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1.  Why interleukin-10 supplementation does not work in Crohn’s disease patients 
Inflammatory bowel diseases (IBD) such as Crohn’s disease (CD) or ulcerative colitis are chronic intestinal disorders, which are on the increase in “Westernised” countries. IBD can be caused by both genetic and environmental factors. Interleukin-10 (IL-10) is an immunoregulatory cytokine that has been identified as being involved in several diseases including IBD. Studies have shown that polymorphisms in the promoter region reduce serum levels of IL-10 and this reduction has been associated with some forms of IBD. Mouse models have shown promising results with IL-10 supplementation, as such IL-10 supplementation has been touted as being a possible alternative treatment for CD in humans. Clinical trials have shown that recombinant human IL-10 is safe and well tolerated up to a dose of 8 μg/kg. However, to date, the results of the clinical trials have been disappointing. Although CD activity was reduced as measured by the CD activity index, IL-10 supplementation did not result in significantly reduced remission rates or clinical improvements when compared to placebo. This review discusses why IL-10 supplementation is not effective in CD patients currently and what can be addressed to potentially make IL-10 supplementation a more viable treatment option in the future. Based on the current research we conclude that IL-10 supplementation is not a one size fits all treatment and if the correct population of patients is chosen then IL-10 supplementation could be of benefit.
doi:10.3748/wjg.v19.i25.3931
PMCID: PMC3703179  PMID: 23840137
Inflammatory bowel disease; Crohn’s disease; Interleukin-10; Recombinant human interleukin-10
2.  Potential prospects of nanomedicine for targeted therapeutics in inflammatory bowel diseases 
Inflammatory bowel diseases (IBDs) such as Crohn’s disease are highly debilitating. There are inconsistencies in response to and side effects in the current conventional medications, failures in adequate drug delivery, and the lack of therapeutics to offer complete remission in the presently available treatments of IBD. This suggests the need to explore beyond the horizons of conventional approaches in IBD therapeutics. This review examines the arena of the evolving IBD nanomedicine, studied so far in animal and in vitro models, before comprehensive clinical testing in humans. The investigations carried out so far in IBD models have provided substantial evidence of the nanotherapeutic approach as having the potential to overcome some of the current drawbacks to conventional IBD therapy. We analyze the pros and cons of nanotechnology in IBD therapies studied in different models, aimed at different targets and mechanisms of IBD pathogenesis, in an attempt to predict its possible impact in humans.
doi:10.3748/wjg.v18.i23.2895
PMCID: PMC3380316  PMID: 22736912
Inflammatory bowel disease; Crohn’s disease; Ulcerative colitis; Tumor necrosis factor-α; Nanomedicine
3.  IL23R and IL12B SNPs and Haplotypes Strongly Associate with Crohn's Disease Risk in a New Zealand Population 
DNA samples from 339 Crohn's disease (CD) and 407 randomly selected controls from the Auckland (New Zealand) IBD project, were genotyped for five common single nucleotide polymorphisms in IL-23R (rs11805303, rs7517847, rs1343151, rs11209026, and rs10889677) and two in IL-12B (rs1363670 and rs6887695). While the IL-12B variants did not show an overall association and other IL23R variants led to minor changes in the risk of CD, rs1343151 and/or rs7517847 variants in the IL-23R gene strongly reduced the risk of developing CD at both allelic and genotype levels. A significantly decreased risk of first diagnosis of childhood CD was observed in individuals carrying the A allele of rs1343151, or between 17–40 y in individuals carrying the G allele in rs7517847 of IL-23R. A significantly decreased risk of ileocolonic or structuring disease was observed in individuals carrying the A allele in either rs11209026 or rs1343151, or the G allele in rs7517847 of IL-23R, and when such individuals did develop the disease, they were unlikely to require a bowel resection. Certain haplotypes very strongly modified risk. There was evidence for interactions of IL-23R variants with the NOD2 wild-type (d/d) genotype. Down-regulating the function of the IL-23R gene may decrease CD risk in the normal population.
doi:10.1155/2010/539461
PMCID: PMC3021847  PMID: 21253534
4.  Recent advances in understanding of interactions between genes and diet in the etiology of colorectal cancer 
At an international level, colorectal cancer (CRC) is a major cause of morbidity and mortality. Diet plays a major etiologic role, and a range of putative dietary carcinogens have been identified. The probability with which these lead to mutations, and thereby cause cancer, is strongly impacted by variants in genes coding for xenobiotic metabolizing or DNA repair enzymes. Nutrient deficiencies also play a role, which will be exacerbated by variants in metabolic genes. However, many of the causal genes in sporadic CRC have hitherto proved elusive. The power of large international collaborations, coupled with genome-wide association studies, has implicated a major functional role of the tumour growth factor-β pathway in CRC susceptibility. Nutrient regulation of gene expression may be especially important here. Future large collaborative studies must consider gene-gene and gene-diet interactions, coupled with high throughput genomic technologies, in order to uncover the relative roles of genetic variants, mutagenic xenobiotics, nutrient imbalance and gene expression in the etiology of CRC.
doi:10.4251/wjgo.v2.i3.125
PMCID: PMC2999172  PMID: 21160819
Transforming growth factor β; Colorectal cancer; Single nucleotide polymorphisms; Genome wide association studies; Gene expression
5.  Tumor Necrosis Factor Receptor Superfamily, Member 1B Haplotypes Increase or Decrease the Risk of Inflammatory Bowel Diseases in a New Zealand Caucasian Population 
Inflammatory bowel diseases (IBDs) comprising Crohn disease (CD) and ulcerative colitis (UC) are chronic inflammatory conditions with polygenic susceptibility. Interactions between TNF-alpha and TNF-alpha receptor play a fundamental role in inflammatory response. This study investigates the role that selected single nucleotide polymorphisms (SNPs) and haplotypes in the TNF-alpha receptor (TNSFRSF1B) gene play in the risk of IBD in a New Zealand Caucasian population. DNA samples from 388 CD, 405 UC, 27 indeterminate colitis patients, and 293 randomly selected controls, from Canterbury, New Zealand were screened for 3 common SNPs in TNSFRSF1B: rs1061622 (c.676T > C), rs1061624 (c.*1663A > G), and rs3397 (c.*1690T > C), using TaqMan technologies. Carrying the rs1061624 variant decreased the risk of UC in the left colon (OR 0.73, 95% CI = 0.54–1.00) and of being a smoker at diagnosis (OR 0.62; 95% CI = 0.40–0.96). Carrying the rs3397 variant decreased the risk of penetrating CD (OR 0.62, 95% CI = 0.40–0.95). Three marker haplotype analyses revealed highly significant differences between CD patients and control subjects (χ2 = 29.9, df = 7, P = .0001) and UC cases and controls (χ2 = 46.3, df = 7, P < .0001). We conclude that carrying a 3-marker haplotype in the TNSFRSF1B gene may increase (e.g., haplotype of GGC was 2.9-fold more in the CD or UCpatients) or decrease (e.g., TGT was 0.47-fold less in UC patients) the risk of IBD in a New Zealand Caucasian population.
doi:10.1155/2009/591704
PMCID: PMC2676325  PMID: 19421420
6.  Single nucleotide polymorphism in the tumor necrosis factor-alpha gene affects inflammatory bowel diseases risk 
AIM: To investigate the role that single nucleotide polymorphisms (SNPs) in the promoter of the tumour necrosis factor-alpha (TNF-α) gene play in the risk of inflammatory bowel diseases (IBDs) in a New Zealand population, in the context of international studies.
METHODS: DNA samples from 388 patients with Crohn’s disease (CD), 405 ulcerative colitis (UC), 27 indeterminate colitis (IC) and 201 randomly selected controls, from Canterbury, New Zealand were screened for 3 common polymorphisms in the TNF-α receptor: -238 G→A, -308 G→A and -857C→T, using a TaqmanR assay. A meta-analysis was performed on the data obtained on these polymorphisms combined with that from other published studies.
RESULTS: Individuals carrying the -308 G/A allele had a significantly (OR = 1.91, χ2 = 17.36, P < 0.0001) increased risk of pancolitis, and a 1.57-fold increased risk (OR = 1.57, χ2 = 4.34, P = 0.037) of requiring a bowel resection in UC. Carrying the -857 C/T variant decreased the risk of ileocolonic CD (OR = 0.56, χ2 = 4.32, P = 0.037), and the need for a bowel resection (OR = 0.59, χ2 = 4.85, P = 0.028). The risk of UC was reduced in individuals who were smokers at diagnosis, (OR = 0.48, χ2 = 4.86, P = 0.028).
CONCLUSION: TNF-α is a key cytokine known to play a role in inflammatory response, and the locus for the gene is found in the IBD3 region on chromosome 6p21, known to be associated with an increased risk for IBD. The -308 G/A SNP in the TNF-α promoter is functional, and may account in part for the increased UC risk associated with the IBD3 genomic region. The -857 C/T SNP may decrease IBD risk in certain groups. Pharmaco- or nutrigenomic approaches may be desirable for individuals with such affected genotypes.
doi:10.3748/wjg.14.4652
PMCID: PMC2738789  PMID: 18698679
Tumour necrosis factor alpha; Single nucleotide polymorphisms; Inflammatory bowel diseases; Crohn’s disease; Ulcerative colitis
7.  Dietary interactions with the bacterial sensing machinery in the intestine: the plant polyphenol case 
There are millions of microbes that live in the human gut. These are important in digestion as well as defense. The host immune system needs to be able to distinguish between the harmless bacteria and pathogens. The initial interaction between bacteria and the host happen through the pattern recognition receptors (PRRs). As these receptors are in direct contact with the external environment, this makes them important candidates for regulation by dietary components and therefore potential targets for therapy. In this review, we introduce some of the main PRRs including a cellular process known as autophagy, and how they function. Additionally we review dietary phytochemicals from plants which are believed to be beneficial for humans. The purpose of this review was to give a better understanding of how these components work in order to create better awareness on how they could be explored in the future.
doi:10.3389/fgene.2014.00064
PMCID: PMC3983525  PMID: 24772116
microbiota; autophagy; phytochemicals; Toll-like receptors; Nod-like receptors
8.  Potential pathway of anti-inflammatory effect by New Zealand honeys 
The role of honey in wound healing continues to attract worldwide attention. This study examines the anti-inflammatory effect of four honeys on wound healing, to gauge its efficacy as a treatment option. Isolated phenolics and crude extracts from manuka (Leptospermum scoparium), kanuka (Kunzea ericoides), clover (Trifolium spp.), and a manuka/kanuka blend of honeys were examined. Anti-inflammatory assays were conducted in HEK-Blue™-2, HEK-Blue™-4, and nucleotide oligomerization domain (NOD)2-Wild Type (NOD2-WT) cell lines, to assess the extent to which honey treatment impacts on the inflammatory response and whether the effect was pathway-specific. Kanuka honey, and to a lesser extent manuka honey, produced a powerful anti-inflammatory effect related to their phenolic content. The effect was observed in HEK-Blue™-2 cells using the synthetic tripalmitoylated lipopeptide Pam3CysSerLys4 (Pam3CSK4) ligand, suggesting that honey acts specifically through the toll-like receptor (TLR)1/TLR2 signaling pathway. The manuka/kanuka blend and clover honeys had no significant anti-inflammatory effect in any cell line. The research found that kanuka and manuka honeys have an important role in modulating the inflammatory response associated with wound healing, through a pathway-specific effect. The phenolic content of honey correlates with its effectiveness, although the specific compounds involved remain to be determined.
doi:10.2147/IJGM.S45839
PMCID: PMC3949697  PMID: 24623989
Leptospermum scoparium; manuka; Kunzea ericoides; kanuka; Trifolium; clover; inflammatory response; phenolics; wound healing
9.  Nutrigenetics, Nutrigenomics, and Selenium 
Selenium (Se) is an important micronutrient that, as a component of selenoproteins, influences oxidative and inflammatory processes. Its’ levels vary considerably, with different ethnic and geographic population groups showing varied conditions, ranging from frank Se deficiencies to toxic effects. An optimum Se level is essential for the maintenance of homeostasis, and this optimum may vary according to life stage, general state of health, and genotype. Nutrigenetic studies of different Se levels, in the presence of genetic variants in selenoproteins, suggest that an effective dietary Se intake for one individual may be very different from that for others. However, we are just starting to learn the significance of various genes in selenoprotein pathways, functional variants in these, and how to combine such data from genes into pathways, alongside dietary intake or serum levels of Se. Advances in systems biology, genetics, and genomics technologies, including genetic/genomic, epigenetic/epigenomic, transcriptomic, proteomic, and metabolomic information, start to make it feasible to assess a comprehensive spectrum of the biological activity of Se. Such nutrigenomic approaches may prove very sensitive biomarkers of optimal Se status at the individual or population level. The premature cessation of a major human Se intervention trial has led to considerable controversy as to the value of Se supplementation at the population level. New websites provide convenient links to current information on methodologies available for nutrigenetics and nutrigenomics. These new technologies will increasingly become an essential tool in optimizing the level of Se and other micronutrients for optimal health, in individuals and in population groups. However, definitive proof of such effects will require very large collaborative studies, international agreement on study design, and innovative approaches to data analysis.
doi:10.3389/fgene.2011.00015
PMCID: PMC3268570  PMID: 22303312
selenium; selenoprotein; nutrigenetics; nutrigenomics
10.  Effect of Sulforaphane on NOD2 via NF-κB: implications for Crohn’s disease 
Background
Sulforaphane has well established anti-cancer properties and more recently anti-inflammatory properties have also been determined. Sulforaphane has been shown to inhibit PRR-mediated pro-inflammatory signalling by either directly targeting the receptor or their downstream signalling molecules such as the transcription factor, NF-κB. These results raise the possibility that PRR-mediated inflammation could be suppressed by specific dietary bioactives. We examined whether sulforaphane could suppress NF-κB via the NOD2 pathway.
Methods
Human embryonic kidney 293T (HEK293T) cells were stably transfected with NOD2 variants and the NF-κB reporter, pNifty2-SEAP. The cells were co-treated with sulforaphane and MDP and secreted alkaline phosphatase (SEAP) production was determined.
Results
We found that sulforaphane was able to significantly suppress the ligand-induced NF-κB activity at physiologically relevant concentrations, achievable via the consumption of broccoli within the diet.
Conclusions
These results demonstrate that the anti-inflammatory role of sulforaphane is not restricted to LPS-induced inflammatory signalling. These data add to the growing evidence that PRR activation can be inhibited by specific phytochemicals and thus suggests that diet could be a way of controlling inflammation. This is particularly important for a disease like Crohn’s disease where diet can play a key role in relieving or exacerbating symptoms.
doi:10.1186/s12950-015-0051-x
PMCID: PMC4335778
Sulforaphane; NOD2; Inflammation; Crohn’s disease
11.  An Investigation into the Association between DNA Damage and Dietary Fatty Acid in Men with Prostate Cancer 
Nutrients  2015;7(1):405-422.
Prostate cancer is a growing problem in New Zealand and worldwide, as populations adopt a Western style dietary pattern. In particular, dietary fat is believed to be associated with oxidative stress, which in turn may be associated with cancer risk and development. In addition, DNA damage is associated with the risk of various cancers, and is regarded as an ideal biomarker for the assessment of the influence of foods on cancer. In the study presented here, 20 men with prostate cancer adhered to a modified Mediterranean style diet for three months. Dietary records, blood fatty acid levels, prostate specific antigen, C-reactive protein and DNA damage were assessed pre- and post-intervention. DNA damage was inversely correlated with dietary adherence (p = 0.013) and whole blood monounsaturated fatty acids (p = 0.009) and oleic acid (p = 0.020). DNA damage was positively correlated with the intake of dairy products (p = 0.043), red meat (p = 0.007) and whole blood omega-6 polyunsaturated fatty acids (p = 0.015). Both the source and type of dietary fat changed significantly over the course of the dietary intervention. Levels of DNA damage were correlated with various dietary fat sources and types of dietary fat.
doi:10.3390/nu7010405
PMCID: PMC4303847  PMID: 25580814
DNA damage; Mediterranean style diet; fatty acids; prostate cancer
12.  Anti-Inflammatory Activity of Fruit Fractions in Vitro, Mediated through Toll-Like Receptor 4 and 2 in the Context of Inflammatory Bowel Disease 
Nutrients  2014;6(11):5265-5279.
Pattern recognition receptors such as Toll-Like Receptor 2 (TLR2) and 4 (TLR4) are important in detecting and responding to stress and bacterial stimuli. Defect or damage in the TLR2 and TLR4 pathways can lead to sustained inflammation, characteristic of inflammatory bowel disease (IBD). The goal of this study was to identify fruit fractions that can be tested further to develop them as complementary therapies for IBD. In order to do this, we identified fruit fractions that mediate their anti-inflammatory response through the TLR4 and TLR2 pathway. Human Embryonic Kidney (HEK)-hTLR4 and hTLR2 cells were stimulated with their respective ligands to induce inflammation. These cells were treated with one of the 12 fractionated fruits and the inflammatory effect measured. 10 of the fruits came up as anti-inflammatory in the hTLR4 assay and nine in the hTLR2 assays. Many of the fruit fractions mediated their anti-inflammatory actions either mainly in their hydrophobic fractions (such as elderberry) or hydrophilic fractions (such as red raspberry), or both. The strongest anti-inflammatory effects were seen for feijoa and blackberry. This study shows that fruits can have multiple fractions eliciting anti-inflammatory effects in a pathway specific manner. This suggests that the compounds found in fruits can act together to produce health benefits by way of reducing inflammation. Exploiting this property of fruits can help develop complimentary therapies for inflammatory diseases.
doi:10.3390/nu6115265
PMCID: PMC4245588  PMID: 25415606
Toll-Like Receptors; inflammatory bowel disease; polyphenols; inflammation
13.  Candidate Genes Involved in Beneficial or Adverse Responses to Commonly Eaten Brassica Vegetables in a New Zealand Crohn’s Disease Cohort 
Nutrients  2013;5(12):5046-5064.
Crohn’s disease (CD) is one of the two manifestations of inflammatory bowel disease. Particular foods are thought with CD to exacerbate their illness. Vegetables, especially Brassicaceae, are often shunned by people with CD because of the negative effects they are alleged to have on their symptoms. Brassicaceae supply key nutrients which are necessary to meet recommended daily intakes. We sought to identify the candidate genes involved in the beneficial or adverse effects of Brassicaceae most commonly eaten, as reported by the New Zealand adults from the “Genes and Diet in Inflammatory Bowel disease Study” based in Auckland. An analysis of associations between the single nucleotide polymorphisms (SNPs) and the beneficial or adverse effects of the ten most commonly eaten Brassicaceae was carried out. A total of 37 SNPs were significantly associated with beneficial effects (p = 0.00097 to 0.0497) and 64 SNPs were identified with adverse effects (p = 0.0000751 to 0.049). After correcting for multiple testing, rs7515322 (DIO1) and rs9469220 (HLA) remained significant. Our findings show that the tolerance of some varieties of Brassicaceae may be shown by analysis of a person’s genotype.
doi:10.3390/nu5125046
PMCID: PMC3875924  PMID: 24352087
Brassicaceae; tolerability; Crohn’s disease; DIO1; HLA
14.  Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn's disease patients 
Human Genomics  2013;7(1):24.
Background
Inflammation is an essential immune response; however, chronic inflammation results in disease including Crohn's disease. Therefore, reducing the inflammation can yield a significant health benefit, and one way to achieve this is through diet. We developed a Mediterranean-inspired anti-inflammatory diet and used this diet in a 6-week intervention in a Crohn's disease population. We examined changes in inflammation and also in the gut microbiota. We compared the results of established biomarkers, C-reactive protein and the micronuclei assay, of inflammation with results from a transcriptomic approach.
Results
Data showed that being on our diet for 6 weeks was able to reduce the established biomarkers of inflammation. However, using transcriptomics, we observed significant changes in gene expression. Although no single gene stood out, the cumulative effect of small changes in many genes combined to have a beneficial effect. Data also showed that our diet resulted in a trend of normalising the microbiota.
Conclusions
This study showed that our Mediterranean-inspired diet appeared to benefit the health of people with Crohn's disease. Our participants showed a trend for reduced markers of inflammation and normalising of the microbiota. The significant changes in gene expression after 6 weeks highlighted the increased sensitivity of using transcriptomics when compared to the established biomarkers and open up a new era of dietary intervention studies.
doi:10.1186/1479-7364-7-24
PMCID: PMC4174666  PMID: 24283712
Inflammation; Crohn's disease; Transcriptomics; Dietary intervention
15.  The Role of Vitamin D Level and Related Single Nucleotide Polymorphisms in Crohn’s Disease 
Nutrients  2013;5(10):3898-3909.
New Zealand has one of the highest rates of Crohn’s Disease (CD) in the world, and there is much speculation as to why this might be. A high risk of CD has been associated with deficient or insufficient levels of Vitamin D (Vit D), lifestyle as well as various genetic polymorphisms. In this study we sought to analyse the relevance of serum Vit D levels, lifestyle and genotype to CD status. Serum samples were analysed for 25-OH-Vitamin D levels. DNA was isolated from blood and cheek-swabs, and Sequenom and ImmunoChip techniques were used for genotyping. Serum Vit D levels were significantly lower in CD patients (mean = 49.5 mg/L) than those found in controls (mean = 58.9 mg/L, p = 4.74 × 10−6). A total of seven single nucleotide polymorphisms were examined for effects on serum Vit D levels, with adjustment for confounding variables. Two variants: rs731236[A] (VDR) and rs732594[A] (SCUBE3) showed a significant association with serum Vit D levels in CD patients. Four variants: rs7975232[A] (VDR), rs732594[A] (SCUBE3), and rs2980[T] and rs2981[A] (PHF-11) showed a significant association with serum Vit D levels in the control group. This study demonstrates a significant interaction between Vit D levels and CD susceptibility, as well as a significant association between Vit D levels and genotype.
doi:10.3390/nu5103898
PMCID: PMC3820050  PMID: 24084050
vitamin D levels; Crohn’s disease; VDR; SCUBE3; PPP6R3; PHF-11; SNPs; lifestyle
16.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease 
Jostins, Luke | Ripke, Stephan | Weersma, Rinse K | Duerr, Richard H | McGovern, Dermot P | Hui, Ken Y | Lee, James C | Schumm, L Philip | Sharma, Yashoda | Anderson, Carl A | Essers, Jonah | Mitrovic, Mitja | Ning, Kaida | Cleynen, Isabelle | Theatre, Emilie | Spain, Sarah L | Raychaudhuri, Soumya | Goyette, Philippe | Wei, Zhi | Abraham, Clara | Achkar, Jean-Paul | Ahmad, Tariq | Amininejad, Leila | Ananthakrishnan, Ashwin N | Andersen, Vibeke | Andrews, Jane M | Baidoo, Leonard | Balschun, Tobias | Bampton, Peter A | Bitton, Alain | Boucher, Gabrielle | Brand, Stephan | Büning, Carsten | Cohain, Ariella | Cichon, Sven | D’Amato, Mauro | De Jong, Dirk | Devaney, Kathy L | Dubinsky, Marla | Edwards, Cathryn | Ellinghaus, David | Ferguson, Lynnette R | Franchimont, Denis | Fransen, Karin | Gearry, Richard | Georges, Michel | Gieger, Christian | Glas, Jürgen | Haritunians, Talin | Hart, Ailsa | Hawkey, Chris | Hedl, Matija | Hu, Xinli | Karlsen, Tom H | Kupcinskas, Limas | Kugathasan, Subra | Latiano, Anna | Laukens, Debby | Lawrance, Ian C | Lees, Charlie W | Louis, Edouard | Mahy, Gillian | Mansfield, John | Morgan, Angharad R | Mowat, Craig | Newman, William | Palmieri, Orazio | Ponsioen, Cyriel Y | Potocnik, Uros | Prescott, Natalie J | Regueiro, Miguel | Rotter, Jerome I | Russell, Richard K | Sanderson, Jeremy D | Sans, Miquel | Satsangi, Jack | Schreiber, Stefan | Simms, Lisa A | Sventoraityte, Jurgita | Targan, Stephan R | Taylor, Kent D | Tremelling, Mark | Verspaget, Hein W | De Vos, Martine | Wijmenga, Cisca | Wilson, David C | Winkelmann, Juliane | Xavier, Ramnik J | Zeissig, Sebastian | Zhang, Bin | Zhang, Clarence K | Zhao, Hongyu | Silverberg, Mark S | Annese, Vito | Hakonarson, Hakon | Brant, Steven R | Radford-Smith, Graham | Mathew, Christopher G | Rioux, John D | Schadt, Eric E | Daly, Mark J | Franke, Andre | Parkes, Miles | Vermeire, Severine | Barrett, Jeffrey C | Cho, Judy H
Nature  2012;491(7422):119-124.
Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy4, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases5. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
doi:10.1038/nature11582
PMCID: PMC3491803  PMID: 23128233
17.  Alternative Sources of Omega-3 Fats: Can We Find a Sustainable Substitute for Fish? 
Nutrients  2013;5(4):1301-1315.
Increasing demand for eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) containing fish oils is putting pressure on fish species and numbers. Fisheries provide fish for human consumption, supplement production and fish feeds and are currently supplying fish at a maximum historical rate, suggesting mass-scale fishing is no longer sustainable. However, the health properties of EPA and DHA long-chain (LC) omega-3 polyunsaturated fatty acids (PUFA) demonstrate the necessity for these oils in our diets. EPA and DHA from fish oils show favourable effects in inflammatory bowel disease, some cancers and cardiovascular complications. The high prevalence of these diseases worldwide indicates the requirement for alternative sources of LC-PUFA. Strategies have included plant-based fish diets, although this may compromise the health benefits associated with fish oils. Alternatively, stearidonic acid, the product of α-linolenic acid desaturation, may act as an EPA-enhancing fatty acid. Additionally, algae oils may be a promising omega-3 PUFA source for the future. Algae are beneficial for multiple industries, offering a source of biodiesel and livestock feeds. However, further research is required to develop efficient and sustainable LC-PUFA production from algae. This paper summarises the recent research for developing prospective substitutes for omega-3 PUFA and the current limitations that are faced.
doi:10.3390/nu5041301
PMCID: PMC3705349  PMID: 23598439
eicosapentaenoic acid (EPA); docosahexaenoic acid (DHA); omega-3; inflammation; dietary fatty acids; fish oils; stearidonic acid; algae
18.  Public Health Pharmacogenomics and the Design Principles for Global Public Goods – Moving Genomics to Responsible Innovation 
PMCID: PMC3606133  PMID: 23531886 CAMSID: cams2807
Genomics and development; genomics without borders; global governance of biotechnology innovation and uncertainty; P5 medicine; public health pharmacogenomics; responsible innovation; STS and organizations; theranostic medicine
19.  Reduced genetic influence on childhood obesity in small for gestational age children 
BMC Medical Genetics  2013;14:10.
Background
Children born small-for-gestational-age (SGA) are at increased risk of developing obesity and metabolic diseases later in life, a risk which is magnified if followed by accelerated postnatal growth. We investigated whether common gene variants associated with adult obesity were associated with increased postnatal growth, as measured by BMI z-score, in children born SGA and appropriate for gestational age (AGA) in the Auckland Birthweight Collaborative.
Methods
A total of 37 candidate SNPs were genotyped on 547 European children (228 SGA and 319 AGA). Repeated measures of BMI (z-score) were used for assessing obesity status, and results were corrected for multiple testing using the false discovery rate.
Results
SGA children had a lower BMI z-score than non-SGA children at assessment age 3.5, 7 and 11 years. We confirmed 27 variants within 14 obesity risk genes to be individually associated with increasing early childhood BMI, predominantly in those born AGA.
Conclusions
Genetic risk variants are less important in influencing early childhood BMI in those born SGA than in those born AGA, suggesting that non-genetic or environmental factors may be more important in influencing childhood BMI in those born SGA.
doi:10.1186/1471-2350-14-10
PMCID: PMC3556300  PMID: 23339409
BMI; Childhood obesity; AGA children; SGA children
20.  Selenium, Selenoprotein Genes and Crohn’s Disease in a Case-Control Population from Auckland, New Zealand 
Nutrients  2012;4(9):1247-1259.
New Zealand has one of the highest incidence rates of Crohn’s Disease (CD), whilst the serum selenium status of New Zealanders is amongst the lowest in the world. A prospective case-control study in Auckland, New Zealand considered serum selenium as a potential CD risk factor. Serum selenium levels were significantly lower in CD patients compared to controls (101.8 ± 1.02 vs. 111.1 ± 1.01 ng/mL) (p = 5.91 × 10−8). Recent detailed studies in the United Kingdom have suggested an optimal serum level around 122 ng/mL, making the average CD patient in New Zealand selenium deficient. Of the 29 single nucleotide polymorphisms (SNPs) tested, 13 were found to significantly interact with serum selenium on CD. After adjustment for multiple testing, a significant interaction with serum selenium on CD was found for three SNPs, namely rs17529609 and rs7901303 in the gene SEPHS1, and rs1553153 in the gene SEPSECS. These three SNPs have not been reported elsewhere as being significantly associated with selenium or CD. It is unclear as to whether lower selenium levels are a cause or an effect of the disease.
doi:10.3390/nu4091247
PMCID: PMC3475235  PMID: 23112913
selenium; Crohn’s Disease; risk factor; single nucleotide polymorphism
21.  Nutrigenetics and Nutrigenomics: Viewpoints on the Current Status and Applications in Nutrition Research and Practice 
Nutrigenetics and nutrigenomics hold much promise for providing better nutritional advice to the public generally, genetic subgroups and individuals. Because nutrigenetics and nutrigenomics require a deep understanding of nutrition, genetics and biochemistry and ever new ‘omic’ technologies, it is often difficult, even for educated professionals, to appreciate their relevance to the practice of preventive approaches for optimising health, delaying onset of disease and diminishing its severity. This review discusses (i) the basic concepts, technical terms and technology involved in nutrigenetics and nutrigenomics; (ii) how this emerging knowledge can be applied to optimise health, prevent and treat diseases; (iii) how to read, understand and interpret nutrigenetic and nutrigenomic research results, and (iv) how this knowledge may potentially transform nutrition and dietetic practice, and the implications of such a transformation. This is in effect an up-to-date overview of the various aspects of nutrigenetics and nutrigenomics relevant to health practitioners who are seeking a better understanding of this new frontier in nutrition research and its potential application to dietetic practice.
doi:10.1159/000327772
PMCID: PMC3121546  PMID: 21625170
Dietetics; Nutrigenetics; Nutrigenomics; Nutrition Research; Personalised nutrition
22.  DNase1: No Association with Crohn's Disease in a New Zealand Population 
ISRN Gastroenterology  2012;2012:826323.
DNase1 has been implicated in a number of immune disorders and is an excellent candidate gene for Crohn's disease (CD). We investigated whether DNase1 SNPs rs1053874 and rs8176938 were associated with CD in a well-characterized New Zealand dataset consisting of 447 cases and 716 controls. Furthermore, we measured serum DNase1 activity levels in a number of CD patients and controls. We did not find any evidence of association for either DNase1 genetic variation or DNase1 activity levels with CD. The lack of association indicates that DNase1 does not play a significant role in predisposing to CD in the New Zealand population.
doi:10.5402/2012/826323
PMCID: PMC3373076  PMID: 22701800
23.  Serum selenium and single-nucleotide polymorphisms in genes for selenoproteins: relationship to markers of oxidative stress in men from Auckland, New Zealand 
Genes & Nutrition  2011;7(2):179-190.
There is controversy as to the recommended daily intake of selenium (Se), and whether current New Zealand diets are adequate in this nutrient. Various functional single-nucleotide polymorphisms (SNPs) polymorphisms may affect the efficacy of Se utilisation. These include the glutathione peroxidases GPx1 rs1050450, GPx4 rs713041, as well as selenoproteins SEPP1 rs3877899, SEL15 rs5845, SELS rs28665122 and SELS rs4965373. This cross-sectional study measured serum Se levels of 503 healthy Caucasian men in Auckland, New Zealand, between ages 20–81. The Se distribution was compared with activities of the antioxidant enzymes glutathione peroxidase and thioredoxin reductase, and DNA damage as measured by the single cell gel electrophoresis assay, both without and with a peroxide-induced oxidative challenge. Serum Se was measured using inductively coupled plasma-dynamic reaction cell-mass spectrometry, while selenoprotein SNPs were estimated using TaqMan® SNP genotyping assays. While antioxidant enzyme activities and DNA damage recorded after a peroxide challenge increased with increasing serum selenium, the inherent DNA damage levels in leukocytes showed no statistically significant relationship with serum selenium. However, these relationships and dietary Se requirements at the individual level were modified by several different SNPs in genes for selenoproteins. The GPx1 rs1050450 C allele was significantly associated with GPx activity. Significant correlations between serum Se level and GPX activity were seen with all genotypes except for homozygous minor allele carriers, while the GPx1 rs1050450 CT genotype showed the highest correlation. Several genotypes showed significant correlations between serum Se and TR activity with SEPP1 rs3877899 GG genotype showing the highest correlation. A significant decreasing trend in DNA damage with increasing serum Se was seen among GPx1 rs1050450 CC and GPx4 rs713041 TT genotype carriers up to a serum Se level of 116 and 149 ng/ml, respectively. In the absence of this genetic information, we would recommend a serum Se concentration in the region of 100–150 ng/ml as providing a useful compromise.
doi:10.1007/s12263-011-0259-1
PMCID: PMC3316745  PMID: 22139612
Selenium (Se); Glutathione peroxidase (GPx); Thioredoxin reductase (TR); Single nucleotide polymorphisms (SNPs)
24.  Association Analysis of ULK1 with Crohn's Disease in a New Zealand Population 
The gene ULK1 is an excellent candidate for Crohn's disease (CD) due to its role in autophagy. A recent study provided evidence for the involvement of ULK1 in the pathogenesis of CD (Henckaerts et al., 2011). We attempted to validate this association, using a candidate gene SNP study of ULK1 in CD. We identified tagging SNPs and genotyped these SNPs using the Sequenom platform in a Caucasian New Zealand dataset consisting of 406 CD patients and 638 controls. In this sample, we were able to demonstrate an association between CD and several different ULK1 SNPs and haplotypes. Phenotypic analysis showed an association with age of diagnosis 17–40 years and inflammatory behaviour. The findings of this study provide evidence to suggest that genetic variation in ULK1 may play a role in interindividual differences in CD susceptibility and clinical outcome.
doi:10.1155/2012/715309
PMCID: PMC3320017  PMID: 22536218
25.  Metallothionein genes: no association with Crohn's disease in a New Zealand population 
Metallothioneins (MTs) are excellent candidate genes for Inflammatory Bowel Disease (IBD) and have previously been shown to have altered expression in both animal and human studies of IBD. This is the first study to examine genetic variants within the MT genes and aims to determine whether such genetic variants have an important role in this disease. 28 tag SNPs in genes MT1 (subtypes A, B, E, F, G, H, M, X), MT2, MT3 and MT4 were selected for genotyping in a well-characterized New Zealand dataset consisting of 406 patients with Crohn's Disease and 638 controls. We did not find any evidence of association for MT genetic variation with CD. The lack of association indicates that genetic variants in the MT genes do not play a significant role in predisposing to CD in the New Zealand population.
doi:10.1186/1477-5751-11-8
PMCID: PMC3280932  PMID: 22284420
Crohn's disease; Metallothioneins; genetic association

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