Colette Deslandres

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

Ulcerative colitis is a chronic, relapsing inflammatory condition of the gastrointestinal tract with a complex genetic and environmental etiology. In an effort to identify genetic variation underlying ulcerative colitis risk, we present two distinct genome-wide association studies of ulcerative colitis and their joint analysis with a previously published scan, comprising, in aggregate, 2,693 individuals with ulcerative colitis and 6,791 control subjects. Fifty-nine SNPs from 14 independent loci attained an association significance of P < 10−5. Seven of these loci exceeded genome-wide significance (P < 5 × 10−8). After testing an independent cohort of 2,009 cases of ulcerative colitis and 1,580 controls, we identified 13 loci that were significantly associated with ulcerative colitis (P < 5 × 10−8), including the immunoglobulin receptor gene FCGR2A, 5p15, 2p16 and ORMDL3 (orosomucoid1-like 3). We confirmed association with 14 previously identified ulcerative colitis susceptibility loci, and an analysis of acknowledged Crohns disease loci showed that roughly half of the known Crohns disease associations are shared with ulcerative colitis. These data implicate approximately 30 loci in ulcerative colitis, thereby providing insight into disease pathogenesis.

Imbalances in Dietary Consumption of Fatty Acids, Vegetables, and Fruits Are Associated With Risk for Crohn's Disease in Children

BACKGROUND AND OBJECTIVES:The role of dietary factors in the etiology of Crohns disease (CD) is inconsistent largely due to difficulties in acquiring valid information on consumption habits. We examined the impact of diet on new onset CD in children using a validated food-frequency questionnaire (FFQ).METHODOLOGY:A case-control study was carried out. Children ≤20 yr, newly diagnosed with CD, were recruited from 3 pediatric gastroenterology clinics across Canada. Population or hospital controls were selected matched to cases for time of diagnosis (±6 months) and area of residence. Dietary consumption 1 yr prior to disease diagnosis was evaluated using a validated FFQ, administered within 1 month of diagnosis. Conditional logistic regression analysis adjusting for potential confounding variables (energy intake, age, gender, body mass index) was carried out.RESULTS: A total of 130 CD patients and 202 controls were studied. Mean age at diagnosis (±SD) was 14.2 (2.7). There were more male patients (59%). Comparing the highest to the lowest levels of consumption, higher amounts of vegetables (OR 0.69, 95% CI 0.33–1.44, P = 0.03), fruits (OR 0.49, 95% CI 0.25–0.96, P = 0.02), fish (OR 0.46, 95% CI 0.20–1.06, P = 0.02), and dietary fiber (OR 0.12, 95% CI 0.04–0.37, P < 0.001) protected from CD. Consumption of long-chain omega-3 fatty acids (LCN-ω-3) was negatively associated with CD (OR 0.44, 95% CI 0.19–1.00, P < 0.001). A higher ratio of LCN-ω-3/ω-6 fatty acids was significantly associated with lower risks for CD (OR 0.32, 95% CI 0.14–0.71, P = 0.02).CONCLUSIONS: Our findings indicate that an imbalance in consumption of fatty acids, vegetables, and fruits is associated with increased risks for CD among Canadian children.

Gene-centric Association Mapping of Chromosome 3p implicates MST1 in IBD pathogenesis

Association mapping and candidate gene studies within inflammatory bowel diseases (IBD) linkage regions, as well as genome-wide association studies in Crohns disease (CD) have led to the discovery of multiple risk genes, but these explain only a fraction of the genetic susceptibility observed in IBD. We have thus been pursuing a region on chromosome 3p21–22 showing linkage to CD and ulcerative colitis (UC) using a gene-centric association mapping approach. We identified 12 functional candidate genes by searching for literature cocitations with relevant keywords and for gene expression patterns consistent with immune/intestinal function. We then performed an association study composed of a screening phase, where tagging single nucleotide polymorphisms (SNPs) were evaluated in 1,020 IBD patients, and an independent replication phase in 745 IBD patients. These analyses identified and replicated significant association with IBD for four SNPs within a 1.2 Mb linkage disequilibrium region. We then identified a non-synonymous coding variant (rs3197999, R689C) in the macrophage-stimulating 1 (MST1) gene (P-value 3.62 × 10–6) that accounts for the association signal, and shows association with both CD and UC. MST1 encodes macrophage-stimulating protein (MSP), a protein regulating the innate immune responses to bacterial ligands. R689C is predicted to interfere with MSP binding to its receptor, suggesting a role for this gene in the pathogenesis of IBD.

Dietary Patterns and Risk for Crohn's Disease in Children

Background: Some dietary foods are considered protective (vegetables and fruits), whereas others (fatty foods) are thought to enhance the risk for Crohns disease (CD). The evidence, however, is inconsistent. Methods: We postulated that specific dietary patterns may influence the risk for CD. A case‐control study was carried out. Newly diagnosed CD cases with population and/or hospital‐based controls ≤20 years were selected from 3 tertiary hospitals across Canada. Predisease diet was assessed using a validated food frequency questionnaire (FFQ) administered within 1 month of diagnosis. Factor analyses and unconditional logistic regression (adjusted) was used to determine gender‐specific dietary patterns and assess associated risks for CD. Odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were estimated. Results: A total of 149 cases and 251 controls were included. The mean age (range) of the cases was 13.3 (2.6‐20 years). There were more boys (61.1%). Four dietary patterns each were observed among both boys and girls. Pattern 1 in girls, characterized by meats, fatty foods, and desserts, was positively associated with CD (OR 4.7, 95% CI 1.6–14.2). Pattern 2, common to both boys and girls, was characterized by vegetables, fruits, olive oil, fish, grains, and nuts and was inversely associated with CD in both genders (girls: OR 0.3, 95% CI 0.1–0.9; boys: OR 0.2, 95% CI 0.1–0.5). Conclusions: Our results suggest that specific dietary patterns could be associated with higher or lower risks for CD in children. Larger prospective studies are required to confirm these findings.

Association between genetic variants in the IL-23R gene and early-onset Crohn's disease: results from a case-control and family-based study among Canadian children.

BACKGROUND AND OBJECTIVES:Interleukin (IL)-23 is a key regulator of inflammation and influences the activities of T-helper 17 (Th-17) lymphocytes. Recent reports indicate that variants in the gene coding for its receptor (IL-23R) are strongly associated with Crohns disease (CD). We investigated whether DNA variants in the IL-23R gene determine susceptibility for CD in Canadian children.DESIGN AND METHODS:A case-control and case-parent trio design was implemented at three pediatric centers across Canada. Cases of CD (≤20 yr) along with their parents and controls were recruited. DNA samples were collected and genotyped for 10 single nucleotide polymorphisms (SNPs) in the IL-23R gene and three common SNPs in the CARD15 gene. Transmission disequilibrium-based tests were applied to the case-parent data and logistic regression models to the case-control data to study the association between the SNPs and CD.RESULTS:A total of 259 CD cases, 139 controls, and 232 families (167 trios and 65 dyads) were studied. The mean age at diagnosis was 13.3 yr (range 2.6–20 yr). The majority of the patients were Caucasian. Case-control analysis revealed significant associations with three SNPs (rs1004819, rs7517847, and rs11209026 [R381Q]) and borderline nonsignificant associations with three other SNPs (rs10489629, rs10889697, and rs11465804) in the IL-23R gene. Having any CARD15 variant was associated with a significant risk for CD (P < 0.0001). Analyses of case-parent data confirmed the findings from the case-control analysis including significant associations with the R381Q SNP (P = 0.002). The common variant in this SNP conferred risk for CD. These associations were largely independent of the CARD15 gene.CONCLUSIONS:Our findings confirm recently reported genome-wide associations between the IL-23R gene and CD. They suggest that the gene is also associated with pediatric-onset CD among Canadian children.

Autophagy Gene ATG16L1 But Not IRGM Is Associated with Crohn's Disease in Canadian Children

Background: Recent genome‐wide studies have implicated the autophagy genes ATG16L1 and IRGM in the pathogenesis of Crohns disease (CD). We investigated whether these genes were associated with CD in Canadian children. Methods: A case‐control study was carried out at 2 pediatric gastroenterology clinics in Canada. Confirmed cases of CD <20 years diagnosed using standard criteria were classified according to the Montreal Classification scheme. Single nucleotide polymorphisms (SNPs) rs2241880 (ATG16L1) and rs10065172 (IRGM) along with CARD15 SNPs, SNP8, SNP12, and SNP13 were genotyped. Results: A total of 289 CD cases and 290 controls were studied. The mean age (±SD) of the cases was 12.1 (±3.5) years of age. Most cases were male (55.4%), had disease location L3 ± L4 (56.7%), and an inflammatory phenotype B1 ± p (87.2%) at diagnosis. rs2241880 (ATG16L1) was strongly associated with CD (allelic P = 1.24 × 10−6). Children with GG genotype had a more than 3‐fold elevated risk for disease as compared to the wildtype AA homozygotes (odds ratio [OR], 3.1; 95% confidence interval [CI], 1.93–4.94; P = 1.8 × 10−6). Association with SNP rs2241880 was specific for ileal disease (with or without colonic involvement) (case‐based allelic P = 0.02; P‐value versus controls = 9.5 × 10−8). The frequency of IRGM SNP rs10065172 was higher in cases but differences with controls were not statistically significant. No interactions between CARD15 and either ATG16L1 or IRGM were evident. Conclusions: We have confirmed associations between CD and ATG16L1 in a pediatric cohort of Canadian children. Associations with IRGM need to be further evaluated in larger studies. (Inflamm Bowel Dis 2008)

Interleukin 10 (IL‐10) gene variants and susceptibility for paediatric onset Crohn’s disease

Background  A recent genome‐wide association study in adult patients with ulcerative colitis (UC) has implicated the interleukin 10 (IL‐10) gene as an important candidate gene. Moreover, a UC‐associated single nucleotide polymorphism (SNP) rs3024405 was also significantly associated with adult Crohn’s disease (CD).

Methotrexate in the treatment of inflammatory bowel disease: An 8‐year retrospective study in a Canadian pediatric IBD center

Background: Methotrexate (MTX) is used as an alternative immunosuppressive treatment for patients with inflammatory bowel disease (IBD). The aim of the study was to evaluate effectiveness and tolerance of MTX for children with IBD. Methods: A retrospective study was conducted in our pediatric IBD center of all children having received MTX for the treatment of their IBD between 2000 and 2008. Remission was defined as discontinuation of steroids and Harvey–Bradshaw Index <4 for Crohns disease (CD) patients or Pediatric Ulcerative Colitis Activity Index (PUCAI) <10 for ulcerative (UC) or indeterminate colitis (IC) patients. Results: Seventy‐five patients had CD, 5 UC, and 13 IC. Mean age at diagnosis was 11 (0.6–17.4) years. Ninety patients were previously treated with purine analogs and 26 with anti‐tumor necrosis factor (TNF). Among patients assessed for effectiveness of MTX (n = 79), clinical remission was observed in 29, 37, 25, and 16% of CD patients (n = 63) and 19, 25, 13, and 7% of patients with UC or IC (n = 16), respectively, 3, 6,12, and 24 months after initiation of MTX. The 1‐year remission rate for CD patients was significantly higher in patients with colonic disease. Forty‐six patients (49%) experienced side effects but only 13 (14%) had to discontinue treatment. Conclusions: The long‐term remission rate with MTX in our pediatric IBD population was low. However, MTX was generally well tolerated and induced and maintained remission in some patients who previously had failed a purine analog and/or anti‐TNF. Prospective controlled trials are indicated to determine the place of MTX in the management of pediatric IBD.

Variants in TRIM22 that affect NOD2 signaling are associated with very early onset inflammatory bowel disease

BACKGROUND & AIMS Severe forms of inflammatory bowel disease (IBD) that develop in very young children can be caused by variants in a single gene. We performed whole-exome sequence (WES) analysis to identify genetic factors that might cause granulomatous colitis and severe perianal disease, with recurrent bacterial and viral infections, in an infant of consanguineous parents. METHODS We performed targeted WES analysis of DNA collected from the patient and her parents. We validated our findings by a similar analysis of DNA from 150 patients with very-early-onset IBD not associated with known genetic factors analyzed in Toronto, Oxford, and Munich. We compared gene expression signatures in inflamed vs noninflamed intestinal and rectal tissues collected from patients with treatment-resistant Crohns disease who participated in a trial of ustekinumab. We performed functional studies of identified variants in primary cells from patients and cell culture. RESULTS We identified a homozygous variant in the tripartite motif containing 22 gene (TRIM22) of the patient, as well as in 2 patients with a disease similar phenotype. Functional studies showed that the variant disrupted the ability of TRIM22 to regulate nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-κB. Computational studies demonstrated a correlation between the TRIM22-NOD2 network and signaling pathways and genetic factors associated very early onset and adult-onset IBD. TRIM22 is also associated with antiviral and mycobacterial effectors and markers of inflammation, such as fecal calprotectin, C-reactive protein, and Crohns disease activity index scores. CONCLUSIONS In WES and targeted exome sequence analyses of an infant with severe IBD characterized by granulomatous colitis and severe perianal disease, we identified a homozygous variant of TRIM22 that affects the ability of its product to regulate NOD2. Combined computational and functional studies showed that the TRIM22-NOD2 network regulates antiviral and antibacterial signaling pathways that contribute to inflammation. Further study of this network could lead to new disease markers and therapeutic targets for patients with very early and adult-onset IBD.

Comparative expression analysis reveals differences in the regulation of intestinal paraoxonase family members.

The paraoxonase (PON) gene cluster contains three members (PON1, PON2, and PON3), located on chromosome 7q21.3-22.1. Until now there has been little insight into their regulation in human intestine. This study was designed to determine the regulation of PONs by oxidative stress and inflammatory factors. Differentiated Caco-2/15 cells, cultured on polycarbonate Transwell filter inserts, exhibited transcripts of the 3 PONs whereas Western blot revealed the protein expression of PON2 and PON3 only. Iron-ascorbate-mediated lipid peroxidation, lipopolysaccharides (LPS), tumor necrosis factor-alpha and interferon-gamma induced differential effects on the gene expression and protein mass of PONs. In particular, LPS down-regulated PON2 protein expression, which was accompanied with decreased levels of IkappaBalpha, the inhibitor of the proinflammatory transcription factor nuclear factor-kappa B (NF-kappaB). Selective inactivation of NF-kappaB by the action of caffeic acid phenethyl ester (CAPE) partially attenuated but did not abolish LPS-triggered decline of PON2. However, the combination of CAPE and antioxidants completely abrogated the negative impact of LPS on PON2. Therefore, our data indicate that oxidative stress and proinflammatory agents selectively affect the expression of PONs. Our findings also suggest that both NF-kappaB pathway and lipid peroxidation are implicated in LPS-dependent diminution of PON2.