an example. Food Funct. 1(1), 60–72 (2010).
   PubMed Web of Science ®Google Scholar
• El-Tawil AM. Zinc supplementation tightens leaky gut in Crohn’s disease. Inflamm. Bowel Dis. 18(2), E399 (2012).
   Google Scholar
• Ainley C, Cason J, Slavin BM, Wolstencroft RA, Thompson RP. The influence of zinc status and malnutrition on immunological function in Crohn’s disease. Gastroenterology 100(6), 1616–1625 (1991).
   PubMed Web of Science ®Google Scholar
• Hering NA, Schulzke JD. Therapeutic options to modulate barrier defects in inflammatory bowel disease. Dig. Dis. 27(4), 450–454 (2009).
   PubMed Web of Science ®Google Scholar
• Suzuki T, Hara H. Role of flavonoids in intestinal tight junction regulation. J. Nutr. Biochem. 22(5), 401–408 (2011).
   PubMed Web of Science ®Google Scholar
• Ho E, Beaver LM, Williams DE, Dashwood RH. Dietary factors and epigenetic regulation for prostate cancer prevention. Adv. Nutr. 2(6), 497–510 (2011).
   PubMed Web of Science ®Google Scholar
• Ho E, Dashwood RH. Dietary manipulation of histone structure and function. World Rev. Nutr. Diet. 101, 95–102 (2010).
   Google Scholar
• Rajendran P, Delage B, Dashwood WM et al. Histone deacetylase turnover and recovery in sulforaphane-treated colon cancer cells: competing actions of 14-3-3 and Pin1 in HDAC3/SMRT corepressor complex dissociation/reassembly. Mol. Cancer. 10, 68 (2011).
   PubMedGoogle Scholar
• Rajendran P, Ho E, Williams DE, Dashwood RH. Dietary phytochemicals, HDAC inhibition, and DNA damage/repair defects in cancer cells. Clin. Epigenetics 3(1), 4 (2011).
   PubMed Web of Science ®Google Scholar
• Rajendran P, Williams DE, Ho E, Dashwood RH. Metabolism as a key to histone deacetylase inhibition. Crit. Rev. Biochem. Mol. Biol. 46(3), 181–199 (2011).
   PubMed Web of Science ®Google Scholar
• Grimoud J, Durand H, de Souza S et al. In vitro screening of probiotics and synbiotics according to anti-inflammatory and anti-proliferative effects. Int. J. Food Microbiol. 144(1), 42–50 (2010).
   PubMed Web of Science ®Google Scholar
• Calder PC. Fatty acids and inflammation: the cutting edge between food and pharma. Eur. J. Pharmacol. 668(Suppl. 1), S50–S58 (2011).
   PubMed Web of Science ®Google Scholar
• Calder PC. The role of marine omega-3 (n-3) fatty acids in inflammatory processes, atherosclerosis and plaque stability. Mol. Nutr. Food Res. 56(7), 1073–1080 (2012).
   PubMed Web of Science ®Google Scholar
• Appleyard CB, Cruz ML, Isidro AA, Arthur JC, Jobin C, De Simone C. Pretreatment with the probiotic VSL#3 delays transition from inflammation to dysplasia in a rat model of colitis-associated cancer. Am. J. Physiol. Gastrointest. Liver Physiol. 301(6), G1004–1013 (2011).
   PubMed Web of Science ®Google Scholar
• Cain AM, Karpa KD. Clinical utility of probiotics in inflammatory bowel disease. Altern. Ther. Health Med. 17(1), 72–79 (2011).
   PubMed Web of Science ®Google Scholar
• Oelschlaeger TA. Mechanisms of probiotic actions – a review. Int. J. Med. Microbiol. 300(1), 57–62 (2010).
   PubMed Web of Science ®Google Scholar
• Mack DR. Probiotics in inflammatory bowel diseases and associated conditions. Nutrients 3(2), 245–264 (2011).
   PubMed Web of Science ®Google Scholar
• Jackson EL, Hamlin PJ, Ford AC. VSL#3 and remission in active ulcerative colitis: larger studies required. Am. J. Gastroenterol. 106(3), 547; author reply 547–548 (2011).
   Google Scholar
• Doherty GA, Bennett GC, Cheifetz AS, Moss AC. Meta-analysis: targeting the intestinal microbiota in prophylaxis for post-operative Crohn’s disease. Aliment. Pharmacol. Ther. 31(8), 802–809 (2010).
   PubMed Web of Science ®Google Scholar
• Hedin CR, Mullard M, Sharratt E et al. Probiotic and prebiotic use in patients with inflammatory bowel disease: a case–control study. Inflamm. Bowel Dis. 16(12), 2099–2108 (2010).
   PubMed Web of Science ®Google Scholar
• Anderson RC, Cookson AL, McNabb WC, Kelly WJ, Roy NC. Lactobacillus plantarum DSM 2648 is a potential probiotic that enhances intestinal barrier function. FEMS Microbiol. Lett. 309(2), 184–192 (2010).
   Google Scholar
• Benjamin JL, Hedin CR, Koutsoumpas A et al. Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn’s disease. Gut 60(7), 923–929 (2011).
   PubMed Web of Science ®Google Scholar
• Quigley EM. Prebiotics and probiotics: their role in the management of gastrointestinal disorders in adults. Nutr. Clin. Pract. 27(2), 195–200 (2012).
   Google Scholar
• Marteau P. Therapy: probiotic-enriched artichokes for abdominal discomfort. Nat. Rev. Gastroenterol. Hepatol. 9(5), 251–252 (2012).
   Google Scholar
• Riezzo G, Orlando A, D’Attoma B et al. Randomised clinical trial: efficacy of Lactobacillus paracasei-enriched artichokes in the treatment of patients with functional constipation – a double-blind, controlled, crossover study. Aliment. Pharmacol. Ther. 35(4), 441–450 (2012).
   PubMed Web of Science ®Google Scholar
• Selma MV, Espin JC, Tomas-Barberan FA. Interaction between phenolics and gut microbiota: role in human health. J. Agric Food Chem. 57(15), 6485–6501 (2009).
   PubMed Web of Science ®Google Scholar
• Tzounis X, Rodriguez-Mateos A, Vulevic J, Gibson GR, Kwik-Uribe C, Spencer JP. Prebiotic evaluation of cocoa-derived flavanols in healthy humans by using a randomized, controlled, double-blind, crossover intervention study. Am. J. Clin. Nutr. 93(1), 62–72 (2011).
   PubMed Web of Science ®Google Scholar
• Qin X. The effect of dietary chemicals on gut bacteria and IBD demands further study. J. Crohns Colitis 5(2), 175 (2011).
   Google Scholar
• Ly NP, Litonjua A, Gold DR, Celedon JC. Gut microbiota, probiotics, and vitamin D: interrelated exposures influencing allergy, asthma, and obesity? J. Allergy Clin. Immunol. 127(5), 1087–1094; quiz 1095–1096 (2011).
   PubMed Web of Science ®Google Scholar
• Weiss ST. Bacterial components plus vitamin D: the ultimate solution to the asthma (autoimmune disease) epidemic? J. Allergy Clin. Immunol. 127(5), 1128–1130 (2011).
   PubMed Web of Science ®Google Scholar
• Triggs CM, Munday K, Hu R et al. Dietary factors in chronic inflammation: food tolerances and intolerances of a New Zealand Caucasian Crohn’s disease population. Mutat. Res. 690(1–2), 123–138 (2010).
   PubMed Web of Science ®Google Scholar
• Ellet S, Ferguson IR, Zhu S et al. Chapter 13. Foodomics to study efficacy of human dietary interventions. In: Nutrigenomics and Nutrigenetics in Functional Foods and Personalized Nutrition. Taylor & Francis, CRC Press, USA (2013).
   Google Scholar